GL1DQR6FRSH6RIWZDUH

8VHU*XLGH

004-994-000 (standard)
004-994-100 (cleanroom)
Copyright © [2006, 2007, 2008] Veeco Instruments Inc.
All rights reserved.

Document Revision History: NanoScope 7.30 Manual

Ref.
Revision Date Section(s) Affected Approval
DCR
G 6-May-2008 7.30 updates Vinson Kelley

F 12-Dec.-2007 Force Volume additions Vinson Kelley

E 8-Nov.-2007 r1sr1 updates Vinson Kelley

D 12-June-2007 5.5, A.7 Vinson Kelley

C April 25, 2007 7.20 updates Vinson Kelley

Notices: The information in this document is subject to change without notice. NO WARRANTY OF ANY KIND IS MADE WITH REGARD TO
THIS MATERIAL, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE. No liability is assumed for errors contained herein or for incidental or consequential damages in connection with the
furnishing, performance, or use of this material. This document contains proprietary information which is protected by copyright. No part of this
document may be photocopied, reproduced, or translated into another language without prior written consent.
Copyright: Copyright © 2004 Veeco Instruments Inc. All rights reserved.
Trademark Acknowledgments: The following are registered trademarks of Veeco Instruments Inc. All other trademarks are the property of their
respective owners.

Product Names:
NanoScope®
MultiMode™
Dimension™
BioScope™
Atomic Force Profiler™ (AFP™)
Dektak®

Software Modes:
TappingMode™
Tapping™
TappingMode+™
LiftMode™
AutoTune™
TurboScan™
Fast HSG™
PhaseImaging™
DekMap 2™
HyperScan™
StepFinder™
SoftScan™

Hardware Designs:
TrakScan™
StiffStage™

Hardware Options:
TipX®
Signal Access Module™ and SAM™
Extender™
TipView™
Interleave™
LookAhead™
Quadrex™

Software Options:
NanoScript™
Navigator™
FeatureFind™

Miscellaneous:
NanoProbe®
Table of Contents

List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Chapter 1 New Features in NanoScope Software . . . . . . . . . . . . . . . . . . . . .1

1.1 New Features in NanoScope v7.30 Software. . . . . . . . . . . . . . . . . . . . . . . 1
1.2 New Features in NanoScope v7.20r1sr1 Software . . . . . . . . . . . . . . . . . . 1
1.3 New Features in NanoScope v7.20r1 Software . . . . . . . . . . . . . . . . . . . . . 2
1.3.1 Newly Supported Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.3.2 Additional New Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
1.4 New Features in NanoScope v7.10 Software. . . . . . . . . . . . . . . . . . . . . . . 3
1.4.1 Newly Supported Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.4.2 Additional New Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.5 New Features in NanoScope v7.00 Software. . . . . . . . . . . . . . . . . . . . . . . 3
1.5.1 Newly Supported Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.5.2 Windows XP Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.5.3 Additional New Features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

Chapter 2 New Features in NanoScope Software . . . . . . . . . . . . . . . . . . . . .5

2.1 Installing the NanoScope Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.1 System Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1.2 Before You Install . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.1.3 NanoScope 7.30 Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
2.2 Getting to Know the NanoScope Software . . . . . . . . . . . . . . . . . . . . . . . 11
2.2.1 Software Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2.2 What is a Workspace? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
2.2.3 The Main Screen Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2.2.4 Menu Bar Items. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2.5 Cursor Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
2.3 Setting up the Workspace. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.1 Create or Open a Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.2 Add Views and Configure the Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3.3 Multiple Users using NanoScope . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
2.3.4 Older Workspaces Unsupported in NanoScope v7.30 and later . . . . . . . . . . 21
2.4 Quick Guide to a 5K Point Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4.1 Starting the NanoScope Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23

Rev. G Nanoscope Software 7.30 User Guide iii

 2.4.2 Preparing a Dimension Series AFM for a Realtime Scan . . . . . . . . . . . . . . . 25
2.4.3 Preparing a MultiMode AFM for a Realtime Scan . . . . . . . . . . . . . . . . . . . . 26
2.4.4 Scanning and Scan Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.4.5 Capturing an Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.4.6 Analyzing an Image with Section Analysis . . . . . . . . . . . . . . . . . . . . . . . . . 31
2.4.7 ASCII Export. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.4.8 High Resolution Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.5 Technical Support at Veeco. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.5.1 Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
2.5.2 Contact Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37

Chapter 3 Realtime Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

3.1 Overview of RealTime Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.1.1 Typical Procedures to Begin to Scan. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.2 Views for Scanning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
3.2.1 Navigate View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
3.2.2 Meter View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.2.3 Point and Shoot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
3.2.4 Cantilever Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
3.2.5 Electric Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.2.6 Scan-Single Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
3.2.7 Scope Trace Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
3.2.8 Main Tab Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
3.2.9 Scan Tab Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
3.2.10 Channels Tab Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
3.2.11 Feedback Controls Tab Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
3.2.12 Other Tab Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
3.3 Tips on Using Realtime. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
3.3.1 Using the Image Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
3.3.2 Multiple Channels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
3.3.3 Hints to Optimize the Engage Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
3.3.4 Tapping Engage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
3.3.5 Scan View Parameters Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
3.3.6 Channels Parameters Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97
3.3.7 Feedback Parameters Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.3.8 Signal Access Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
3.4 Force Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
3.4.1 Force Curves Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
3.4.2 Ramp Parameter List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
3.4.3 Ramp Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
3.4.4 Mode Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
3.4.5 Auto Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
3.4.6 Channel (1, 2 or 3) Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
3.4.7 Feedback Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
3.4.8 Ramp Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
3.5 Force Volume . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .112
3.5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112

iv Nanoscope Software 7.30 User Guide Rev. G

 3.5.2 Varieties of Force Volume Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
3.5.3 A Force Volume Imaging “Jump Start”. . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
3.5.4 Sample Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
3.5.5 Force Volume Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
3.5.6 Force Volume Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
3.5.7 Force Volume Display and Interpretation . . . . . . . . . . . . . . . . . . . . . . . . . . 132
3.5.8 Force Volume Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
3.5.9 Force Volume Sample Parameter Settings. . . . . . . . . . . . . . . . . . . . . . . . . . 139
3.5.10 Fluid Cell Preparation for Force Volume . . . . . . . . . . . . . . . . . . . . . . . . . 140
3.5.11 Force Volume Image File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
3.6 Piezoresponse Force Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143
3.7 Surface Potential Detection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
3.7.1 Surface Potential Detection Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
3.7.2 Surface Potential Detection—Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
3.7.3 Surface Potential Detection — Voltage Application . . . . . . . . . . . . . . . . . . 152
3.7.4 Surface Potential Detection — Procedure. . . . . . . . . . . . . . . . . . . . . . . . . . 154
3.7.5 Surface Potential Detection Pointers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155
3.8 NanoScope V Controller Lock-In . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
3.8.1 Mode-specific behavior . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
3.8.2 Generic Sweep Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
3.8.3 Drive Output Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
3.8.4 Lock-Input Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
3.9 High Speed Data Capture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
3.9.1 Channel Selection Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
3.9.2 Trigger Controls Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
3.9.3 Status Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
3.9.4 Point And Shoot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
3.10 Pulse Counting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Chapter 4 File Navigation and Browsing . . . . . . . . . . . . . . . . . . . . . . . . . . .171

4.1 The Browse Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
4.1.1 Image Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
4.1.2 Exporting Images. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
4.1.3 Image Processing Add View Commands . . . . . . . . . . . . . . . . . . . . . . . . . . 178

Chapter 5 Display Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .181

5.1 Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
5.1.1 Using the Image Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
5.1.2 Dual-Scan Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
5.1.3 Triple-Scan Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
5.2 Multiple Channel Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
5.2.1 Eight Channel Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
5.2.2 Analyzing Captured Multichannel Images . . . . . . . . . . . . . . . . . . . . . . . . . 189
5.3 3D Surface Plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
5.3.1 Parameters in the 3D Surface Plot Inputs . . . . . . . . . . . . . . . . . . . . . . . . . . 192

Rev. G Nanoscope Software 7.30 User Guide v

 5.4 Zoom . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
5.5 High Speed Data Capture Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194

Chapter 6 Analysis Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197

6.1 Depth. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
6.1.1 Depth Theory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
6.1.2 Depth Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
6.1.3 Depth Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
6.2 Power Spectral Density . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
6.2.1 PSD and Surface Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
6.2.2 PSD and Flatness. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
6.2.3 Performing a Spectral Density Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
6.2.4 Changing Parameters of the Spectrum Plot. . . . . . . . . . . . . . . . . . . . . . . . . 210
6.3 Roughness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
6.3.1 Roughness Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
6.3.2 Roughness Procedures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
6.3.3 Roughness Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
6.4 Section. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
6.4.1 Sectioning of Surfaces: Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
6.4.2 Section Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
6.4.3 Section Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
6.5 Step . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
6.5.1 Step Interface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
6.6 Width. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
6.6.1 Width Theory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
6.6.2 Width Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
6.6.3 Width Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
6.7 XY Drift . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240
6.7.1 Offline XY Drift Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 240

Chapter 7 Modify Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243

7.1 Image Filtering using Data Matrix (Kernel) Operations. . . . . . . . . . . . 244
7.2 Clean Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
7.3 Crop and Split . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
7.3.1 Crop and Split Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
7.3.2 Crop and Split Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
7.4 Erase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 254
7.5 Flatten . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
7.5.1 Flatten Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 258
7.5.2 Flatten Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
7.5.3 Flatten View Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
7.6 Gaussian . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
7.6.1 Gaussian Filter Panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264

vi Nanoscope Software 7.30 User Guide Rev. G

 7.6.2 Gaussian Kernel Algorithm. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
7.6.3 Lowpass Gaussian Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266
7.6.4 Highpass Gaussian Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
7.6.5 Procedure for the Gaussian Command . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
7.7 Lowpass . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
7.8 Median . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
7.9 Plane Fit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
7.9.1 Fitted Polynomials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
7.9.2 Plane Fit Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 276
7.9.3 Plane Fit Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 278
7.10 Spectrum 2D. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
7.10.1 Spectrum 2D Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
7.10.2 Spectrum 2D View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
7.10.3 Example 1—Simplifying an Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
7.10.4 Example 2—Highlighting Features Using 2D Spectrum Modification . . 285
7.10.5 Example 3—Removing External Noise . . . . . . . . . . . . . . . . . . . . . . . . . . 287
7.11 Subtract Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Chapter 8 AutoProgram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .293

8.1 Creating an AutoProgram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
8.2 Example command: Flatten . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
8.3 Example command: Depth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 298
8.4 Example command: Roughness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
8.5 Running AutoProgram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300

Chapter 9 Recipes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .303

9.1 Starting the Recipe Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
9.1.1 Menu Bar Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
9.2 Creating a Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
9.3 Running a Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
9.3.1 Report files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
9.4 Meta tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
9.4.1 Special Meta Tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
9.5 Recipe Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
9.5.1 Alignment/Origin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
9.5.2 Auto Tune . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 313
9.5.3 Capture Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
9.5.4 Image Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
9.5.5 Image Export . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 316
9.5.6 Image Set (offline). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
9.5.7 Load Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
9.5.8 Measurement . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
9.5.9 My Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318

Rev. G Nanoscope Software 7.30 User Guide vii

 9.5.10 Real-time Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
9.5.11 Report . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
9.5.12 Site. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
9.5.13 Site Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
9.6 Example 1: Teach and Run a Basic Recipe. . . . . . . . . . . . . . . . . . . . . . 322
9.6.1 Teach a Real-time Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
9.6.2 Run the Real-time Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 326
9.6.3 Add an Additional Site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
9.6.4 Teach an Offline Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328

Chapter 10 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331

10.1 Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
10.1.1 Remove File on Close . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
10.2 Programmed Move (Dimension Series Only). . . . . . . . . . . . . . . . . . . 333
10.2.1 Programmed Move Panels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
10.2.2 Procedure for Teaching a Programmed Move. . . . . . . . . . . . . . . . . . . . . . 336
10.2.3 Procedure to Remove a Programmed Option . . . . . . . . . . . . . . . . . . . . . . 336
10.2.4 Procedure to Insert a Step into an Existing Program Sequence . . . . . . . . 337
10.2.5 Procedure To Run a Series of Programmed Moves. . . . . . . . . . . . . . . . . . 337

Appendix A File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339

A.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
A.2 File Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
A.3 Data File Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
A.3.1 Header Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
A.3.2 Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
A.3.3 Control-Z (Ctrl-Z) Character . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
A.3.4 Padding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
A.3.5 Raw Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 344
A.4 Converting Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
A.4.1 Preparing Data for Spreadsheets (Summary) . . . . . . . . . . . . . . . . . . . . . . . 345
A.4.2 Preparing Data for Image Processing (Summary) . . . . . . . . . . . . . . . . . . . 345
A.4.3 Converting Data Files into ASCII . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
A.5 Converting Raw Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
A.5.1 Data Organization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
A.5.2 Calculating Scaling Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
A.5.3 Calculating Raw Data Values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349
A.5.4 Force Curve File Format Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
A.5.5 Force Volume File Format Information . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
A.6 Electrochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
A.6.1 EC File Format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
A.6.2 Data Conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
A.7 General Format for CIAO Parameter Objects . . . . . . . . . . . . . . . . . . . 353
A.7.1 Value Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
A.7.2 Scale Parameters. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354

viii Nanoscope Software 7.30 User Guide Rev. G

 A.7.3 Select Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 354
A.7.4 Procedures to Interpret Data in a Height Image . . . . . . . . . . . . . . . . . . . . . 355

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .357

Rev. G Nanoscope Software 7.30 User Guide ix

x Nanoscope Software 7.30 User Guide Rev. G
List of Figures
Chapter ii List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Chapter 1 New Features in NanoScope Software . . . . . . . . . . . . . . . . . . . . . . . 1

Chapter 2 New Features in NanoScope Software . . . . . . . . . . . . . . . . . . . . . . . 5

Figure 2.1a Administrator Warning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Figure 2.1b Welcome to NanoScope 7 Dialog Box . . . . . . . . . . . . . . . . . . . . . 7
Figure 2.1c Installation Type Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Figure 2.1d System Information and Recommendations Dialog Box . . . . . . . 8
Figure 2.1e Destination Location Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . 8
Figure 2.1f Select Features Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Figure 2.1g Calibration file location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Figure 2.1h Ready to Install Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure 2.1i Progress Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Figure 2.1j Installation Complete Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 11
Figure 2.2a Workspace Nodes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Figure 2.2b Screen Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Figure 2.2c Functions Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14
Figure 2.2d Permit Multiple Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
Figure 2.2e Realtime Workspace Functions Submenu . . . . . . . . . . . . . . . . . 16
Figure 2.3a New Realtime Screen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Figure 2.3b Older workspaces are not be supported . . . . . . . . . . . . . . . . . . . 21
Figure 2.3c Import confirmed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Figure 2.4a NanoScope Software Window . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Figure 2.4b Microscope Select Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 2.4c Equipment Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Figure 2.4d Add Realtime Views Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . 25
Figure 2.4e Status Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Figure 2.4f Change Filename. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Figure 2.4g NanoScope Image View Window. . . . . . . . . . . . . . . . . . . . . . . . 30
Figure 2.4h Color Scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Figure 2.4i Section Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Figure 2.4j The ASCII Export Command . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Figure 2.4k The File Export Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Figure 2.4l Sample ASCII Image File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Figure 2.4m Microscope Select . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35

Rev. G Nanoscope Software 7.30 User Guide xi

List of Figures

Figure 2.4n System Component Designation . . . . . . . . . . . . . . . . . . . . . . . . 35

Figure 2.4o Set the SCAN DATA LIMITS to SYSTEM MAXIMUMS for
images with more than 1 M data points. . . . . . . . . . . . . 36

Chapter 3 Realtime Views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39

Figure 3.1a Manual Scanning in Realtime . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Figure 3.2a Navigate Menu Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Figure 3.2b Navigate View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Figure 3.2c Engage Stage-Motor Settings Dialog Box. . . . . . . . . . . . . . . . . 45
Figure 3.2d Meter View and Docking RealTime Status Window. . . . . . . . . 46
Figure 3.2e Point and Shoot View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Figure 3.2f Ramp Parameters > Mode > XY move on surface . . . . . . . . . . 49
Figure 3.2g Tapping Cantilever in Mid-air . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Figure 3.2h Tapping Cantilever on Sample Surface . . . . . . . . . . . . . . . . . . . 50
Figure 3.2i Cantilever Tune Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Figure 3.2j Cantilever Tune Method Comparison . . . . . . . . . . . . . . . . . . . . 53
Figure 3.2k Typical Generic Sweep . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Figure 3.2l Electric Tune Generic Sweep while adjusting the
Drive Amplitude and Drive Phase. . . . . . . . . . . . . . . . . 55
Figure 3.2m Scan-Single and Main Controls . . . . . . . . . . . . . . . . . . . . . . . . 56
Figure 3.2n Scope Grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Figure 3.2o Scope Grid Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Figure 3.2p Main Controls Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Figure 3.2q Select Scan View Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Figure 3.2r Scan Tab Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Figure 3.2s Aspect Ratio Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Figure 3.2t Scan Angle Rotated Example. . . . . . . . . . . . . . . . . . . . . . . . . . . 63
Figure 3.2u Channels Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Figure 3.2v Feedback Controls Tab in TappingMode. . . . . . . . . . . . . . . . . . 69
Figure 3.2w Interleave Lift Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Figure 3.2x Lift Scan Height Illustrated . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Figure 3.2y Lift Start Height Illustrated . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Figure 3.2z Other Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Figure 3.3a Real Time Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Figure 3.3b Color Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Figure 3.3c Color Adjust Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Figure 3.3d Image Cursor Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Figure 3.3e Grid Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Figure 3.3f Default Configuration Settings Window . . . . . . . . . . . . . . . . . . 85
Figure 3.3g Add Views to Realtime1 Dialog Box . . . . . . . . . . . . . . . . . . . . 86
Figure 3.3h Add Views to Realtime1 Menu . . . . . . . . . . . . . . . . . . . . . . . . . 87
Figure 3.3i Select SCAN 8 CHANNELS in RealTime view . . . . . . . . . . . . . . 87
Figure 3.3j Scan-Dual View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Figure 3.3k Scan Triple view and Location of Channel 2 and 3 Parameters 89

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 List of Figures

Figure 3.3l Scan 8 Channels RealTime view. . . . . . . . . . . . . . . . . . . . . . . . 90

Figure 3.3m Tapping Engage Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Figure 3.3n Tip Amplitude While Approaching the Sample Surface . . . . . . 93
Figure 3.3o Select OUTPUT 1 DATA TYPE . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Figure 3.3p Input signal selection shown with the SCM module connected . 99
Figure 3.3q Output signal selection: left: tapping; right SCM. . . . . . . . . . . . 99
Figure 3.4a Bar Graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
Figure 3.4b Force Curve. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Figure 3.4c Realtime Force Curve . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Figure 3.4d Force Curve Cursors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Figure 3.4e Update Sensitivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
Figure 3.4f Deflection Sensitivity Dialog Box. . . . . . . . . . . . . . . . . . . . . . . 103
Figure 3.4g Ramp Parameter List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Figure 3.4h Ramp Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Figure 3.5a Force Curve with Both Extending and Retracting Traces (top) 113
Figure 3.5b The Force Volume Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
Figure 3.5c Force Volume Parameter Window . . . . . . . . . . . . . . . . . . . . . . 116
Figure 3.5d Calibrating Deflection as Displacement . . . . . . . . . . . . . . . . . . 120
Figure 3.5e A Force Volume Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Figure 3.5f Force Volume Parameters Window . . . . . . . . . . . . . . . . . . . . . . 122
Figure 3.5g Image Scan Time versus Samples per line and Z scan rate. . . . 124
Figure 3.5h Data center and Z display are Controlled by Cross-hairs . . . . . 127
Figure 3.5i Z Display and Data center in Relation to Cursor. . . . . . . . . . . . 128
Figure 3.5j CAPTURE LAST Assists Collecting Non-Square
Force Volume Data (see text for discussion) . . . . . . . . 129
Figure 3.5k Example of Excessive Adhesion. . . . . . . . . . . . . . . . . . . . . . . . 131
Figure 3.5l Force Volume Slices - Block Height Represents Deflection. . . 133
Figure 3.5m Force Volume: multi-layered polyethylene . . . . . . . . . . . . . . . 134
Figure 3.5n Retracting Slices: Adhesion vs. Z Positions 1-4
in Figure 3.5m . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
Figure 3.5o Iso-Force Surfaces: Bacteriorhodopsin Adsorbed to Mica.. . . 137
Figure 3.5p Force Volume Data File Structure. . . . . . . . . . . . . . . . . . . . . . . 141
Figure 3.6a Select Piezo Response for MICROSCOPE MODE . . . . . . . . . . . 144
Figure 3.6b Scan Parameter List including Piezoresponse variables. . . . . . 145
Figure 3.7a LiftMode Principles Used in Surface Potential Detection . . . . 148
Figure 3.7b Simplified Block Diagram of Surface Potential Detection. . . . 148
Figure 3.7c Force as a Function of Voltage . . . . . . . . . . . . . . . . . . . . . . . . . 149
Figure 3.7d VAC at w, DVDC = 2V. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Figure 3.7e Major Force Component in Phase with VAC at
Frequency ω, DVDC = 2V . . . . . . . . . . . . . . . . . . . . . . 151
Figure 3.7f VAC at ω, DVDC = -2V . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Figure 3.7g Major Force Component 180° Out of Phase with VAC at
Frequency w, DVDC = -2V . . . . . . . . . . . . . . . . . . . . . 151
Figure 3.7h VAC at w, DVDC= 0V . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

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List of Figures

Figure 3.7i Force at frequency of 2w, DVDC = 0V . . . . . . . . . . . . . . . . . . 152

Figure 3.7j Electrically Connecting a Sample to the Piezo Cap
(MultiMode) or Chuck (Dimension) . . . . . . . . . . . . . . 152
Figure 3.7k Electrically Isolating a Sample from the Piezo Cap
(MultiMode) or Chuck (Dimension) . . . . . . . . . . . . . . 153
Figure 3.7l Sample Bias . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Figure 3.8a The Generic Lock-In, shown configured for TappingMode
imaging. The DDS 1 output is routed to the Tapping
Piezo and the lock-in input is set to monitor the vertical
photodetector signal. . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Figure 3.8b Buttons to enable/disable the lock-in and to set parameters
for main and interleave modes. . . . . . . . . . . . . . . . . . . 160
Figure 3.8c The Generic Sweep window may be accessed from the
lock-in panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Figure 3.8d The Drive Output panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Figure 3.8e The Lock-In Input panel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163
Figure 3.9a High Speed Data Capture window . . . . . . . . . . . . . . . . . . . . 164
Figure 3.9b Abort box. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
Figure 3.9c Point and Shoot - High Speed Data Capture . . . . . . . . . . . . . . 168
Figure 3.10a Pulse Counter Enabled. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169

Chapter 4 File Navigation and Browsing . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171

Figure 4.1a Select VIEW > BROWSE to Open the Browse Window. . . . . . 172
Figure 4.1b Browse Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Figure 4.1c Browse for Folder Window Open Upon Clicking Directory. . 173
Figure 4.1d Browse Column Configuration . . . . . . . . . . . . . . . . . . . . . . . . 173
Figure 4.1e Thumbnail Images in the Browse Window . . . . . . . . . . . . . . . 174
Figure 4.1f Sorting Thumbnails . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Figure 4.1g Capture File Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Figure 4.1h Selecting the Display Channel and Color Table for the Icons. 176
Figure 4.1i Exporting Multiple Images from the Image Browse Window . 177
Figure 4.1j Image Processing Functions Menu. . . . . . . . . . . . . . . . . . . . . . 178
Figure 4.1k Adding Offline Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Figure 4.1l Add Offline Views Window . . . . . . . . . . . . . . . . . . . . . . . . . . . 179

Chapter 5 Display Commands. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181

Figure 5.1a Open NanoScope File Dialog Box. . . . . . . . . . . . . . . . . . . . . . 182
Figure 5.1b Image for Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Figure 5.1c Image Click . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Figure 5.1d Image Adjustment Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Figure 5.1e Image Cursor Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Figure 5.1f Captured Dual-Scan Image . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
Figure 5.1g Captured Triple-Scan Image . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Figure 5.2a Multi-Channel offline view . . . . . . . . . . . . . . . . . . . . . . . . . . 189

xiv Nanoscope Software 7.30 User Guide Rev. G

 List of Figures

Figure 5.3a 3D Surface Plot Window. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191

Figure 5.5a HSDC Offline Display Window . . . . . . . . . . . . . . . . . . . . . . . . 194

Chapter 6 Analysis Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .197

Figure 6.1a Depth Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
Figure 6.1b Functions Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Figure 6.1c Depth Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Figure 6.1d Depth Histogram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Figure 6.1e Grid Parameters Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Figure 6.2a Waveform Surfaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Figure 6.2b Progressive Data Sampling . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Figure 6.2c Epitaxial Gallium Arsenide Image . . . . . . . . . . . . . . . . . . . . . . 206
Figure 6.2d PSD Plot for Terraced Sample . . . . . . . . . . . . . . . . . . . . . . . . . 206
Figure 6.2e PSD Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Figure 6.2f Power Spectral Density Histogram . . . . . . . . . . . . . . . . . . . . . . 209
Figure 6.2g Select Show All On/Off Check Boxes . . . . . . . . . . . . . . . . . . . 209
Figure 6.2h Spectrum Plot Parameter Menu . . . . . . . . . . . . . . . . . . . . . . . . 210
Figure 6.2i Color Menu Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Figure 6.2j Filter Menu Items . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
Figure 6.2k Scale Settings Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
Figure 6.2l Line Style Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 212
Figure 6.2m User Preferences Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Figure 6.3a Basic Roughness Measurements . . . . . . . . . . . . . . . . . . . . . . . . 214
Figure 6.3b Roughness Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Figure 6.3c Input On Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Figure 6.4a Section Analysis Orientation . . . . . . . . . . . . . . . . . . . . . . . . . . 222
Figure 6.4b Section Command Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223
Figure 6.4c Mouse Drawing Line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Figure 6.4d Section View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Figure 6.4e Configure Columns Window . . . . . . . . . . . . . . . . . . . . . . . . . . 227
Figure 6.4f Grid Parameters Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Figure 6.5a Step Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 230
Figure 6.5b Level Option Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Figure 6.5c Grid Parameters Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 233
Figure 6.6a Depth Histogram Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
Figure 6.6b Width Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 236
Figure 6.6c Depth Histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Figure 6.6d Grid Parameters Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
Figure 6.7a XY Drift View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241

Chapter 7 Modify Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .243

Figure 7.1a Median Filter Example. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Figure 7.1b 3 x 3 Pixel Matrix . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Rev. G Nanoscope Software 7.30 User Guide xv

List of Figures

Figure 7.1c Gaussian Filter Example . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245

Figure 7.2a Clean Image Diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
Figure 7.2b Clean Image Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
Figure 7.2c Image of Figure 7.2b after 1 clean operation. . . . . . . . . . . . . . 248
Figure 7.3a Initial Crop and Split Window . . . . . . . . . . . . . . . . . . . . . . . . 251
Figure 7.4a Erase Options Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
Figure 7.4b Effect of the Erase Interpolation on a Rectangular Area. . . . . 255
Figure 7.5a Image Flattened . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Figure 7.5b Raw Image of Syndiatatic Polystyrene (500nm). . . . . . . . . . . 259
Figure 7.5c Flattened Image of Syndiatatic Polystyrene (500 nm). . . . . . . 260
Figure 7.5d Flatten View. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Figure 7.6a Larger Filter Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Figure 7.6b Smaller Filter Size . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263
Figure 7.6c Gaussian Filter Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 264
Figure 7.6d Views of Diffraction Grating . . . . . . . . . . . . . . . . . . . . . . . . . . 267
Figure 7.6e Magnetic Domains in a Permalloy Specimen . . . . . . . . . . . . . 268
Figure 7.6f Gaussian Highpass-Filtered Images . . . . . . . . . . . . . . . . . . . . . 269
Figure 7.7a Lowpass Image Display. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
Figure 7.8a # Different Pixel Arrays of the Same Image . . . . . . . . . . . . . . 272
Figure 7.8b Median View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Figure 7.9a Visual Representation of Plane Fit. . . . . . . . . . . . . . . . . . . . . . 274
Figure 7.9b Saddle Image Before Plane Fit . . . . . . . . . . . . . . . . . . . . . . . . 276
Figure 7.9c Plane Fit View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Figure 7.9d Plane Fit Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Figure 7.9e Plane Fit Inputs Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . 278
Figure 7.10a The Spectrum 2D View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 281
Figure 7.10b Select BOX or STOPBAND . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Figure 7.10c DELETE, SET COLOR and CLEAR ALL buttons are active
inside a passband or STOPBAND window. . . . . . . . . . . 282
Figure 7.10d Horizontal Passband Box Illustration . . . . . . . . . . . . . . . . . . 286
Figure 7.10e Vertical Passband Box Illustration. . . . . . . . . . . . . . . . . . . . . 287
Figure 7.10f Spectrum 2D Hot Spots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
Figure 7.11a Effects of Image Subtraction . . . . . . . . . . . . . . . . . . . . . . . . . 289
Figure 7.11b Subtract Image View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Figure 7.11c Subtract Image after channel 2 (right) was subtracted
from channel 1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291

Chapter 8 AutoProgram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 293

Figure 8.1a Open Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
Figure 8.1b Create AutoProgram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Figure 8.1c Include Selected Image Box . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Figure 8.1d Add Views to be Included in an AutoProgram . . . . . . . . . . . . 296
Figure 8.2a Specify a Flatten Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Figure 8.3a Specify a Depth Measurement . . . . . . . . . . . . . . . . . . . . . . . . . 298

xvi Nanoscope Software 7.30 User Guide Rev. G

 List of Figures

Figure 8.4a Specify a Roughness Measurement for Inclusion in an

AutoProgram. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Figure 8.5a Add Files Dialog Box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Figure 8.5b Log File View Property Sheet. . . . . . . . . . . . . . . . . . . . . . . . . . 301

Chapter 9 Recipes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .303

Figure 9.1a Recipe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
Figure 9.2a File Browse Button . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
Figure 9.3a Recipe Runner Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
Figure 9.6a Example 1, Basic Outline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Figure 9.6b Navigate Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324
Figure 9.6c Recipe Runner Window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Figure 9.6d Add Files to the Image List. . . . . . . . . . . . . . . . . . . . . . . . . . . . 329

Chapter 10 Tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .331

Figure 10.1a Remove File on Close Menu Item . . . . . . . . . . . . . . . . . . . . . 332
Figure 10.2a Selecting Programmed Move . . . . . . . . . . . . . . . . . . . . . . . . . 334
Figure 10.2b Programmed Move File Name Selection . . . . . . . . . . . . . . . . 334
Figure 10.2c Programmed Move Window . . . . . . . . . . . . . . . . . . . . . . . . . 335
Figure 10.2d Stage Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Figure 10.2e Stage Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
Figure 10.2f Programmed Move Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338

Chapter A File Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .339

Figure A.3a Single and Two-Image Data File Structure . . . . . . . . . . . . . . . 341
Figure A.3b Example of a Two-image Header File . . . . . . . . . . . . . . . . . . 342
Figure A.4a The ASCII Export Command. . . . . . . . . . . . . . . . . . . . . . . . . . 346
Figure A.4b The File Export Dialog Box. . . . . . . . . . . . . . . . . . . . . . . . . . . 347
Figure A.5a Exported image data organization . . . . . . . . . . . . . . . . . . . . . . 348
Figure A.7a Sample Parameter List for an Image File. . . . . . . . . . . . . . . . . 355

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .357

Rev. G Nanoscope Software 7.30 User Guide xvii

List of Figures

xviii Nanoscope Software 7.30 User Guide Rev. G

Chapter 1 New Features in NanoScope
Software

1.1 New Features in NanoScope v7.30 Software

• Harmonic Force Microscopy (HarmoniX)—optional. See the HarmoniX User Guide,
Veeco p/n 004-1024-000.

• Offline Modify command Clean Image function. See Clean Image: Section 7.2.

• Offline Modify command Guassian function. See Gaussian: Section 7.6.

• Dimension Heater/Cooler Support. See Support Note 441, Dimension Heater/Cooler.

• Closed Loop Force Volume. See Page 116.

• 5K x 5K image is available on all 8 channels.

• Starting with NanoScope 7.30, older workspaces are not supported. See Older
Workspaces Unsupported in NanoScope v7.30 and later: Section 2.3.4.

• Dark Lift. See Application Modules NanoScope Software Version 7, Rev. B or later,
Veeco p/n 004-1020-000.

1.2 New Features in NanoScope v7.20r1sr1 Software

• EnviroScope STM and Electrochemistry support. See the EnviroScope Using a
NanoScope V Controller Instruction Manual, Veeco part number 004-1008-000 and the
Electrochemical SPM NanoScope Software v7 manual, Veeco part number 004-1016-
000.

• TR TUNA. See the Applications Modules NanoScope Software v7 manual, Veeco part
number 004-1020-000.

• Piezo Response improvements. See the NanoScope V Controller Manual, Veeco part
number 004-992-000, Revision E or later.

• MultiMode Closed Loop XYZ. See MultiMode Closed Loop Scanner, Veeco Support
Note 013-431-000.

• Many other smaller features and bugs fixed. See the Research 7.20 Release Notes.

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New Features in NanoScope v7.20r1 Software

1.3 New Features in NanoScope v7.20r1 Software

1.3.1 Newly Supported Hardware

NanoScope v7.20r1 supports additional hardware. This includes:

• EnviroScope using a NanoScope V Controller.

• BioScope (SZ) using a NanoScope V Controller.

• MS10 dedicated STM.

• Serial communication for the Universal Bipotentiostat

See the appropriate manuals, EnviroScope Manual, BioScope SZ Instruction Manual, Scanning
Tunneling Microscope Operation Manual and Universal Bipotentiostat for details.

1.3.2 Additional New Features

Additional new features, described in the NanoScope v7.20 release notes. These include:

• Pulse Counting

• Improved Width Offline function

• Spectrum 2D

• Nanoindentation

• Piezo response imaging. See the NanoScope V Controller Manual for information about
this mode.

• Torsion TUNA (Tunneling Atomic Force Microscopy) imaging. See the Applications
Modules NanoScope Software v7 Manual and Support Note 416, Revision H or later,
TRmode NanoScope Version 7 for information about this mode.

• Offline feature ROUGHNESS revised.

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New Features in NanoScope v7.10 Software

1.4 New Features in NanoScope v7.10 Software

1.4.1 Newly Supported Hardware

NanoScope v7.10 supports additional hardware. This includes:

• Dimension 5000 microscope.

See the appropriate manual, Dimension 5000 using a NanoScope V Controller Instruction Manual
for details.

1.4.2 Additional New Features

Additional new features, described in the NanoScope v7.10 release notes. These include:

• Recipes

• CROP AND SPLIT Offline View replaces ZOOM

• XY to Z Coupling with Ramp mode

• TIFF Export

1.5 New Features in NanoScope v7.00 Software

1.5.1 Newly Supported Hardware

NanoScope v7.0 supports new hardware. This includes:

• NanoScope V Controller.

• BioScope II.

See the appropriate manuals, NanoScope V Controller Manual, and BioScope II User Manual for
details.

1.5.2 Windows XP Support

NanoScope v7.0 runs on Windows XP.

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1.5.3 Additional New Features

Additional new features, described in the NanoScope v7.0 release notes and the NanoScope V
Controller Manual, are included in this manual. These include:

• Eight channel support.

• High resolution imaging.

• Signal Access Software.

• Surface Potential Detection

• Generic Lock-In

• High Speed Data Capture

• Force Volume.

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Chapter 2 Getting Started with
NanoScope v7.30 Software

The focus of this manual is the NanoScope software version 7. It is a reference to the tasks related
to your NanoScope system. The material provides an overview (i.e., theory and applications),
procedures, interface definitions and optimization tips.

Refer to the following sections to begin to understand the NanoScope software:

• Installing the NanoScope Software: Section 2.1

• Getting to Know the NanoScope Software: Section 2.2

• Setting up the Workspace Section 2.3

• Quick Guide to a 5K Point Image: Section 2.4

• Technical Support at Veeco: Section 2.5

2.1 Installing the NanoScope Software

2.1.1 System Requirements

CAUTION: Contact Veeco Technical Support (see Contact Information Section

2.5.2) before attempting to increase the RAM of your system. Failure
to do so could cause irreparable damage to your system.

The 7.10 version of software requires the following:

• A minimum computer configuration of 3.0GHz

• 1GB RAM (2GB recommended)

• G550 Video

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2.1.2 Before You Install

CAUTION: Ensure you have backed up all critical data onto external media before
installing the NanoScope 7.30 software.

1. If you are upgrading from a previous version of NanoScope, ensure you are starting with a
working version. The settings from the working version will be used for the new version.

2. Note that some of the installation screen views may not appear, or may appear slightly
different, depending on your particular system configuration.

3. Ensure you are logged in as Administrator on the local workstation.

2.1.3 NanoScope 7.30 Installation

Note: Most systems are configured on the microscopes prior to delivery.

1. Insert the NanoScope 7.30 CD-ROM in your CD drive, open the CD-ROM files, open the
v730 folder, and select the Setup.exe icon.

If you do not have Administrator privileges on your workstation, a WARNING will appear on the
screen and installation will discontinue (see Figure 2.1a).

Figure 2.1a Administrator Warning

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2. The Welcome to NanoScope 7 dialog box will open (see Figure 2.1b). Click NEXT.

Figure 2.1b Welcome to NanoScope 7 Dialog Box

3. After accepting the license agreement, the Installation Type dialog box will open (see
Figure 2.1c). Click NEXT.

Figure 2.1c Installation Type Dialog Box

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4. Install Shield then checks your system and, if needed, makes recommendations. See Figure
2.1d.

Figure 2.1d System Information and Recommendations Dialog Box

5. After choosing a destination location (see Figure 2.1e), click NEXT.

Figure 2.1e Destination Location Dialog Box

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6. Select the features you wish to install (see Figure 2.1f) and click NEXT.

Figure 2.1f Select Features Dialog Box

7. Browse to find calibration files or leave it blank for factory defaults. See Figure 2.1g. Click
NEXT.

Figure 2.1g Calibration file location

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8. The Ready to Install dialog box will display:

Figure 2.1h Ready to Install Dialog Box

9. Installation of the NanoScope V7.20 software will then continue. A progress box, shown in
Figure 2.1i, appears:

Figure 2.1i Progress Dialog Box

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10. When the NanoScope V7.30 installation is complete, the following dialog box will appear:

Figure 2.1j Installation Complete Dialog Box

11. Click FINISH to complete the installation.

2.2 Getting to Know the NanoScope Software

Start the NanoScope software by double-clicking on the desktop shortcut labeled NanoScope 7.30.

2.2.1 Software Interface

The NanoScope software contains two modes of operation: Realtime (i.e., all operations related to
controlling the microscope) and Image Processing or Offline (i.e., analysis and modification of
captured images). In previous versions of NanoScope software, these modes were separate work
environments. With versions 6 and 7, both work environments have been combined into a
“workspace.”

2.2.2 What is a Workspace?

A workspace is a configuration of views and parameters in the NanoScope software. Within the
workspace window, the user configures a hierarchy of commands (i.e., nodes) for running the
microscope and processing images. Auto programs are run in the order that commands are
configured.

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The behavior and appearance of the workspace window may be controlled using the Workspace >
Preferences menu or by right-clicking in the workspace window.

Figure 2.2a Workspace Nodes

Parent
Node

Child
Node

Nodes

The top level node is known as the parent node and each node underneath is known as a child node
(see Figure 2.2a). Parent nodes are usually the name for the microscope mode (e.g., Realtime) or a
file name of an image within the workspace. Parent nodes are the higher level nodes for auto
programs. Child nodes, also known as “views,” are typically associated with a window that is used
to carry out an analysis, image processing, or Realtime control function of the software.

Each node may be renamed, deleted and grouped. Node names may be preceded by an icon and/or
lines indicating the relative positions of nodes in the hierarchy.

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2.2.3 The Main Screen Elements

Workspace Window The left pane in the client window for viewing and configuring a
series of views.
Client Window A central window for viewing all Realtime graphical displays, input
parameters, results parameters and graphs.
Menu Bar A group of items for executing commands or viewing files.

Toolbar A group of icons for executing commands or viewing dialog boxes

to configure input parameters.
Status Bar A read only list that displays the stage X, Y, Z coordinates and
enabled functions (e.g., Capture: On).
RT Status Window A dockable window in the client window displaying information
about the sample during Realtime.
Browse Window A dockable window in the client window for browsing files. Avail-
able in list or thumbnail format.
Help Window A dockable window in the client window for displaying the Help
screen.

Start Real Time

Complete the following to open the NanoScope software:

1. Double-click the Real Time (shown) icon or click RealTime > Start Realtime.

2. The default screen appears with menu items (File, View, Help, etc.), a blank workspace and
a toolbar (see Figure 2.2b).

Note: Select File > Open Workspace to open a previously created workspace file.

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Figure 2.2b Screen Elements

Menu Bar

Toolbar

Workspace
Name

Workspace
Window

Status Bar

Functions Menu

The Functions menu is accessed by right-clicking on a parent node (i.e., Realtime or a filename). It
includes specific elements for viewing multiple windows, renaming views, grouping views, and
adding and deleting views. This menu also includes the command for running an Auto Program
(i.e., Run AutoProgram) where the image processing commands may be run in a series on
multiple images and results may be saved in a data file (see Figure 2.2c).

Figure 2.2c Functions Menu

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Menu Items

Add View Accesses a submenu of Realtime or offline commands.

Add Group Adds a Group node to the workspace for creating a defined set of
child nodes.

Delete Deletes the currently selected node in the workspace. If changes

were made, a prompt appears to save the view.

Delete Sub Items Deletes the items listed under the currently selected node in the
workspace. If changes were made, a prompt appears to save the
view.

Change Title Allows for the selected view title to be changed.

Permit Multiple Views Selecting this item allows for multiple views to appear in the client
window (see Figure 2.2d).

Assign File Allows the user to Assign a File to a node. Used to replace missing
files.

Create Auto Program Allows you to create a new Auto Program based on analysis done
on a node.

Edit AP Attributes If the currently selected node is in Auto Program, this parameter
allows you to edit the Auto Program properties.

Run Auto Program Accesses the Auto Program Results view to run the selected image
processing commands.

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Figure 2.2d Permit Multiple Views

Scan
View Meter
View

Navigate
View

Functions Submenu

The Functions submenu allows for adding new views to the workspace in the Add View command
(see Figure 2.2e).

Figure 2.2e Realtime Workspace Functions Submenu

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Functions Submenu Items

The Add View submenu includes commands for running the microscope, analyzing and reporting.
Selecting a command adds the item name and icon as a new child node to the workspace window.
Click on a node to invoke the view in the client window.

Depending upon the microscope type and mode (i.e., Realtime and Image Processing), each
workspace has unique commands in the Add View submenu. For the Realtime functions Add View
submenu, see Figure 2.2e. For more detailed descriptions about the views, see Chapter 3.

Quick Key Commands

Many commands have quick key commands (series of keys to enter in place of using the mouse).
You can open menus, access panels and execute commands with the keys or combination of
keystrokes. In the NanoScope software, the quick keys are designated by an underlined letter in
the command name (e.g., R is the quick key in Realtime).

To activate a quick key command, press the Alt button then the quick key, or select the command
with the mouse and press the indicated quick key.

Quick keys only apply when in an active box, menu, panel or window that is currently visible on
the screen. Active panels are designated in color with a highlight on the panel title or with a heavy
frame around the panel.

2.2.4 Menu Bar Items

The initial menu bar includes: File, View and Help to begin the process of initializing and opening
files in the client window. Once a workspace is open an expanded toolbar exists for running and
configuring the microscope to scan or process images.

The menu items include:

• File—Accesses menu selections for opening, saving and printing files and documents.

• View—Accesses menu selections allowing you to choose display properties.

• RealTime—Accesses menu selections to administer commands during data collection.

• Acquire—Accesses all Realtime Views.

• Offline—Accesses all Offline Views.

• Tools—Accesses menu items for selecting and calibrating various settings.

• Window—Accesses menu selections for arranging windows.

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• Help—Accesses menu items for initializing and displaying the help screen, Technical
Support contact information, probe purchase information and NanoScope information
about your system.

2.2.5 Cursor Types

Within captured images, it may be necessary to do analysis or modification on a selected area or

exclude this area from the analysis. Cursors allow for specifying this information.

The cursor types are as follows:

• Lines—Selecting specific data (e.g., lengths of features or sectioning features) along

the line.

• Boxes—Selecting specific areas on the display for including or excluding data.

• Grid Markers—Horizontal or vertical line cursors within histograms and spectrum

graphs for choosing data ranges or making measurements.

Using a Slider Cursor

In a graph or histogram, position the mouse within the blank area between the axis and the edge of
the graph and drag the slider along the graph to position the cursor. The mouse cursor will change
to .

Positioning a Line or Box Cursor

• Click and drag the image to draw a line or box cursor.

• To resize an existing line or box cursor, click and drag on a corner edge or end of the
object. Cursor will change to or .

• To move an existing object, click and drag the center of the object to the desired
location. The cursor will change to .

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Setting up the Workspace

2.3 Setting up the Workspace

2.3.1 Create or Open a Workspace

1. A workspace can be opened or created by selecting one of the following:

• File > New Workspace.

• File > Open Workspace and browse to open an existing workspace.

• File > Select the Workspace Name from the Recent files list.

Note: A new blank space will automatically display when version 7 is opened.

2. To begin Realtime operations, open a Realtime node. Select RealTime > Start Realtime or
click the NanoScope icon.

A Real Time node appears in the workspace, along with a dialog box allowing you to add views to
the Real Time node.

2.3.2 Add Views and Configure the Workspace

1. Position the mouse on the Realtime icon and right-click to view the functions menu (see
Figure 2.3a).

2. If one of the views (Scan-Single, Scan-Dual, or Scan-Triple) does not appear

automatically, in the functions menu, select Add View and one of the scan views or click the
Scan button.

3. Add the following views to your workspace to set up the hardware for scanning:

• Meter View—for verifying the laser signal on the cantilever. (If desired, the View >
Real Time Status window can be opened in place of the Meter View).

• Navigate View—for setting the tip to sample focus, locate tip and stage alignment (not
present for MultiMode).

4. Customize your workspace with any additional views using the same procedure as in Step 2.

Note: In the Functions menu, select Permit Multiple Views for allowing several
windows to display.

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2.3.3 Multiple Users using NanoScope

The NanoScope computer can save multiple user preferences/settings in the computer registry.
Once a user sets up an account on the computer, several settings are automatically saved for the
user. These settings include:

• Previous image file type

• Previous directories

• Browse window settings

• Option to disable video while scanning

• Section View results to display

• Location of Abort dialog box

• Review curve settings

• Force Filter settings

• Help settings

• Script directory

• Track ball on

• Default Parameter dialog box location

• Point and Shoot View settings

• Sweep dialog box settings

• Workspace settings

• Image control settings

• Grid control settings

• Meter View control settings

• Color control settings

• Z center control settings

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Figure 2.3a New Realtime Screen

Right-click on
the Realtime node
to view the
Functions Menu

Select to
Add Views
to the Work-
Space

Realtime Workspace

Scanning ImageView

Scan Controls

2.3.4 Older Workspaces Unsupported in NanoScope v7.30 and later

Starting with V7.30 older workspaces will not be supported. See Figure 2.3b.

Figure 2.3b Older workspaces are not be supported

To import an older NanoScope workspace:

1. Open the older version of Nanoscope.

2. Open the workspace you would like to get parameter values from.

3. Ensure that you are in RealTime Mode.

4. Go to FILE > SAVE AS...

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5. You will be prompted to save to a (settings) .bag file.

6. Open the newer version of Nanoscope.

7. Go to Realtime mode.

8. Go to Open...

9. Select settings type, (settings)*.bag files.

10. Select the bag file saved from the older version.

11. You should get the confirmation message shown in Figure 2.3c.

Figure 2.3c Import confirmed

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Quick Guide to a 5K Point Image

2.4 Quick Guide to a 5K Point Image

The following procedures provide quick steps for using NanoScope 7 software. Follow these steps
to quickly scan a sample and then capture and analyze an image. Along the way, you’ll see how
NanoScope 7 software works, learn some useful tricks, and find out how to learn more later.

If you have used the “classic” NanoScope software, you’ll see that the new interface is Microsoft
Windows-based.

This section is not intended to teach a new user how to run an AFM, but only to introduce
experienced users to NanoScope version 7.

2.4.1 Starting the NanoScope Software

After the software installation is complete, you are ready to start the NanoScope software and add
some views to the software workspace.

1. To start the NanoScope software, double-click the NanoScope 7.3 startup icon on the
computer desktop. You will see the NanoScope software window (see Figure 2.4a), which
can span one or two monitor displays. This large window will contain all the areas and views
you use to control the microscope and analyze your results.

Figure 2.4a NanoScope Software Window

2. Notice the white area on the left side of the NanoScope software window. This white area is
the “workspace.” This area acts as an organizer for operations you use in the software—
including scanning and analysis. Each item in the workspace has a view window that lets you
set parameters, perform actions, or view results. The sequence of items in the workspace is
important only for Auto Programs that use offline functions.

3. Select Tools > Select Microscope to open the Microscope Select dialog box, shown in
Figure 2.4b.

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Figure 2.4b Microscope Select Dialog Box

In the Microscope Select dialog box:

a. You can add a new set of hardware configuration parameters by clicking New, or edit
the parameters of the selected microscope by clicking Edit. The parameters include
things such as the controller and vision system.

b. In the Equipment dialog box, choose the microscope you are using (see Figure 2.4c). If
you are using a MultiMode AFM, select the scanner you plan to use (Scanner button).

Note: Select the Advanced button to view all equipment parameters.

Figure 2.4c Equipment Dialog Box

4. Click the yellow Realtime icon in the toolbar. This adds a “Realtime” group and a Scan
View to the workspace. It may take a moment the first time Realtime is added. A dialog box
(see Figure 2.4d) will appear giving you the option to add more views.

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Figure 2.4d Add Realtime Views Dialog Box

5. Right-click on Real Time1 in the workspace and select Permit Multiple Views from the
pop-up menu. When this item is enabled (that is, has a check mark next to it), you can have
several views open at the same time.

Note: Areas in the NanoScope software window can be resized and moved to make it
easier for you to use. When you reopen the software, it will remember your
changes. Drag the edge of an area to resize it. Drag the title bar or double raised
lines on an area to move it to another edge of the window or to make it a
floating window. (In Microsoft Windows terminology, these areas are
“dockable.”) Click the “X” in the upper-right corner to close an area. Use the
View, File, or Scan menu to open an area. For details about the areas of the
NanoScope software window, see Section 2.2.

If you are using a Dimension Series AFM, continue with the steps in Preparing a Dimension Series
AFM for a Realtime Scan. If you are using a MultiMode AFM, skip to Scanning and Scan
Parameters Section 2.4.4.

2.4.2 Preparing a Dimension Series AFM for a Realtime Scan

Once you’ve created the workspace, prepare the system to scan. This includes selecting the
operation mode, aligning the laser, adjusting the photodetector, locating the cantilever tip with the
optical microscope, and focusing the optical microscope on the surface. If you have not yet learned
these procedures, refer to your Dimension Microscope Manual and/or SPM Training Notebook.

For details on using the Realtime Scan Views, see Chapter 3.

1. Click the Scan group or one of the Scan views (Scan-Single, Scan-Dual, Scan-Triple or
Scan 8 Channels) in the workspace to see one of the Scan Views. In the Scan Parameters
window, set the Microscope mode parameter to Tapping or Contact.

2. Mount the probe into the cantilever holder

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3. Mount the cantilever holder onto the end of the scanner head.

4. Align laser on cantilever.

5. Click Meter in the workspace or check View -> Real Time Status to see the Meter View.
Turn the two screws on the side of the scanner to adjust the laser position in the
photodetector. In the Meter View, the location of the red dot and the values at the bottom of
the display change.

6. Click Navigate in the workspace to see the Navigate window. This view shows the video
and stage controls. Activate the track ball by checking the box next to TRACKBALL inside
the Navigate window.

7. Click the Locate Tip icon in the toolbar or the Locate Tip button within Navigate View.
Slide the illumination value to the right until the probe area is visible. Using the two
adjustment screws to the left of the optical objective of the microscope, center the tip of the
cantilever under the crosshairs.

8. Focus on the tip end of the cantilever either by using the trackball while holding down the
bottom-left button or by using the optical Focus mouse controls. Click and hold the large
arrow keys to move the focus up or down. The speed is controlled by the sliding bar or by
typing a value from 0 to 100. Click OK to set the focus and enter Focus Surface mode.

When you leave Locate Tip mode, the optics move to a focus position, typically 1mm below
the tip. To set this, select Tools > Engage Settings > General > Sample clearance.

9. Focus the optics on the sample surface using either the trackball or the Z Motor arrows in
the Navigate View. To use the track ball, check the trackball box, and roll the trackball up
or down while holding down the bottom-left button. To use the Z Motor arrows, click and
hold them down. You can use the speed controls in the Z Motor area to adjust the speed.
This adjustment raises or lowers the Z stage on which the SPM and optics are mounted.

10. Move the x-y stage to align the desired location on the sample under the crosshairs either by
using the trackball without holding down any buttons or by using the XY Stage arrows in the
Navigate View.

11. If you are using TappingMode, click the Tune icon. Check your parameters in the Auto
Tune list.

12. Click the Auto Tune button. Notice that the status bar at the bottom of the NanoScope
software window says “Cantilever Tuning” during automatic tuning. When tuning is
complete, click Exit in the Cantilever Tune dialog box. Proceed to Section 2.4.4, "Scanning
and Scan Parameters".

2.4.3 Preparing a MultiMode AFM for a Realtime Scan

Once you’ve created the workspace, prepare the system to scan. This includes selecting the
operation mode, mounting the probe, selecting the scanner, mounting the sample, aligning the laser,

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and adjusting the photodetector. If you have not yet learned these procedures, refer to your
Multimode Manual and/or SPM Training Notebook.

1. Click Scan or Scan-Single in the workspace to see the Scan View. In the Scan Parameters
List, under the Other tab, set the Microscope mode parameter to TAPPING or CONTACT.

2. Change the mode switch on the base of the microscope. Set it to TM_AFM if you are using
TappingMode. Set it to AFM & LFM mode if you are using Contact mode.

3. Mount the probe into the cantilever holder.

4. Put the cantilever holder in the SPM head. Secure the holder by tightening the screw in the
back of the SPM head.

5. Choose a scanner (A, E, or J) by clicking on Tools > Select Scanner. Mount and plug the
scanner into the base. Attach the corresponding springs to the microscope base.

6. Mount sample onto scanner.

7. Place SPM head on scanner, making sure there is enough clearance between the tip and the
sample.

8. Align laser.

9. Adjust the photodiode signal.

10. If you are using TappingMode, click the Tune icon. Check your parameters in the Auto Tune
list.

11. Click the Auto Tune button in the Cantilever Tune dialog box. Notice that the status bar at
the bottom of the NanoScope software window says “Cantilever Tuning” during automatic
tuning. When tuning is complete, click Exit in the Cantilever Tune dialog box.

2.4.4 Scanning and Scan Parameters

Next, you set scan parameters and scan the sample.

1. In the Scan-Single or the Scan Parameters window, use the following initial parameter
settings in the Scan tab. These values may already be set; they are handy starting values.

Scan size: 1µm

Aspect Ratio: 1.00
X offset: 0nm
Y offset: 0nm
Scan angle: 0.00 °
Scan rate: 2Hz

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2. Most of these commonly-used parameters are also shown on the Main tab. You can right-
click on the field in the Main tab to open a dialog box that allows you to change which
parameters are shown on the Main tab.

3. To collect 5K points of data per line, set the following parameters in the Scan tab:

Aspect ratio: 8.00 (4.00 if Lines is 1024; 1.00 if Lines is

5120) and you want square pixels
Samples/line: 5120
Lines: 640, 1280 or 5120

Note: You can use the mouse to adjust the value in many parameter fields. Click on
the value and drag the mouse left to decrease the value or right to increase the
value.

The Aspect ratio controls the X:Y ratio of the pixels in the displayed image. Because there is
an 8:1 ratio between 5120 samples/line and 640 lines, using an Aspect ratio of 8 causes the
pixels displayed in the image to be square.

4. For TappingMode, use the following initial parameter settings in the Feedback tab:

SPM feedback: Amplitude

Integral gain: 1.0
Proportional gain: 5.0

5. For Contact mode, use the following initial parameter settings in the Feedback tab:

Integral gain: 5.0

Proportional gain: 10.0
Deflection setpoint: 0V (vertical deflection = -2V (before engage)

6. Click the Engage button in the Main tab or click the Engage icon. Scan lines appear in the
Scan View once the tip engages and scanning begins.

7. Click the Scope button. Check to see whether the trace and retrace lines are tracking each
other well. They should have a similar shape, but they may not overlap each other
horizontally or vertically. Adjust the Scan rate, Integral gain, Proportional gain, and/or
Setpoint (that is, Amplitude setpoint for TappingMode and Deflection setpoint for Contact
Mode) parameters. Once the trace and retrace are tracking well, your tip is scanning the
sample surface.

8. At this point, you may want to adjust the Scan size, X offset, Y offset, and Scan angle (Scan
Tab) parameters to locate the scan over features of interest. If you increase the Scan size,
remember that the Scan rate should be lowered.

Note: You can zoom in on the scan image by selecting the Zoom button below the
image. Then, use your mouse to drag a box outline over the area you want to
zoom in on. Click Offset to offset the center position of your scan.

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 Getting Started with NanoScope v7.30 Software
Quick Guide to a 5K Point Image

9. With a 5K image, it may be useful to zoom in on the scan without changing the scan size.
Select the Data Zoom button above the image. Use your mouse to drag a box outline on the
image (begin by clicking where you want the center of the box to be). When you release the
left button, you will be zoomed in (scan size of image display will change) but the scanner
will remain scanning the original scan size. At this point you can choose to “pan” over to
other areas of the total scan. Select the Pan button and click and hold the left mouse button as
you move the mouse. The left arrow button above the image allows you to go back to the
original scan and the right arrow button allows you to go to more zoomed in scans (if you
have done multiple zooms). You may also choose to physically change the scan size or X/Y
offsets by using the Zoom or Offset.

2.4.5 Capturing an Image

Once you have adjusted the scan parameters, you can capture a scanned image. Perform these steps
once a scan you want to capture is in progress.

1. You can capture a scan in any one of three ways:

• From the menu bar, select RealTime > Capture.

• From the menu bar, select RealTime > Capture Now.

• On the Main Tab in the Scan View, click the Capture button.

• Click the Capture icon in the toolbar.

The scan will continue. Notice that the status bar at the bottom of the NanoScope window (see
Figure 2.4e) says “Capture: On.” When the current scan is complete, the image will be stored
automatically in the Capture Directory with the file name indicated in the status bar. The file
name and directory can be changed by selecting Realtime > Capture Filename from the menu
bar (see Figure 2.4f).

Figure 2.4e Status Bar

Capture Status

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Quick Guide to a 5K Point Image

Capture Now, and Capture Last save as much of the image buffer as possible including parts of it
that were generated with different parameters such as gains, setpoints, etc., so some of the
information in the header may be incorrect for some parts of the saved image.

Figure 2.4f Change Filename

2. In the Image Browser area (see Figure 2.4g), check to see if you are looking at the Capture
Directory. If not, select the Capture Directory icon, shown at left, (or click the “...” button
and select the Capture Directory, which is usually D:\Capture). If you don’t see the Image
Browser, choose View > Browse.

Figure 2.4g NanoScope Image View Window

Image
Browse
Area

Image View

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 Getting Started with NanoScope v7.30 Software
Quick Guide to a 5K Point Image

3. Double-click the image you just captured. The image opens in the Image View window (see
Figure 2.4g). Notice that the image filename and an image view are added to your
workspace.

4. If you need to change the CONTRAST or COLOR TABLE, right-click on the color scale of the
Image window, and change the appropriate values in the Color Scale popup window. The
Color Table may also be changed by clicking and holding the color bar, then dragging the
mouse left or right.

Note: To rename image files, you can use File > Save As, use Explorer to rename the
file, or right-click on the image in the image browser and select Move.

Figure 2.4h Color Scale

2.4.6 Analyzing an Image with Section Analysis

After opening the captured image, you can analyze the image. In this example, the Flatten filter
and Section analysis views are used.

1. Right-click on the name of the image in your workspace. Choose Add View > Flatten from
the pop-up menu, select Offline > Flatten from the menu bar, or click the Flatten icon.

The Flatten filter can be used to remove image artifacts due to vertical (Z) scanner drift, image
bow, skips, and anything else that may have resulted in a vertical offset between scan lines.
Refer to Flatten on page 257 for a detailed description of Flatten.

2. Set the input parameters for the filter. For example, you can choose the order of the
polynomial to use to fit scan lines.

3. Click Execute.

4. To restore to the original data, click Reload. Then change the parameters and click Execute
again.

5. Right-click on the name of the image in your workspace again. Choose Add View > Section
from the pop-up menu, select Offline > Section from the menu bar, or click the Section icon.
Section analysis allows you to easily make depth, height, width, and angular measurements.

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Quick Guide to a 5K Point Image

6. Drag a line across the image. A vertical cross section along that line is shown in the upper
graph area, shown in Figure 2.4i. The lower graph also shown in Figure 2.4i, shows the
power spectrum (Fourier Transform) of the cross section.

7. In the upper grid, drag the two cursors around to make measurements. You can grab two or
more measurement cursors from the outside of the grid. You will see the cursor change from
a to a , at which point you can grab the measurement cursors. The results area at the
bottom of the view shows various measurements at the marker position.

Note: Section can have three horizontal lines or 3 rotating lines or one rotating box. It
can have three sets of grid markers on one image cursor or one set of grid
markers on each image cursor.

8. If you would like to make an Average Section, right-click on the image, select Rotating Box.
After drawing the box, you can make it rotate by holding down the shift key while grabbing
anywhere in the box.

Figure 2.4i Section Analysis

2.4.7 ASCII Export

When transporting the results of using NanoScope software to another computing platform, the
most generic format is an ASCII text file. The File > Export > ASCII command builds such a file.

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Quick Guide to a 5K Point Image

1. Select a directory, then an image file within it, from the file browsing window at the right of
the NanoScope Version 7 main window. Right-click in the thumbnail image to open the
menu shown in Figure 2.4j.

Figure 2.4j The ASCII Export Command

2. Click Export > ASCII to open the Export dialog box (see Figure 2.4k).

Figure 2.4k The File Export Dialog Box

3. Select the Units in which to record the data in the new file by checking the appropriate
boxes. DISPLAY exports the image data in the displayed units, e.g. Height is exported in

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Quick Guide to a 5K Point Image

metric (nm), Phase in degrees, Frequency in Hz... NATIVE exports the data in raw (unscaled)
Volts. LSB exports the data in bits.

4. You can also export image HEADER, RAMP, or TIME information by selecting those check
boxes.

5. Click Save As..., designate a directory path and filename, and click Save.

Figure 2.4l shows the start of an exported ASCII image file saved without a header.

Figure 2.4l Sample ASCII Image File

2.4.8 High Resolution Imaging

Your controller can collect data at a maximum rate of 5120 x 5120 points per image for all 8
simultaneous channels. This increase makes re-imaging at higher resolution unnecessary in most
situations.

Note: Images with more than 1 million data points require that the SCAN DATA
LIMITS parameter in the Equipment panel be set to SYSTEM MAXIMUMS:

1. Click the TOOLS drop-down menu, then SELECT MICROSCOPE..., shown in Figure 2.4m, to
specify your SPM.

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Quick Guide to a 5K Point Image

Figure 2.4m Microscope Select

2. Click EDIT in the Microscope Select panel to open the Equipment panel, shown in Figure
2.4n.

Figure 2.4n System Component Designation

3. Click ADVANCED and set the SCAN DATA LIMITS parameter to SYSTEM MAXIMUMS. See
Figure 2.4o.

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Technical Support at Veeco

Figure 2.4o Set the SCAN DATA LIMITS to SYSTEM MAXIMUMS for images with more than 1 M data points.

4. Click OK to close the Equipment panel. Click OK to close the Microscope Select panel.
The NanoScope software will close all open RealTime and Offline panels before re-entering
RealTime.

2.5 Technical Support at Veeco

Your satisfaction and productivity regarding Veeco products and documentation are absolutely
essential.

2.5.1 Technical Support

Click Help > TECHNICAL SUPPORT for Veeco SPM technical support contact information.

Phone: 1-800-873-9750 (or 805-967-1400), Option 4, then Option 5.

e-mail: spmhelp@veeco.com.

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Technical Support at Veeco

2.5.2 Contact Information

Mailing Address

Technical Documents, Technical Support or Bug Reports at Veeco

Veeco Instruments Inc.
112 Robin Hill Rd.
Santa Barbara, CA 93117

E-mail: help@veeco.com

Voice Phone

(805) 967-1400, (800) 873-9750

Fax

(805) 967-7717

E-Mail (Documentation Feedback only)

TechPubsSBO@veeco.com

World Wide Web

http://www.veeco.com

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38 Nanoscope Software 7.30 User Guide Rev. G

Chapter 3 Realtime Views

The RealTime Views control the Real time collection of data. Each part of the screen is an integral
part of the scanning process. For more information on controlling views and the workspace,
reference Chapter 2.

For general procedures in setting the parameters and data definitions, refer to the following
sections:

• Overview of RealTime Views: Section 3.1

• Views for Scanning Section 3.2

• Tips on Using Realtime Section 3.3

• Force Curves Section 3.4

• Force Volume Section 3.5

• Piezoresponse Force Microscopy Section 3.6

• Surface Potential Detection Section 3.7

• NanoScope V Controller Lock-In Section 3.8

• High Speed Data Capture Section 3.9

• Pulse Counting Section 3.10

Note: If you have never used an AFM before, refer to your microscope manual or
contact Veeco for training.

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Overview of RealTime Views

3.1 Overview of RealTime Views

The Scan View includes all SPM parameters previously found in the RealTime control panels. The
settings and parameters configure the microscope and NanoScope controller signals to optimize
each scan.

You can access Realtime views such as Scan-Single, Scan-Dual, Scan-Triple, Meter, Navigate,
Video, and Point and Shoot by any of the following methods (see Figure 3.1a):

1. Right-click on RealTime in the workspace and select the desired view from the Add View
menu.

2. Click on the desired view icon in the RealTime tool bar.

3. Select a view from the Acquire menu.

Figure 3.1a Manual Scanning in Realtime

3.1.1 Typical Procedures to Begin to Scan

Set Scan parameters to affect piezo movement and data collection. The Scan functions control the
type of scan to run, how large the scan is, its angle, scan rate, and number of samples per scan line.
Prior to scanning a sample, the user must have knowledge of the following:

• Basic SPM processes

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 Realtime Views
Overview of RealTime Views

• Microscope safety, handling and tip/probe handling procedures (see your system
manual)

• Sample handling procedures

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Views for Scanning

3.2 Views for Scanning

The general interface views associated with configuring parameters for scanning include:

• Navigate View Section 3.2.1

• Meter View Section 3.2.2

• Point and Shoot View Section 3.2.3

• Cantilever Tune Section 3.2.4

• Scan-Single Interface Section 3.2.6

• Scope Trace Plot Section 3.2.7

• Main Tab Interface Section 3.2.8

• Scan Tab Interface Section 3.2.9

• Channels Tab Interface Section 3.2.10

• Feedback Controls Tab Interface Section 3.2.11

• Other Tab Interface Section 3.2.12

3.2.1 Navigate View

Use the Navigate commands to locate the tip, focus on the surface, enable the trackball and move
the stage. Use the Navigate View (previously the Realtime > Stage menu commands) to position
the tip, locate a surface position for referencing Z height and move the stage for scanning the
sample surface.

To access the Navigate View, click on the Navigate node in the Real Time workspace. If the
Navigate node is not present, right-click Real Time in the workspace to view the functions menu.
Select Add View > Navigate and the Navigate View appears in the client window.

Navigate Commands

The Navigate commands allow you to focus surface or locate the tip (see Figure 3.2a). To view the
Navigate commands select Tools > Stage or the command icons for Focus Surface or Locate Tip.

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 Realtime Views
Views for Scanning

Figure 3.2a Navigate Menu Commands

Figure 3.2b Navigate View

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Realtime Views
Views for Scanning

Using the Navigate View

CAUTION: If Locate Tip is not accomplished before Focus Surface, there is a

danger of crashing the tip during Engage.

Access the Navigate View at any time when the stage movement or focus surface and locate tip
settings are necessary.

Note: Some microscope options, such as Engage and Withdraw, are unavailable
when the Navigate View is active. You must select another view, such as the
Scan View, to enable these options.

1. Access Locate Tip and Focus Surface in the Navigate View or select the appropriate icons.

2. Select the Locate Tip button and focus on the tip using the trackball or arrow keys. When
finished, click the Ok button.

3. For Focus Surface, use the trackball or arrow keys to move the stage in X, Y or Z directions.

Navigate View Parameters:

XY Stage Motion Controls the horizontal, vertical and diagonal movement of

the stage.
Speed Buttons allow for setting slow (S), medium (M) and fast
(F) stage speeds by entering a speed value to the right of
the buttons or using the scroll bar then select the S, M or F
button.
Z Motion Up and down arrow keys control the height movement of
the tip toward or away from the stage.
Trackball Enables or disables the X, Y stage and Z cantilever move-
ment by using the trackball.
Camera Controls the magnification used to view the stage or tip.
Range: High Mag, Low Mag.
Illumination Sets the light intensity in the optics.

Zoom Changes the optical field of view (i.e., without stage or tip
movement).
Vision System Displays the surface (in focus surface mode) or tip (in
locate tip mode) and tip on the surface (in Realtime scan-
ning mode).

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Views for Scanning

SPM Parameters

To access the SPM Parameter controls, select Tools > Engage Settings > General or right-click in
Navigate View and select Edit SPM Parameters (see Figure 3.2c). Parameter Controls are:

• Sample Clearance

• SPM Safety

• SPM Engage Step

• Load/Unload Height

• SPM exclusion limit

• Sew tip

• Trigger safety

Figure 3.2c Engage Stage-Motor Settings Dialog Box

3.2.2 Meter View

Access the Meter View (select Acquire > Meter) to view the photodetector signal, RMS
amplitude, horizontal and vertical deflection signals, and the signal sum. The meter can also be
viewed in the docking RealTime status window.

Meter View Interface

• Photodetector Signal—Red dot that corresponds to the positioning of the laser on the
photodetector.

• Signal Sum—Horizontal meter that displays the sum of the voltage response from the
laser in all 4 sections of the photodetector.

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Views for Scanning

• Vertical Deflection—Corresponds to the voltage for vertical displacement of the laser

signal. Should be “0” for centering.

• Horizontal Deflection—Corresponds to the voltage for the horizontal displacement of

the laser signal. Should be “0” for centering.

• RMS Amplitude—Root mean square (RMS) signal measured at the detector

(TappingMode only).

Figure 3.2d Meter View and Docking RealTime Status Window

Photodetector signal

Signal Sum

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Views for Scanning

3.2.3 Point and Shoot View

The Point and Shoot View allows you to select specific points on an image (see Figure 3.2e). Use
Point and Shoot to capture an image and/or collect a force curve for every point you designate.

When you click a point on an image, a crosshair (+) marks the location. You can designate
individual points, or use the tools in the Point and Shoot View to assign multiple points
simultaneously.

Figure 3.2e Point and Shoot View

Controls and Parameters

Image/Scan Allows you to switch to Image/Scan mode. Use Image/

Scan mode to adjust scan parameters in any scan view.
Ramp/Force Curve Allows you to switch to Ramp/Force Curve mode. Use
Ramp/Force Curve mode to adjust the ramp settings. You
can select points on an image, ramp each point, and create
a force curve for each point.
Image Channel Select the channel to use for the image.

Ramp Channel Select the channel to use for the ramp display.

Multiple Shoot Number of force curves collected at each point, 100 max.

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Capture Image and Click this button to capture an image and save it in the
Ramp Capture Directory, and to then capture a force curve at
each designated point.
Capture Image Click this button to capture an image and save it in the
Capture Directory. After the capture the software switches
to Ramp/Force Curve mode.
Ramp Click this button to ramp a variable determined from the
force curve menu at each point.
Capture Click this button to ramp each point, capture the ramp/
force curve, and save it in the Capture Directory.
Point Parameters Image Cursor Mode Settings:
Mark Only—Select points of interest on the image.
M/Ramp—Select points of interest. Software will auto-
matically ramp each point.
M/R/Capture—Select points of interest. Software will
automatically ramp each point and capture a ramp/force
curve.
Line Parameters Draw a line to select specific points on an image.
Point Number—Number of points in the line.
Spacing—The distance in nm between each point. All
points are equidistant.
Clear Path—This button clears the current line and asso-
ciated points.
Convert to Points—Places a + in the location of each
point in the line. The line disappears.
Box Parameters Draw a box in the area you want to place a group of points.
You can use the parameters below to create a grid of
points.
Row Number—Designates the number of rows of points
in the grid.
Column Number—Designates the number of columns of
points in the grid.
Row Space (nm)—Designates the distance in nm between
each row of the box.
Col Space (nm)—Designates the distance in nm between
each column of the box.
Clear Path—This button clears the current box and asso-
ciated points.
Convert to Points—Places a + in the location of each
point in the grid. The box disappears.
Clear All Marks Removes all user-defined marks from the Point and Shoot
image.
Save Marked List... Save the marks on the image as Path Files (*.psm).

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Views for Scanning

Load Marked List... Opens and loads a previously saved Path File (*.psm)
which contains marks on a Point and Shoot image.
Note: If there are points on the image prior to selecting this
option, when this button is selected the saved marks will
appear in addition to the previous marks.

Two options are available for moving, in XY, from one point to another:

1. XY MOVE ON SURFACE: OFF - Move with tip at home (lift) height.

2. XY MOVE ON SURFACE: ENABLED - Move on surface with Z feedback on See Figure 3.2f.

Figure 3.2f Ramp Parameters > Mode > XY move on surface

3.2.4 Cantilever Tune

The Cantilever Tune command allows determination of the cantilever resonant frequency and the
setting of the operating point for TappingMode feedback (see Figure 3.2g). Cantilever Tune
sweeps the cantilever drive frequency over a selectable range, then displays plots of the cantilever
amplitude and phase versus drive frequency. This command is enabled only when the Microscope
mode parameter on the Other Controls panel is set to Tapping. On Small Sample MultiMode
SPMs, verify that the switch located on the base is toggled to TM AFM before selecting the
Cantilever Tune command.

Note: The sweep channel is determined by the data selection in the Channel 1,
Channel 2, or Channel 3 control panels.

Figure 3.2g shows how the maximum amplitude is attained in air at the cantilever natural
resonance. Figure 3.2h shows the amplitude is reduced when it is in contact with the sample
surface.

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Figure 3.2g Tapping Cantilever in Mid-air

Laser

Photodiode
Detector

Tapping Piezo

Cantilever
Resonant
Deflection

Figure 3.2h Tapping Cantilever on Sample Surface

Laser

Photodiode
Detector

Tapping Piezo

Cantilever
Resonant
Deflection

In TappingMode, the optical lever technique reflects a laser beam off the back of the oscillating
cantilever, thence to a segmented photodiode. The differential signal between the top and bottom
photodiode segments provides a sensitive measure of cantilever deflection. As the sample is
scanned, analog circuitry determines the RMS value of the rapidly changing cantilever deflection
signal. The RMS value of the cantilever deflection signal corresponds to the amplitude of the
cantilever oscillation. Changes in amplitude of the cantilever oscillation are controlled by the
feedback system to track the sample surface.

Access the Cantilever Tune dialog box by selecting the Tune icon or by selecting
Cantilever Tune... from the Realtime menu.

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Views for Scanning

Figure 3.2i Cantilever Tune Dialog Box

Auto Tune
Parameters

Auto
Tune But-

Mode Box More Button

Select Cantilever Tune Dialog Box Definitions:

Mode box Toggles the Auto Tune signal from the main to interleave sig-
nals.
Settings:
Main— Displays the set of parameters applied to the main scan
(see Section 3.2.8).
Interleave—Displays a duplicate set of parameters applied
only to the interleaved portions of the scan.

Auto Tune Button Executes the automatic tuning procedure: the cantilever is
excited through a range of frequencies beginning at the Start
frequency and ending at the End frequency.

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Auto Tune Parameters:

Start Frequency Starting point of the Auto Tune frequency sweep.

End Frequency Ending point of the Auto Tune frequency sweep.
Target Amplitude Targeted output signal amplitude at the photodiode detector. This value
should not be confused with Drive amplitude, which is the amplitude applied
directly to the cantilever itself (see Drive amplitude).
Range and Settings: 0.00 to 8.00 V
Note: Dimension Series SPMs, nominal = 500mV
Small Sample MultiMode SPMs, nominal = 500mV
Peak Offset Percentage of cantilever’s free-air resonant frequency to be automatically off-
set. Peak offset is used to compensate for changes in resonance before engage-
ment due to the tip’s interaction with the surface after engagement.
Range and Settings: 0 to 50%; typical value = 5%
Minimum Q Q is the value defined by the amount of oscillation it takes for a wave to drop
to 1/e (e = 2.718) of its amplitude value (i.e. a wave with an amplitude of ten
would have a Q of 10/e, or 3.6788). Minimum Q establishes a minimum
“width of peak” value allowed by the AutoTune function. Peaks not meeting
the Minimum Q may be ignored by setting the Smash Q factor.
Smash Width Factor The width of the area beneath the wave smashed (set to zero) when a peak not
meeting the Minimum Q requirement is found.
Note: This parameter does not appear if Minimum Q is 0.

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Views for Scanning

3.2.5 Electric Tune

Theory

When evaluating Surface Potential, you can now tune the cantilever electrically. Traditional
cantilever tune oscillates the cantilever via tapping piezo material (see Figure 3.2j). Electric Tune
sweeps the frequency of the electric field surrounding the cantilever. The force of the electric field
moves the cantilever. The cantilever amplitude is then plotted in the Generic Sweep dialog box.

Figure 3.2j Cantilever Tune Method Comparison

Traditional Cantilever Tune Electric Tune

Electric Field

Piezo Material Oscillates the Cantilever Electric Field

Change the Electric Field Frequency

to Oscillate the Cantilever

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Views for Scanning

Procedure

1. While evaluating Surface Potential in Realtime mode, select RealTime > Generic Sweep.
The Generic Sweep dialog box will display.

Figure 3.2k Typical Generic Sweep

Interleave Mode

2. Select Interleave as the Mode (see Figure 3.2k).

3. In the Generic Sweep dialog box, set the Sweep parameters Input igain and Input pgain to
0. This disables the Surface Potential feedback loop, which works to keep the cantilever's
amplitude at zero.

4. You can adjust several parameters to acquire interesting data:

• Try changing the Data Scale, Drive Phase and Drive Amplitude (see Figure 3.2l).

• Try changing the channel. For example, the Data Type can be changed to Potential
Input.

• Try sweeping another channel. For example, set the Graph parameter Sweep Output to
Bias (see Figure 3.2l).

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Views for Scanning

Figure 3.2l Electric Tune Generic Sweep while adjusting the Drive Amplitude and Drive Phase

Note: Remember to re-enable the Input gains before collecting further Surface
Potential data.

3.2.6 Scan-Single Interface

The Scan-Single display includes an image viewer, color bar, scope viewer, vision control viewer
(for systems configured with vision controls), and numerous parameters to configure Realtime data
collection. Most SPM operators use only a few of these parameters to obtain images. The
parameters within each tab are also microscope-specific or level-access dependent and may be
greyed out or hidden, depending on microscope configuration.

Scan-Single Interface:

Image Window During scanning, the Realtime image of the sample appears along with a cur-
sor. The cursor moves along the image vertically to show the engaged tip
position on the surface. The Measure button allows you to make line mea-
surements. The Data Zoom button allows you to “zoom in” to a smaller view,
but doesn’t change the scan size. The Pan button allows you to pan over to
other areas of the total scan if you are zoomed in.

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Color Bar Sets the color table for viewing height data in the image window. Left-click
on the color bar and drag the mouse left or right.

Image Parameters Configure options below the image window to select the channel and image
display values, (e.g. Data type, Line direction, Data scale, and so on).

Vision Window The Vision window displays the Optics or Scope data. Select the Video or
Scope or Line Plot button.

Figure 3.2m Scan-Single and Main Controls

User-Defined Parameters in the Scan View

Clicking on a parameter and then dragging the mouse back and forth increases or decreases a
parameter value much like an old analog slider. The significance, range of acceptable values, and
specific information about control panel parameters are discussed in this section.

Parameters listed in the Scan-Single tabs depend on the microscope selected and the Show All
Items function (right-click on parameter list windows > Show All). Parameters necessary for one
style of microscope are not applicable to another. For example, the Drive frequency and Drive
Amplitude parameters are enabled on the Feedback tab only when the mode is set to
TappingMode.

Some users find operating an SPM less confusing if the number of parameters is limited to only the
most essential ones. For this reason, The Main tab in the Scan View contains user specified
parameters.

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Views for Scanning

3.2.7 Scope Trace Plot

Select the Scope button in Scan-Single (see Figure 3.2m) for a scope to display a plot versus the
probe position in an oscilloscope-type format on the image display (see Figure 3.2n).

Note: The Scope view is selected by default.

Figure 3.2n Scope Grid

Scope Trace Interface

By right-clicking the Scope grid, you will get a menu of different options (see Figure 3.2o).

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Views for Scanning

Figure 3.2o Scope Grid Parameters

These menu options allow you to make the following changes:

Color Allows operator to change color of:

• Curve (data)

• Text

• Background

• Grid

• Minor Grid

• Markers

Filter Typically used for a Profiler Scan.

• Type—Allows the user to plot the mean, maximum or

minimum y-value per x-value.

• Points—Allows user to plot multiple vertical axis (y) values

at each horizontal axis (x) value. Select 4K, 8K, 16K or 32K
Points to limit the display to 4, 8, 16 or 32 times 1024 points.

Minor Grid Places a minor grid in the background of the Vision Window.

Scale Allows user to auto scale, set a curve mean, or set their own data range.

X Translate Offsets the curve by placement of vertical cursor on the grid. Grab vertical
cursor in the space above the grid and pull down onto grid.

Y Translate Offsets the curve by placement of horizontal cursor on the grid. Grab hori-
zontal cursor in the space next to the grid and pull onto grid.

Line Style For each curve, operator can choose, connect, fill down, or point.

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User Preferences Restore—Reverts to initial software settings

Save—Saves all changes operator has made during this session. This
becomes the new default settings.

Copy Clipboard Copies the grid image to the Microsoft Clipboard.

Print Prints out the current screen view to a physical printer.

Export Exports data in bitmap, JPEG or XZ data format.

Active Curve Determines which curve you are analyzing.

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3.2.8 Main Tab Interface

Figure 3.2p shows an example of parameter controls and settings for scanning in TappingMode.

Figure 3.2p Main Controls Panel

Engage Button The Engage command brings the tip into contact with the sample surface and
starts the Realtime imaging process.
Withdraw Button The Withdraw command stops the scanning process and withdraws the tip
from the surface.
Frame Down Button The Down command restarts the Realtime scan at the top of the frame. This
allows you to go directly to the start of the frame and not have to wait for the
previous frame to end.
Frame Up Button The Up command restarts the Realtime scan at the bottom of the frame. It is
an easy way to begin to view an entire Realtime frame from the bottom. By
clicking on this button, the Realtime scan restarts and moves up at the bottom
of the frame. This allows you to go directly to the start of the frame and not
have to wait for the previous frame to end.
Capture Button The Capture command stores the image data of the current scan. During the
image scanning process, the cursor moves up and down a square image frame.
When the cursor moves up or down one complete frame the Capture is com-
plete and an image file is saved.
Abort Capture The Abort Capture command (on the toolbar) stops the capture process.

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Procedures to Set the Main Tab

The parameters in the Main Control panel (see Figure 3.2q) are unique to your specific needs.
Configure specific parameters as follows:

1. Right-click in the Main Control panel.

2. In the Parameter list, verify each Scan View tab name.

3. Expand the desired tab name by clicking on the plus (+) sign next to each name (i.e., Scan,
Feedback, Interleave, etc.) to view a list of parameters.

4. Highlight the desired parameters for viewing on the Main Controls tab.

Note: Only eight parameters may be selected. Therefore, take note of the most used
parameters to view in the Main Controls tab.

5. With the parameter selected, click the double arrows (<<) to position the selected parameter.

6. Repeat Step 2 - Step 5 for displaying eight main controls parameters for viewing during the
scanning process.

Select OK to accept the changes or Cancel to revert to the previous view.

Figure 3.2q Select Scan View Controls

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3.2.9 Scan Tab Interface

The Scan tab (see Figure 3.2r) includes parameters influencing piezo movement and data
acquisition, as well as the ability to execute non-square scans. This Tab panel is probably the most
frequently used panel, as it controls what type of scan to run, how large the scan is, its angle, scan
rate, and number of samples per scan line.

Figure 3.2r Scan Tab Parameters

Scan Tab Parameters

Scan size Determines the size of the scan by controlling the voltage applied to the
X and Y piezos.
Range or Settings:

• 0 to 440V

• 0 to XXµm (scanner-dependent)

The units of this parameter are volts if the Units parameter (Other Con-
trols panel) is set to Volts. The units are linear distance (nm or µm) if
the Units parameter is set to Metric.

See also, Optimizing the Scan Size Parameter on page 95.

Aspect ratio Controls the width-to-height size ratio of scans. Set Aspect ratio to 1.00
for square scans. An Aspect ratio of 2.00 yields scanned images having
width equal to twice the height.
Range or Settings: (depends upon the number of scan lines) 1 to 256.

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Figure 3.2s Aspect Ratio Example

4.00

8.00
1.00

16.00

Figure 3.2t Scan Angle Rotated Example.

X offset, Y offset Controls the center position of the scan in the X and Y directions,
respectively.
Range or Settings: ±220V; ± XXµm (dependent on Scan size and
scanner).

See also, Optimizing the X Offset, Y Offset Parameter on page 96.

Scan angle Controls the angle of the X (fast) scan relative to the sample.
Range or Settings: 0 to 359° (Any angular value can be entered with
the keyboard)
Changing this parameter can dramatically affect the quality of
images due to tip effects (tip side wall angle).
Setting this parameter to a setting besides 0 or 90° may reduce the
maximum allowable Scan size 10-20 percent due to corner con-
straints (see Figure 3.2t).

Scan rate The Scan rate sets the number of fast scan lines performed per sec-
ond. When the Scan rates are low, it can take a fairly long time to
scan an entire frame. For example, with the Scan rate set to 0.5Hz
and the Number of samples set to 512, it can take over 17 minutes
to capture a single image.
Range or Settings: 0.1-237Hz, depending on the number of
Samples/line.

See also, Optimizing the Scan Size and Scan Rate Parameters on page 96.

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Lines Selects the number of lines to scan in a frame. The Lines parameter
reduces resolution along the Y axis. It also speeds imaging (or frame
rate) and reduces the size of the resulting image file.
Range or Settings: 2 to 1024. The maximum number of lines may be
limited by the value for Samples/line.

Tip velocity Velocity of the tip (in µm/s) as it scans over the surface.
When Tip Velocity is changed, the Scan Rate adjusts automatically.

Samples/line Selects the number of sample data points per scan line.
When this parameter is changes, the number of scan lines per image
(Lines) are automatically adjusted to maintain the same ratio
between the samples/line and lines per image.
Range or Settings: 128 to 16384. This setting influences the mem-
ory size of captured files and image resolution (see Table 3.2a).

Table 3.2a File Size/Samples per line

File size (for square

Samples/line value scans, including 8K
header)
128 40Kb
256 136Kb
512 520Kb

Note: Samples/line should be kept at 512 or higher for high resolution scans. To
increase the frame rate (rate at which complete images are generated), the
Lines parameter should be reduced. When the Lines parameter is reduced, file
sizes in Table 3.2a are reduced accordingly.

Slow scan axis Allows the slow scan to be disabled, causing the fast scan to be
repeated continuously at the same position. This means that the image
displays the same line continuously. Images may be presented either as
“true” X-Y renderings of the sample surface (Enabled), or as
“stretched” single-line scans of length equal to the Scan size (Dis-
abled).
Range or Settings:

• Enabled—Sample is scanned in the slow scan

direction. (This is the normal setting of this parameter.)

• Disabled—No scanning of the sample in the slow

direction is performed. The fast scan is repeated at the
same position.

Note: Disabling the Slow scan axis and viewing the Scope Mode display is a
convenient way of setting the Feedback Gain parameters.

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The advantage of using the Slow Scan Axis > Disabled parameter is to emphasize one area (line) to
adjust SPM parameters. For example, an area of the image appears fuzzy (suggesting SPM
parameters are not optimized for the sample). Disable the Slow Scan Axis, view the image in
Scope mode, and reconfigure scan parameters to optimize the scan.

Note: Setting the Slow scan axis parameter to Disable stops the slow scanning of the
piezo, but does not stop the movement of the Realtime display in Y. Lines are
replicated in the Y direction.

3.2.10 Channels Tab Interface

The Channels tab (see Figure 3.2u) consists of parameters for eight channels. Each channel
represents a unique scanning image. Up to eight data Channels may be opened by selecting each
channel and choosing a data type to view simultaneously. Channels are numbered 1, 2, 3... and
feature their own control panels. When a Data type is selected on a Channel, its image appears on
the Display Monitor. It is possible to have up to eight separate images from each scan. For example,
a TappingMode scan might simultaneously present a Height image on Channel 1, a Deflection
image on Channel 2, and an Amplitude image on Channel 3.

Parameters shown on each Channel control panel vary slightly, depending upon the type of
microscope selected and its operating mode.

Figure 3.2u Channels Tab

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Channel Tab Parameters

Data Type Settings vary, depending upon the microscope selected and operating mode
as shown in the field descriptions below. The Data type parameter may
receive: no data (Off); sample-height data (Height); cantilever oscillation
amplitude data for TappingMode (Amplitude); cantilever deflection data
(Deflection); STM current data (Current); phase data (Phase).

See also, Optimizing the Data Type Parameters on page 97.

Data Type Range or Settings

Amplitude (TappingMode The RMS of the cantilever amplitude signal is displayed and captured.
and Force Mode only)

Current (STM only) Data displayed and captured is the tunneling current generated by the pream-
plifier. (When set to Current, the units of the data are nA.)

TM Deflection Cantilever deflection signal data is displayed and captured. (When set to TM
Deflection, the units of the data are in distance or volts.)

Height The Z piezo voltage set by the feedback calculation in the Digital Signal Pro-
cessor (DSP) is displayed. (The displayed data comes from the voltage output
to the Z piezo.) Units are distance (e.g., nm, µm, etc.). Standard imaging of
topography.

Off Channel is turned off.

Phase (MFM, EFM) Phase data from oscillating TappingMode tips, generally used with Magnetic
Force Microscopy (MFM) and Electrical Force Microscopy (EFM), is dis-
played and captured. This setting appears when the microscope is configured
with an Extender™ Electronics Module.

Potential (EFM) Surface potential data is displayed. (For detailed information on Surface
Potential or EFM features, see Support Note 231, Electric Force Microscopy
on the MultiMode Systems.)

Deflection Cantilever deflection signal data is displayed

Friction Torsional deflection signal data is displayed

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Data scale The Data Scale controls the Z scale corresponding to the full height of the dis-
play and color bar.
Range or Settings:

• 0.0067 to 440V (Data type set to height, Units are set to

volts).

• XX to XXX µm (Scanner dependent; where Data type is set to

height, Units set to metric).

• XX to XXX µm (Sensitivity dependent; where the Data type

is set to deflection or amplitude; Units are set to metric).

• 0.00003815 to 2.5V or 20V (Data type set to amplitude; Units

set to volts or deflection)

• 0.0031 to 200nA (Data type set to current; Units are set to

metric).

• 0.0003052V to 20V (Data type set to current; Units are set to

volts).

See also, Optimizing the Data Scale Parameters on page 97.

Data center Offsets centerline on the color scale by the amount entered.
The Data Center offset does not become a permanent part of the data.
Range or Settings:

• ± 220V

Line direction Selects the direction of the fast scan data collection that is displayed in the
image.
The feedback calculation is always performed regardless of the scan direction.
This parameter simply selects whether the data is collected on the trace or the
retrace. This parameter selects the relative motion of the tip to the sample.
Range or Settings:

• Trace—Data is collected when the relative motion of the tip is

left to right as viewed from the front of the microscope.

• Retrace—Data is collected when the relative tip motion is

right to left as viewed from the front of the microscope.

Scan line The scan line controls whether data from the Main or Interleave scan line is
displayed and captured.
Range or Settings: Main or Interleave

This parameter is not selectable when the Interleave mode parameter is set to Disable. The system is locked
on the Main scan lines whenever the interleaved mode is turned off.

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Realtime Planefit Applies a software leveling plane to each Realtime image, removing up to first-
order tilt. Three types of planefit are available to each Realtime image.
Range or Settings:

• None—Only raw, unprocessed data is displayed.

• Offset—Takes the Z-axis average of each scan line, then subtracts

it from every data point in that scan line.

• Line—Takes the slope and Z-axis average of each scan line and
subtracts it from each data point in that scan line. This is the
default mode of operation, and should be used unless there is a
specific reason to do otherwise.
Offline Planefit Applies a software “leveling plane” to each captured image for removing up to
first-order tilt. Three types of planefit are available to each Offline image.
Range or Settings:

• None—Only raw, unprocessed data is displayed.

• Offset—Captured images have a DC offset removed, but they are

not fitted to a plane.

• Full—A best-fit plane which is derived from the data file

subtracted from the captured image.
See also, Optimizing the Offline Planefit Parameter on page 97.

3.2.11 Feedback Controls Tab Interface

The Feedback Controls parameters allow for monitoring the signals between the NanoScope
Controller and the cantilever. These signals adjust the setpoint, oscillation frequency, drive
voltage, Z response for surface tracking, and output voltages. The purpose of the Feedback
Controls is to maintain a constant setpoint (deflection, amplitude, or current) in the Feedback
Loop for tip/sample control and tracking optimization. Parameters listed in the Feedback tab
depend on the microscope selected and the Show All Items function (right-click on parameter list
windows > Show All).

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Figure 3.2v Feedback Controls Tab in TappingMode

Feedback Control Parameters

Z Modulation (Fluid TappingMode Allows the user to add the drive oscillation signal to the Z piezo
only) voltage. This parameter is used to set up fluid cell oscillation in
any Dimension system for Fluid TappingMode.
Range or Settings:

• Enabled—Enables Z modulation. Drive

oscillation signal (Drive Frequency) is added to Z
piezo voltage. When enabled, the Z limit must
be set ≤ 420V.

• 0—Disables the Z modulation (i.e., no additional

signal is added to Z piezo voltage).

The desired Drive amplitude and Drive frequency voltages

(Realtime > View > Sweep > Cantilever Tune) need to be set
for Fluid TappingMode operation.

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SPM feedback Selects the signal to be used for tip feedback according to the
selected Microscope mode parameter (Other Controls panel).
For Contact AFM, the choice defaults to Deflection; however,
for TappingMode, you may select either the TM Deflection or
the Amplitude. STM offers two choices of feedback: Linear and
Log.
Range or Settings:

• TappingMode—Amplitude, TM Deflection-
Phase (Forcemod only)

• Contact Mode—Deflection only

• STM—Linear, Log

Linear—The linear difference between the instantaneous tun-

neling current and the Setpoint current is used in the feedback
calculation.
Log—The difference between the log of the instantaneous tun-
neling current and the log of the Setpoint current is used in the
feedback calculation.

See also, Optimizing the STM Feedback Parameters on page 98.

Input Feedback Controls Frequency Modulation (MFM or EFM) and Surface

Potential.

Integral Gain Controls the amount of integrated error signal used in the feed-
back calculation.
Range or Settings: 0 to 1024

See also, Optimizing the Integral and Proportional Gain on page 98.
Gain settings vary, depending upon the scanner used, the sample and scanner sensitivity. See Table 3.2b for
approximate, nominal values (assumes a Scan rate of ≈ 2.5Hz).

Table 3.2b Typical Integral Gain Ranges:

Contact AFM and

Scanner TappingMode STM
Forcemod
Aa 4.0 - 20.0 0.4 - 2.0 0.3 - 5.0

a. For atomic-scale images, scan rate must be increased to approximately

60 Hz.

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Proportional Gain Controls the amount of the proportional error signal used in the
feedback calculation. The Proportional gain term in the feed-
back calculation has equal gain at all frequencies; therefore, it
has a dominating effect over the Integral gain for high frequen-
cies (scan rates).
Range or Settings: 0 to 1024
(Typical settings for the Proportional gain parameter are 35-
100% more than Integral gain values).

Setpoint The meaning of this parameter depends on the operating mode of

the microscope as follows:
Amplitude Setpoint (TappingMode)—defines the amplitude of
the cantilever oscillation signal to be maintained by the feedback
loop. (Range: 0.00 to 10.00V)
Deflection Setpoint (Contact Mode)—Controls the deflection-
signal level used as the constant desired voltage in the feedback
loop. (Range: -12.00 to 12.00 V)
Current Setpoint (STM)—Controls the constant current main-
tained by the feedback loop. (Range: 0.0 to 100.0nA)

Drive frequency (TappingMode and Selects the oscillation frequency applied to the piezoelectric
Force Mode only) crystal that vibrates the cantilever.
Range or Settings: 0.00 to 250MHz
The Center frequency is adjusted with the Cantilever Tune
command to find the resonance frequency of the cantilever. The
maximum cantilever oscillation amplitude occurs at its resonant
frequency. The software sets the Drive frequency equal to the
current Center frequency value when the Ok button in the Can-
tilever Tune control panel is pressed.

Drive Phase (TappingMode and Force Selects the phase of the drive voltage applied to the piezoelectric
Mode only) crystal that vibrates the cantilever.

Drive amplitude (TappingMode and Selects the amplitude of the drive voltage applied to the piezo-
Force Mode only) electric crystal that vibrates the cantilever.
Range or Settings: 0.00 to 20.00V
The Drive amplitude is also adjusted with the Cantilever Tune
command. Increasing the Drive amplitude increases the cantile-
ver-oscillation amplitude. The cantilever-oscillation amplitude is
increased to an appropriate level with the Cantilever Tune com-
mand. In AutoTune, the Drive Amplitude automatically adjusts
to get a cantilever oscillation (rms amplitude) equivalent to the
user’s Target amplitude.

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Bias Controls the sign and magnitude of the bias voltage applied to the
sample.
Range or Settings: -10.00 to 10.00V
When used with STM, typical settings for the Bias voltage
parameter are 20 to 100mV for conductive samples and up to
several volts with poorly conducting samples. Positive settings of
the Bias voltage item correspond to negative current (electrons)
tunneling from the tip into the sample on heads with the Bias
applied to the Sample or Tip.

Analog 1, 3, 4 This voltage has no effect on the operation of the standard micro-
scope, but is useful in custom applications.
Range or Settings: -10.00 to 10.00V. These settings are only
displayed with either NSIV or NSIIIA with Quadrex
extender.

Aux Lockin Directs an external input signal through the auxiliary lock-in
amplifier.

Drive Phase The phase of the AC bias signal applied to stimulate piezore-
sponse.

Lockin BW The bandwidth of the effective bandpass filter centered on the

TTL level reference frequency (i.e., the cantilever drive fre-
quency in the NanoScope Controller) used by the main lock-in
amplifier.

Lateral 16x Gain Increases the lateral gain 16 times. This should be set to
Disabled for most applications.
Range or Settings: Disabled, Enabled

Linked Parameters Range or Settings

Several parameters (e.g. Z modulation, SPM Feedback, etc.) are highlighted by dark gray or green
background. Dark grey indicates that the parameters are coupled with the equivalent values in the
Feedback controls. By selecting (left-click) the Interleave parameters, the grey field turns green,
indicating that the Feedback and Interleave parameters are decoupled and the value in those
parameters will be used as feedback during the interleave scan line.

Interleave Mode

• Interleave—Adds a second, interleaved set of lines to the scan, which can be accessed
from the Channel panel and captured as data. Invoking Interleave reduces the slow axis
speed by one-half and doubles the capture time.

• Lift—A variant of Interleave, the Lift option uses the first set of scan lines to detect the
surface, then lifts the probe above the sample surface on the interleaved set of scan lines
according to the Lift start height and Lift scan height parameter settings. During the

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Interleaved scan, the tip mimics the surface topography from the previous surface scan
line (see Figure 3.2w).

Figure 3.2w Interleave Lift Mode

• Disabled—Turns off the interleave scanning.

Lift scan height Specifies the tip’s height above the sample surface during interleaved scans.
This parameter is in effect ONLY when the Interleave mode parameter is set
to Lift (see Figure 3.2x).
Range or Settings: XXµm (Scanner dependent)
The maximum meaningful value of the parameter depends on the Z voltages
applied in the Main scan line and the maximum voltage that the system can
output. The maximum voltage that can be applied to the piezo is ±220V. It
will be lower if the Z voltage is restricted by the Z limit parameter.

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Figure 3.2x Lift Scan Height Illustrated

Lift start height Specifies the height that the tip is to be lifted above the sample surface at the
start of each interleaved scan. Generally, this parameter serves to lift the tip
clear of any contamination layers present on the sample before assuming its
Lift scan height during interleaved scans. This parameter is in effect ONLY
when the Interleaved mode parameter is set to Lift. This parameter defines
an offset from the Z voltage, or height, applied to the piezo on the Main scan
line.
Range or Settings: XXµm (Scanner dependent)

Figure 3.2y Lift Start Height Illustrated

Tips for Using the Lift Start Height Parameter

• This value can be left at zero for TappingMode and STM. It is generally only used for
Contact AFM to break the tip free of the adhesive force produced by the water layer
before settling to the final tip height.

The tip will go through this height at the start of every lifted scan line, then proceeds to the lift scan
height for the rest of the scan line.

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3.2.12 Other Tab Interface

The Other Controls parameters set the type of microscopy, Z tracking limits, units to use in
measuring and other parameters specific the to microscope mode (i.e., the parameters that appear in
the Other Controls panel will vary from one microscope to another). In the Workspace menu,
select Real Time1. In the Realtime Scan-Single window, select the Other tab.

Figure 3.2z Other Tab

Parameters in the Other Controls Tab:

Microscope mode Selects the type of microscopy to be employed. Switching this parameter
enables/disables other parameters. Also, on MultiMode SPMs, any change
to the Microscope mode must be accompanied by use of the mode selector
switch on the microscope’s base.
Range or Settings:
Contact, Tapping or STM

Z limit Permits attenuation of maximum allowable Z voltage and vertical scan range
for achieving higher resolution (smaller quantization) in the Z direction.
Range or Settings:
11 to 440V (with Units set to Volts) for the XY Closed loop head
11 to 330V (with Units set to Volts) for the XYZ Closed loop head

Note: In previous software versions, engaging with Z LIMIT ≠ Z

max could result in a tip crash and the operator was warned by
a message on the screen. Engage in versions 7.0 and later is
always done with Z LIMIT = Z MAX. Therefore the warning is
no longer needed.

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FM igain Integral gain for Frequency modulation. Controls the feedback loop that uses
phase electronics.

FM pgain Proportional gain for Frequency modulation. Controls the feedback loop that
uses phase electronics.

Deflection Limit Use this parameter for attenuating the input voltage signal (appears only
when performing Contact AFM). Appears as TM Deflection Limit in Tap-
ping mode.
Range or Settings:

• 2.500V to 20.0V for regular imaging

• 24.58V in Force Mode only

Amplitude Range Use this parameter for attenuating the input voltage signal (appears only for
TappingMode or STM).
Range or Settings:

• 1000, 2000, 3000 or 4000mV for regular imaging

Illumination Controls the fiber optic illumination of the sample in Dimension series
microscopes.
Range or Settings: 0 to 100, recommended range is 20 to 50

Units Selects whether the units of certain scan parameters are in Volts or in units of
Metric distance (nm, etc.). Parameters affected include Scan size, X Offset,
Lift start height and Lift scan height, Y Offset, Data Scale, Z Limit, Z Scan
Start, Ramp Size, Column Step and Row Step.
Range or Settings:

• Volts—Parameters are in Volts.

• Metric—Parameters are in units of distance (nm, µm, etc.)

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Engage Setpoint (Tap- Allows the user to correct for loss of tracking on engage due to sample dif-
pingMode only) ferences. The automatic Engage procedure establishes the setpoint voltage at
the smallest possible value that detects the sample surface, resulting in a
value that protects both the sample surface and the cantilever tip. However,
this value may not be sufficient for optimal surface tracking on all samples.
The setpoint voltage determined by the automatic Engage procedure will be
multiplied by the Engage Setpoint value, increasing or decreasing tapping
force.
Range or Settings:
0.5 through 2.0. A value of 1.0 results in no change to the tapping force. Val-
ues less than 1.0 increase the tapping force and values greater than 1.0
decrease the tapping force. A value of 0.9 is nominal for most samples.
Example of Engage Setpoint
The Engage Setpoint for a particular sample may be empirically deter-
mined. Procedures are as follows:
1. Set the Engage Setpoint to 1.0 and engage on the sample.

2. After engagement, make note of the Setpoint parameter.

3. While watching the scan, adjust the Setpoint value until the tip
tracks the surface correctly. Calculate the following:

(Setpoint value/Starting Setpoint value) = Engage Setpoint

(For optimal value, take the average of several engages on a selec-
tion of samples or different areas of the same sample).

Bidirectional scan When the Bidirectional scan parameter is Enabled, data from both Trace and
Retrace scans are used to capture frames in half the normal time. Images
have alternately shifted lines, which cause features to lose some of their lat-
eral definition; however, data may be used for metrological analysis. Use to
save time while capturing images.
Range or Settings:
Enabled or Disabled
When Enabled, features shown in images lose some lateral definition, mak-
ing point-to-point measurements inadvisable. Vertical data, however, is unaf-
fected.
Use the Scan line shift parameter to readjust images with the Bidirectional
scan parameter Enabled. This will shift scan lines relative to one another to
restore some lateral definition in features.

Scan line shift Use the Scan Line Shift parameter to shift trace and retrace lines relative to
one another by up to 5 pixels in either direction. Units are in pixels and range
from -5 to +5. Scan line shift is used for readjusting images captured when
the Bidirectional scan parameter is Enabled.
Range or Settings: -5 to +5
This parameter is generally only for images that have been captured with the
Bidirectional scan parameter set to Enabled.

Tip Serial Number Saves input in the image header (Ciao Scan List) for users who keep a tip fil-
ing system. This is to keep track of the tips used for certain images.

Serial Number Scanner Calibration file.

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Min. Engage Gain Allows user to engage tip in constant height mode. In constant height mode,
(STM only) the gains (feedback) is disabled. However, the Min. Engage Gain parameter
provides for gain during engagement.

Strip Chart Rate Frequency of (Z-position, deflection) data point acquisition.

Range: 1kHz
Typical value: 100Hz

Strip Chart Size Time interval over which (Z-position, deflection) data points are displayed.
Typical value: Tens of seconds.
Note: Although the strip chart collects and displays data over the time inter-
val defined by clicking Start, then later, Stop, this data is not saved for sub-
sequent use until the Capture icon is clicked. If Capture is clicked while
strip chart data is being taken, what is saved begins at the start of the chart
(sooner than the icon is clicked).

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3.3 Tips on Using Realtime

Refer to the following Realtime commands available on the NanoScope software:

• Using the Image Interface Section 3.3.1

• Multiple Channels Section 3.3.2

• Hints to Optimize the Engage Button Section 3.3.3

• Tapping Engage Section 3.3.4

• Scan View Parameters Tips Section 3.3.5

• Channels Parameters Tips Section 3.3.6

• Feedback Parameters Tips Section 3.3.7

• Signal Access Software Section 3.3.8

3.3.1 Using the Image Interface

There are various commands available for use during a Realtime scan. Below is a description of
these commands (see Figure 3.3a).

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Figure 3.3a Real Time Window

Buttons

• Measure: Allows you to draw a line to make measurements.

• Pan: From a zoomed image, the user can pan around to other areas of the original
image.

• Data Zoom: Left-click, hold, and drag out a box. Release the mouse button and the
image will automatically zoom in to the area of the box. The original scan size remains
the same.

• Zoom: Allows you to zoom in on a region of interest.

• When you select Zoom a bounding box appears on the image display. Left-click on
the outer edge of the box to resize.

• Left-click in the center to reposition.

• Click the Execute button to zoom in. This updates the Scan size and X and Y
Offset parameters.

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• Execute: Executes the Zoom and Offset commands. You must select the Zoom or
Offset button for the Execute button to appear.

• Offset: Allows you to center the scan at the region of interest.

• When you select Offset a crosshair displays at the center of the image.

• Left-click and hold the crosshair to reposition it.

• Click the Execute button to center the scan. This updates the X and Y Offset
parameters.

Right-Clicking on the Image

By right-clicking on the image, you will get a menu that allows you to perform the following tasks:

• Copy Clipboard: Copies the image to the Microsoft™ clipboard.

• Tooltip Info Level:

• Basic

• Medium

• Advanced

• None

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Right-Clicking on the Color Bar

Right-clicking on the color bar along the right side of the image (see Figure 3.3a) will produce a
Color Scale button (see Figure 3.3b). Clicking on this Color Scale button will open the Color
Adjust menu, shown in Figure 3.3c, where you can perform the following image adjustments:

Figure 3.3b Color Button

a. You can adjust the color by changing the Contrast or Offset settings.

• Contrast—Number (-10 to +10) designates contrast of colors in displayed image

(e.g., 0 shows little change, while 10 shows highest contrast).

• Offset—Number (-128 to +128) designates offset of colors in displayed image

(e.g., 120 shows illuminated background on image).

• Table—Number (0 to 24) designates which color table will be used.

b. Clicking the Color Reset button will change all the current readings to the default
settings.

Figure 3.3c Color Adjust Menu

c. To change the color table, position the mouse over the color bar on the right side of the
image. Click and hold the left mouse button, then drag the mouse from left to right to
scroll through the different color tables or set the table number in the Color Adjust
window.

Using the Mouse Within a Captured Image in Measure Mode

Left-click anywhere in image Creates a line of X length, at Xo of angle in the image window.
window, drag line out, and
release

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Place cursor on line Displays length and angle values of line in the image window.

Place cursor on line, click Allows you to drag the line anywhere in the image window.
and hold left button, and
drag

Click and hold on either end Changes length and/or the angle of the line.
of line and drag

Right-click Clicking the right mouse button when the cursor is on the line
accesses the Image Cursor menu (see Figure 3.3d).

• Delete—Deletes the line.

• Flip Direction—Switches the line end to end.

• Show Direction—Adds small arrowhead to the line to

indicate its direction.

• Set Color— Allows you to change the color of the

line.

• Clear All—Deletes the line.

Figure 3.3d Image Cursor Menu

Using the Grid Display

Measurement cursors for the Scope View are provided to the left and right of the Grid Display. You
can bring the cursors into the grid by placing the mouse cursor outside of the grid, clicking and
holding the left mouse button, and dragging them onto the grid. When you place the mouse cursor
onto a measurement cursor, the cursor will change from a plus sign to a horizontal or vertical
arrowhead cursor, which indicates you can grab and drag this cursor.

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Right-clicking on the grid will bring up the Grid Parameters menu (see Figure 3.3e) and allow
you to make the following changes:

Color Allows operator to change the color of the:

• Curve (data)

• Text

• Background

• Grid

• Minor Grid

• Markers
Filter Typically used for a Profiler Scan.

• Type—Allows the user to plot the mean, maximum or

minimum y-value per x-value.

• Points —Allows user to plot multiple vertical axis

(y-)values at each horizontal axis (x-)value. Select 4K,
8K, 16K or 32K Points to limit the display to 4, 8, 16
or 32 times 1024 points.
Minor Grid Places a minor grid in the background of the Vision Window.

Scale Allows user to auto scale, set a curve mean, or set their own data
range
Translate Offsets the curve by the placement of a horizontal cursor on the grid

Line Style For each curve, the operator can choose a connect, fill down, or point
line.
User Preferences Restore—Reverts to initial software settings
Save—Saves all changes operator has made during this session. This
becomes the new default settings.
Copy Clipboard Copies the grid image to the Microsoft Clipboard

Print Prints out the current screen view to a physical printer

Export Exports data in bitmap, JPEG or XZ data format

Active Curve Determines which curve you are analyzing

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Figure 3.3e Grid Parameters

Default Configuration Settings

NanoScope software, starting with version 7.10, remembers your customized configurations, both
RealTime and Offline. You may customize your use of this feature by selecting Tools > Options >
Default Configuration Settings... This will open the Default Configuration Settings window
shown in Figure 3.3f.

Figure 3.3f Default Configuration Settings Window

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Default Configuration Settings Buttons

• Do not use Default Configuration Settings—Turns off the Default Configuration

Settings feature and opens views using factory settings.

• Use configuration settings, do not save new settings when closing views—Uses your
customized settings but does not save the current settings for future use.

• Save Cursor Settings—Saves the cursor locations. Cursors will appear when you open
the same view at a later time. This only works well if you open a view with the same
horizontal and vertical resolution.

3.3.2 Multiple Channels

It is often helpful to view more than one channel of data simultaneously. Scan-Dual, Scan-Triple
and Scan 8 Channels can be selected upon first opening RealTime by clicking on the appropriate
check boxes in the Add Views to Real Time1 dialog box (see Figure 3.3g).

Figure 3.3g Add Views to Realtime1 Dialog Box

If you are already in Real Time, you can also access multiple channel views by right-clicking on the
Real Time icon in the Real Time workspace (see Figure 3.3h).

• Click Add View > Scan-Dual to add a window with two channels displayed.

• Click Add View > Scan-Triple to add a window with three channels displayed.

• Click Add View > Scan 8 Channels to add a window with eight channels displayed.

Note: To open a single channel, click Add View > Scan Display.

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Figure 3.3h Add Views to Realtime1 Menu

Realtime Icon
in Workspace

You may also access multiple channel view by clicking ACQUIRE > SCAN-DUAL, SCAN-TRIPLE or
SCAN 8 CHANNELS from the Menu Bar. See Figure 3.3i.

Figure 3.3i Select SCAN 8 CHANNELS in RealTime view

Image controls are displayed beneath each image (see Figure 3.3j).

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Figure 3.3j Scan-Dual View

right-click in title bar

Scan Controls

In Scan-Triple the Scan Line, Scan Direction, Data Scale, Data Center, Realtime Planefit, and
Offline Planefit settings are not displayed below the images and must be accessed using the
parameters list to the right of the image display (see Figure 3.3j and Figure 3.3k). To make this
parameter list visible, right-click in the title bar of the Scan-Dual or Scan-Triple windows and
select SHOW PARAMETER LIST 1 and/or SHOW PARAMETER LIST 2. You may also select Scan
Parameter List from the workspace to make additional Scan Parameters visible.

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Figure 3.3k Scan Triple view and Location of Channel 2 and 3 Parameters
right-click in the title bar

Channels 2 and 3 Parameters

Note: All four channel display options are included among the Realtime views
presented as options to include in the workspace upon first opening the
RealTime workspace (see Figure 3.3g).

Scan 8 Channels

The Scan 8 Channels window is shown in Figure 3.3l. All active channels have an associated
thumbnail down the left-hand side of the Scan 8 Channels window, shown in Figure 3.3l. The
currently displayed channel is highlighted. The image parameters may be set independently for all
eight channels including data type and scale, plane fitting and color table. See Channel Settings in
Figure 3.3l. Settings common to all channels can be set through the Scan Parameter List.

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Figure 3.3l Scan 8 Channels RealTime view

Currently displayed channel

Currently displayed channel

Channel settings

Typical examples of the use of multiple channels:

• To simultaneously monitor both a TappingMode height image and a phase image of the
same region.

• To simultaneously collect a topography and MFM image.

3.3.3 Hints to Optimize the Engage Button

• When used with stepper-motor-engagement microscopes, the tip is lowered under
program control. While the tip is being engaged, the tip travel distance is shown in the
status bar. When the surface is detected, the workstation beeps, starts the RealTime
imaging process, and displays Engaged in the status bar.

• During automatic engagement, the tip will travel a preset distance (200µm for
Dimension AFMs, 125µm for MultiMode AFMs). If the sample surface is not detected
in this distance, an error message will be displayed.

• If the tip is on the surface and the Z center voltage indicates that the piezo is near full
extension or retraction, the tip may be withdrawn and re-engaged to center the Z center
voltage. Alternatively, the Tip Up and Tip Down subcommands of the Motor command
can be used to center the Z voltage. If the Z center position indicates that the scanner is
retracted, click the Tip Up button until Z center is near 0V (0.50V).

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• Pressing Ctrl-F will cause a false engage to occur after the SPM safety height is
recycled for Dimension, causing the Realtime software to start scanning independently
of whether the surface has been detected or not.

3.3.4 Tapping Engage

The Tools > Engage Settings > Tapping... window is designed to assist users in controlling key
parameters associated with surface engagement during TappingMode. By using the Tapping
Engage panel, however, users may minimize engagement times or tapping forces for specific
conditions (e.g., TappingMode in fluids, etc.).

CAUTION: Adjustment of the Tapping Engage parameters can decrease

engagement times during TappingMode by speeding the tip’s travel to
the surface and decreasing the number of test probes. Although this
may save time, it also endangers the tip. You should always default to
more conservative settings when in doubt; otherwise, you risk
breaking tips.

Tapping Engage Panel

The Tapping Engage panel shown in Figure 3.3m illustrates recommended parameter values for
most conditions. These settings yield an engagement time of 20 - 40 seconds.

Figure 3.3m Tapping Engage Window

Setpoint values represent percentages of a setpoint established internally by the software for
engagement purposes (generally, about 90 percent of the tip’s free-air amplitude). These values
should not be confused with the Setpoint value indicated on the Feedback panel.

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Parameters in the Tapping Engage Panel

Delta setpoint

Amount the setpoint is adjusted during each false engage test.

Note: While in TappingMode, this tests for false engagement and assists in engaging
the tip on the sample surface. Tests for false engagement help to avoid artifacts
produced by light scatter, fluid film damping, etc. Therefore, a setting of 0.00
(no test for false engagement) is not recommended.

Range and Settings:

• ± 0—0.25 (default: 0.02) A value of 0.25 (corresponds to ±25%) is the recommended

maximum. If set to 0.00, the system will not test for false engagement.

Final delta setpoint

Percentage of setpoint value (internally set) to be used after tests for false engagement are
concluded. This is the amount of temporary “overdrive” used by the system to verify whether the
sample is, in fact, engaged by the tip. If this test is passed, the setpoint is restored to the last value
used during false engagement tests.

Range and Settings:

• 0.00—0.50 (corresponding to 0 to 50 percent)

Note: This value is usually set equal to the Delta setpoint. It represents a cumulative
value which is eventually reached in a series of Delta setpoint increments
(rather than one, single test). For example, with an engage delta setpoint of 0.02
and a final delta of 0.10, five extra tests will be run after “engagement” to
verify that the tip is actually on the surface (0.10 ÷ 0.02 = 5).

Note: If problems persist with false engagement, set the Final delta setpoint to a
value that is 2-3 times the engage delta setpoint.

Test threshold slope

Slope value obtained by dividing the change in Z piezo voltage by the change in setpoint, which
ultimately represents an envelope within which engagement is detected.

Range and Settings:

• 0.11—1000 (default: 100)

Note: Because changes in Z piezo voltage units occur approximately 200 times per
unit change of setpoint, slope values tend to be between 5—1000.

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Note: The higher the slope value, the greater the chance of “false engagement.”
Lower values are recommended for most applications. Using much lower
values may reduce tip life.

Test threshold dZ

Similar to Test threshold slope, above. Engage occurs when either Test threshold slope > dZ/dA
(change in Z with respect to Amplitude - shown as Slope test in Figure 3.3n) or Test threshold dZ
> dZ. The probe tip tapping amplitude drops markedly when the tip contacts the surface.

Range and Settings:

• 0.0—2000nm (typical value: 25nm)

Figure 3.3n Tip Amplitude While Approaching the Sample Surface


3ETPOINT 6

/FF SURFACE

: 6


3LOPE TEST

Engage min setpoint [%]

Lowest allowable percentage of setpoint value (internally set) used during engagement,
representing the “last word” in tip-sample force. This value overrides other parameters determining
setpoint during engagement.

Range and Settings:

• 10—90. (typical value: 25).

Note: Lower values may endanger the tip and/or sample, as higher tip-sample forces
will be employed.

Note: Higher values represent lower, more conservative tip-sample forces; however,
very high values will increase false engagements.

TM engage gain

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Integral gain value used during TappingMode engagement. Once the surface is engaged, gain
values revert to those displayed on the Feedback panel.

Range and Settings:

• 0.0100—10.00 (typical values: 0.5-2)

Hints for optimizing the TM Engage Gain

• As TM engage gain is increased, the tip’s vertical velocity downward increases. This
parameter may be used to speed the engagement process and save time; however, if set
too high, the tip and sample may be damaged.

• During engagement, gain values (Integral and Proportional) displayed on the

Feedback panel are not utilized. Instead, the software sets its own integral gain based
on this parameter.

• With normal (non-fluid) samples, higher values tend to accelerate engagement speed at
the cost of endangering tips and samples. Use of a higher gain may be recommended for
TappingMode scanning of hard samples in fluid; however, gain should be increased
cautiously.

• Use of lower gain values will tend to increase engagement times; however, lower values
are recommended for soft, delicate samples where impact is to be minimized.

Sew tip

Controls use of sewing during the engagement process to detect the surface. Sewing consists of
moving the tip vertically with the Z piezo while lowering it toward the surface. If the surface
position is well known, sewing may be triggered to save time.

Range and Settings:

• Yes—Turns sewing on. This is the normal, default mode.

• No—Turns sewing off.

Note: Only used for testing purposes; typically results in a damaged tip.

• Triggered—Turns sewing on when the RMS amplitude reaches the specified Sewing
trigger value. The Triggered switch is used to protect tips and samples and to decrease
engagement time.

Sewing trigger [%]

Percentage of oscillation amplitude required to trigger sewing. This parameter is enabled only
when the Sew tip parameter has been set to Triggered. Default setting is 98; not recommended at
values less than 90.

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Range and Settings:

• 1—100; default setting = 98.

Note: Regardless of setting, this parameter may be overridden by the Trigger safety
parameter.

Trigger safety [for Dimension series microscopes only]

Minimum height above sample surface at which sewing is turned on. This parameter overrides the
SEWING TRIGGER parameter.

Range and Settings:

0—100 μm; typical setting = 20 μm

CAUTION: To avoid damaging the tip or sample, the Trigger safety should be set
to a value greater than the height of the tip, or the maximum peak-to-
valley distance of surface features, whichever is greater. This
parameter consists of a height above the surface as determined during
the TOOLS/STAGE > FOCUS SURFACE... command.

Pre engage setpoint [%]

Used to set the setpoint of the tip prior to engagement by reducing the setpoint relative to the RMS
amplitude.

Range and Settings

• 30—100; default = 90.

Note: The usable range of this parameter is generally from 85 to 95. This represents
the starting value for the engagement cycle (see beginning of this section).

3.3.5 Scan View Parameters Tips

Optimizing the Scan Size Parameter

• The Scan size and offsets can be set by using the Zoom and Offset subcommands in
Scan View or in tabbed panels.

• Non-zero X and Y offsets reduce the maximum Scan size. Each volt of X or Y offset
reduces the maximum scan size by 2V.

• Having a non-zero Scan angle will reduce the maximum allowable Scan size.

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• The maximum Scan size will also decrease as the Scan rate increases.

Optimizing the X Offset, Y Offset Parameter

• These parameters use the sample as the position reference. Therefore, a more negative
X offset value will move a feature in the current image to the left on the Image display
Similarly, a more negative Y offset moves a feature in the current image down on the
Image display.

• Using the left-arrow and right-arrow keys when the cursor is in these parameters will
decrement and increment these parameters by 10% of the Scan size.

• Using the Zoom or Offset subcommands automatically changes the value of X and Y
offsets.

Optimizing the Scan Size and Scan Rate Parameters

• The Scan size and height of features on the sample will affect the maximum Scan rate
that should be used on a given sample. Scan rate should be set to a rate that allows the
tip to closely track the sample surface in both trace and retrace. In general, larger scans
and taller features require slower scan rates.

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3.3.6 Channels Parameters Tips

Optimizing the Data Type Parameters

• The system can display up to three Realtime images on the Display Monitor.

• The Data type parameter does not switch the operating mode of the instrument, it
simply changes the source of the data displayed.

Optimizing the Data Scale Parameters

• Data beyond the setting of the Data scale is clipped for the RealTime display. Captured
data, however, is not clipped. Independent of the settings of this parameter, the captured
data will be correct unless it exceeds the maximum vertical range of the scanner.

• Each Data type retains separate settings for Data scale.

• Data Center is used to manually offset the trace data when Realtime Planefit is set to
none.

The conversion of volts to nm or nA, is dependent on the value Sensitivity Detector parameters in
the Tools > Calibrate > Detector panel.

For example, nanometers of cantilever deflection are calculated using the Sensitivity parameter in
the Force Calibrate panel.

Optimizing Realtime Planefit Parameters

The setting of Realtime Planefit only affects the displayed data. It does not affect the captured data
The parameters are described below.

• None displays the raw data in the scope display.

• Offset applies a zero order correction to each line of data so that the average height of
the line is centered in the scope display.

• Line applies a 1st order correction, removing both tilt and offset from each line of data.

Note: If features are not evenly spaced along the scan line, using Realtime Planefit
Line can result in artificial tilting of the scan line.

Optimizing the Offline Planefit Parameter

• The None option should only be used in special cases. The Offset and Full options
provide greater dynamic range in the data to reduce round-off and other errors in
subsequent calculations.

• The Offline > Modify > Flatten and Planefit commands can also be used to level the
data after it has been captured.

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3.3.7 Feedback Parameters Tips

Optimizing the STM Feedback Parameters

• Log mode is preferable for most STM samples, because the tip responds in a more
symmetric manner (i.e., the same going up and coming down). Log mode tends to
linearize the entire feedback loop since Z ≈ ln(i). The asymmetric response of the
Linear setting distorts data.

Optimizing the Integral and Proportional Gain

• The Integral gain is usually the major contributor to the performance of the feedback
loop due to its “long term” influence. For this reason, it is usually adjusted before
proportional gain.

• The integral term in the feedback calculation has the highest gain at low frequencies,
and its effects diminish with increasing frequency.

• A nominal Integral gain value may be obtained by slowly increasing the value until the
piezo begins to oscillate, then decreasing the value until oscillation ceases. Oscillation
effects are best viewed using Scope Mode and show up first in error signal (i.e
deflection or amplitude).

• The Proportional gain parameter is typically set to 35 to 100% more than the Integral
gain value.

3.3.8 Signal Access Software

Signal Access Software allows selected signals to be copied, at 10 micro-second intervals, to the
Output 1/2 connectors on the front of the NanoScope V Controller. To use this feature:

1. Select the OUTPUT 1 and/or OUTPUT 2 DATA TYPE. See Figure 3.3o. INPUT allows selected
input signals to be copied to the Output 1/2 connectors. OUTPUT allows selected output
signals to be copied to the Output 1/2 connectors.

2. Select, using the OUTPUT 1/2 DATA field, the signal that you wish to be copied. See Figure
3.3p and Figure 3.3q.

a. These menu options are also available in the Scan Parameter List.

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Figure 3.3o Select OUTPUT 1 DATA TYPE

Figure 3.3p Input signal selection shown with the SCM module connected

Figure 3.3q Output signal selection: left: tapping; right SCM.

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3.4 Force Curves

Force Curves ramp tip-sample separation while holding the X, Y position constant in the center of
the previous scan. The scanner’s vertical position is plotted versus either the cantilever deflection
(Contact AFM), or the amplitude of the cantilever oscillation (TappingMode). Alternatively, the
cantilever deflection or oscillation amplitude can be plotted relative to a user-designated input
signal.

3.4.1 Force Curves Procedure

Ramp Settings

To obtain force curves, it is necessary to first engage in Scan Mode using one of the Scan Views
(see Preparing a Dimension Series AFM for a Realtime Scan Section 2.4.2), then switch to
Ramp mode. If you want to calibrate deflection sensitivity, use a hard sample in the following
procedure.

1. Activate Ramp mode (this causes the system to stop scanning, and the probe to position
above the center of the previous image):

a. Click the Ramp node in the workspace or any visible ramp plots.

Or

b. Add the Ramp Parameter List and Ramp Plot(s) to the workspace. Right-click
Realtime or click the Acquire menu, and select Ramp Parameter List and Ramp
Plot. It is possible to view three Ramp Plots at a time by adding ramp plots to the
workspace. Arrange the Ramp Plot(s) and Ramp Parameter List so that all are
viewable.

Note: See Ramp Parameter List Section 3.4.2 - Feedback Panel Section 3.4.7 for a
thorough discussion of the Ramp Parameter List Parameters. When in Ramp
mode, a ramp- specific menu also displays, the Ramp menu. See Ramp Menu
Section 3.4.8 for more information.

2. Enter the following parameter settings in the designated panels of the Ramp Parameter
List:

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a. In the Ramp panel select:

Parameter Setting
Ramp output Z
Ramp size 1.00µm
Z scan start 0nm
Scan rate 1.00Hz
Number of samples 512

b. In the Channel 1 panel select:

Parameter Setting
Data Type Deflection
X Data Type Z
Display Mode Deflection vs. Z

Gather Force Curves

1. Select Ramp > Run continuous from the menu bar.

2. While watching the Ramp Plot and the Real Time Status bar graph (see Figure 3.4a),
increase the Z Scan Start to move the tip closer to the sample.

Figure 3.4a Bar Graph

3. When the force curve suddenly rises, the tip has reached the surface (see Figure 3.4b).

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Figure 3.4b Force Curve

4. Click the Capture icon to save the force curve. Make note of the file name in the status bar
(lower right corner of the window).

Calibrate Deflection Sensitivity

It is often necessary to calibrate the deflection sensitivity of a force curve. The deflection
sensitivity depends upon several factors, such as the position of the laser spot on the cantilever, so it
needs to be calibrated each time you change the probe. Use the following procedure to determine
the deflection sensitivity:

1. Move two cursors onto the Deflection vs. Z plot (see Figure 3.4c).

Figure 3.4c Realtime Force Curve

2. Arrange the cursors so that they surround the contact (steepest) portion of the graph
(see Figure 3.4d).

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Figure 3.4d Force Curve Cursors

3. Select Force > Update Sensitivity. The software will automatically calculate the deflection
sensitivity.

Figure 3.4e Update Sensitivity

4. Click OK to accept this deflection sensitivity in the dialog box that displays, and it will
automatically be entered into the Sens. DeflSens parameter in the Channel Data panel to the
right of the plot (see Figure 3.4c).

Figure 3.4f Deflection Sensitivity Dialog Box

5. Replace the hard sample with the sample you wish to analyze. The deflection sensitivity will
remain applicable as long as the position of the laser spot on the cantilever does not change.

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3.4.2 Ramp Parameter List

When you open Ramp Parameter List, the Ramp Parameter List box displays (see Figure 3.4g).
All force curve parameters can be set in the Ramp Parameter List. The Ramp Parameter List is
sectioned into seven panels. The parameters in each panel are defined in the following sections:

• Ramp Panel on page 106

• Mode Panel on page 108

• Auto Panel on page 109

• Channel (1, 2 or 3) Panels on page 110

• Feedback Panel on page 111

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Figure 3.4g Ramp Parameter List

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3.4.3 Ramp Panel

Ramp Output: Specifies the Ramp Channel.

Ramp Size: Specifies the range of the Ramp Channel. Visible only if the Ramp Channel
parameter is set to Z. Settings depend on the specified units.

Z Scan Start: Visible only if the Ramp Channel parameter is set to Z and TRIGGER MODE is OFF.
Z scan start is the bottom position of the Z-axis scan as represented on the Real Time status bar.
When the Ramp node is first accessed during imaging, this value is automatically set to the Z
Center Position.

Note: The value of this parameter will need to be increased to move the sample closer
to the cantilever in the case where there is no deflection of the cantilever for a
displacement of the sample.

• Range and Settings: The range of this parameter depends on the scanner. The units of
this parameter are volts or nanometers, depending on the setting of the Units parameter.

Note: While the user is ramping Z in Ramp Mode, some feedback parameters are
inactive.

Scan Rate: The Scan Rate sets the ramping rate. Changing this value effects the Forward and
Reverse Velocities.

Forward Velocity: Forward Velocity of the tip (in µm/s) as it approaches the surface. Increasing
this value increases the Scan Rate.

Reverse Velocity: Reverse Velocity of the tip (in µm/s) as it retracts from the surface.

X Offset: Controls the position of the range in the X direction.

Y Offset: Controls the position of the range in the Y direction.

Number of samples: Number of data points collected during each upward (retraction) and
downward (extension) travel cycle of the piezo. The Number of samples parameter sets the pixel
density of the force curve. This parameter does not change the Z scan size.

• Range or Settings: 16 to 19,968 data points displayed per extension and retraction cycle.

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Spring Constant: Records the spring constant of the cantilever that is currently being used. This
parameter is input by the user and is recorded along with each force plot captured. It is used for
Offline analysis of the force plot. It is not critical to set the Spring constant in Realtime, since it
can be altered in the Offline analysis of the captured force plot. The Spring constant is necessary to
display a graph of force vs. separation if UNITS is set to FORCE.

Plot Units: Switches parameters in the control panels between units of Volts (V), Metric (nm or
µm), or Force (nN). Changing this parameter also changes the setting of the Units parameter on the
Scan Parameter panel.

• Range or Settings: Volts (V), Metric (nm) or Force (nN)

Display Mode: The portion of a tip’s vertical motion to be plotted on the force graph.

• Range or Settings:

• Extend—Plots only the extension portion of the tip’s vertical travel.

• Retract—Plots only the retraction portion of the tip’s vertical travel.

• Both—Plots both the extension and retraction portions of the tip’s vertical travel.

• If a channel other than Z is chosen, Display mode will not be available in Offline
view.

X Rotate: Allows the user to move the tip laterally, in the X direction, during indentation. This is
useful since the cantilever is at an angle relative to the surface. One purpose of X Rotate is to
prevent the cantilever from plowing the surface laterally, typically along the X direction, while it
indents in the sample surface in the Z direction. Plowing can occur due to cantilever bending during
indentation or due to X movement caused by coupling of the Z and X axes of the piezo scanner.
When indenting in the Z direction, the X Rotate parameter allows the user to add movement to
scanner in the X direction. X Rotate causes movement of the scanner opposite to the direction in
which the cantilever points. Without X Rotate control, the tip may be prone to pitch forward during
indentation. Normally, it is set to about 22.0º.

• Range or Settings: 0 to 50º; most effective values are between 15 and 25º.

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3.4.4 Mode Panel

Trigger Mode: Limits the amount of force exerted by the tip upon the sample. It is possible to
operate the trigger independent of drift (Relative) or at some arbitrarily fixed point (Absolute)
depending on the trigger settings.

Data Type: Channels may be assigned for triggering to any input signal available including:
Deflection, Amplitude, Phase or Friction data.

Trig Threshold: The value of the cantilever deflection, as measured by the photodetector, desired
for the indentation or scratch. The Trigger threshold defines the maximum force applied to the
sample corresponding to the upper right-most point on the force plot.

• Range or Settings: -10V to +10V, depending on the Deflection Limit. Try 0.5V to 1.0V.

Trig Direction: Determines the direction of the trigger and allows for a Positive, Negative, or
Absolute trigger slope. In this way, the trigger may be configured to activate on either the positive
or negative direction of the force curve.

Z position - 0.10 µm/div Z position - 0.10 µm/div

Negative Trigger Direction Positive Trigger Direction

Start Mode: Start mode allows you to switch between the various force modes without returning to
image mode.

• Range or Settings:

• CALIBRATE—Produces standard force plots. Includes the ability to continuously

cycle the tip up and down.

• STEP—Produces standard force plots, with added control to step the tip towards the
surface.

• MOTOR STEP—Tip is stepped towards surface using the motor.

• INDENT—Starts optional nanoindentation mode. Available only in TappingMode.

End Mode: Determines the location of the tip when the microscope is returned to Image mode.
Choices include Extended, Retracted, or Surface.

Z Step Size: The change in tip height per step when using force step.

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Auto Start: When enabled, autostarts ramping when entering from Image mode. If off, you must
start ramping by clicking the Continuous or Single icon, or by selecting the proper menu selection
under the Ramp menu.

Surface Delay: Specifies a delay when the tip reaches the point closest to the sample.

• Range or Settings: 0 to 200 seconds

Retracted Delay: Similar to Surface delay, this value specifies the duration of the delay when the
piezo is at the top of the cycle (farthest away from the sample).

• Range or Settings: 0 to 200 seconds

Auto Offset: Because of Z drift (thermal drift, piezo drift, etc.), the sample will sometimes drift out
of Z range. When enabled, Auto Offset uses the Setpoint value from Image mode to Feedback and
find the surface and resume ramping. The Auto Offset feature is a form of drift correction.

Note: Uses Feedback parameters from Scan settings.

Strip Chart Rate: Frequency of (Z-position, deflection) data point acquisition for strip chart (only
available for Picoforce and Nanoman).

• Range: 0.01Hz to 1kHz. Typical value: 100Hz.

Strip Chart Size: Time interval over which (Z-position, deflection) data points are displayed in the
strip chart.

• Range: 10 to 360,000,000 sec. Typical value: 100 sec.

Note: Although the strip chart collects and displays data over the time interval
defined by clicking Start, then later, Stop, this data is not saved for subsequent
use until the Capture icon (shown) is clicked. If Capture is clicked while strip
chart data is being taken, what is saved begins at the start of the chart (sooner
than the icon is clicked).

3.4.5 Auto Panel

The Auto Panel parameters are only applicable when Autoramping.

Columns: Number of points in the Y axis.

Rows: Points in the X axis.

Column Step: Offset distance between points in the X direction.

Row Step: Offset distance between points in the Y direction.

Threshold Step: The trigger point at which the deflection or the current activates the position
change.

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Capture: State is either ENABLED or OFF. When ENABLED, the software records and stores the ramp
data for each data point in the matrix of rows and columns.

3.4.6 Channel (1, 2 or 3) Panels

Data Type: Channels may be assigned to any input signal available including: Deflection,
Amplitude, Phase, Friction and so on. Any channel may be switched to Off, however, at least one
channel is always on.

X Data Type: Type of data that the channel data is being compared to. This data displays on the X-
Axis of the scope grid.

Data Scale: Voltage range for the vertical axis of the force curve plot.

Note: This can be overridden by selecting Auto Scale On for the plot.

Data Center: Offsets centerline of scan by the amount entered.

Note: The Data center offset does not become a permanent part of the data.

• Range or Settings: Depends upon the input signal, generally ± one-half of data scale
maximum.

Deflection Sens.: Defines the conversion factor from cantilever deflection signal voltage to
nanometers of cantilever displacement (in nm/V) using data in the contact region of a force plot.

Plot Invert: Inverts data along the Y-axis, effectively turning valleys into mounds and vice versa.

Ave. Points: Averages multiple points to smooth the curve.

Effective BW: A display (you cannot input a value to it) representing the sampling frequency with
display averaging taken into account:

Effective BW = (force plot sampling rate)/(Ave. Points)

Phase Offset: Shift horizontal position of plot to compensate for averaging of endpoint data.

Note: The numerical values of the two Phase Offset parameters can be ignored; set
them to whatever values minimize the apparent hysteresis. Particularly when
Forward Velocity and Reverse Velocity are unequal, the same numerical
value for each Phase Offset may not correspond to an identical displacement
on each axis.

Display Mode: The data types to be plotted on the force graph. E.g. Amplitude vs. Z.

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3.4.7 Feedback Panel

Only the Force Curve-applicable menu parameters are described below:

Deflection Setpoint: Defines the deflection signal, and therefore the tip-sample force, maintained
by the feedback loop.

• Range or Settings: ± 12.0V maximum

3.4.8 Ramp Menu

While the microscope is engaged and in Realtime mode, opening the Ramp parameters will display
the Ramp Menu.

Figure 3.4h Ramp Menu

Ramp Menu Definitions

Run Continuous: The tip is continuously lowered and raised by a distance equal to the Ramp size.
This is the normal, default motion during Force Calibrate. “Raising” and “lowering” are relative
to your system (e.g., On Dimension Series SPMs, the tip is raised and lowered to the surface;
however, other SPMs raise and lower the sample beneath the tip).

Run Single: Lowers and raises tip once by a distance equal to the Z scan size, then halts.

External Trigger: (Not available)

Stop: Halts all tip movement.

Retract: The Z-axis piezo retracts to its limit in preparation for Approach Continuous. This
command does not initiate motor movements.

Approach Continuous: The tip lowers to the surface and raises in a controlled series of steps, then
indexed by the Z step size (see Scan Mode panel) distance. This process continues downward until
the tip encounters the surface. When tip deflection exceeds the Threshold Step amount, Approach
Continuous halts and the resulting force curve displays.

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Approach Single: The tip is lowered to the surface and raised in a single, controlled step. This
process is halted if the surface is encountered by the tip, causing deflection exceeding the Step
threshold amount. The resulting force curve is displayed.

Note: For both Approach Continuous and Approach Single, if Start mode =
MOTOR STEP, the motor is stepped towards the surface, not the Z piezo.

Auto ramp: Begins auto ramping as defined by the parameters specified in the Auto Panel.

3.5 Force Volume

3.5.1 Introduction

NanoScope Force Volume (FV) imaging with the atomic force microscope (AFM) combines force
measurement with topographic imaging. Typical AFM images depict the topography of a surface
by measuring the action of a feedback loop to maintain a constant tip/sample interaction as the tip
is scanned across the surface. The force volume data set combines nearly simultaneously measured
topographic and force information into a single data set allowing the microscopist to test for
correlations between forces and surface features.

A single force curve records the force imposed on the tip as it approaches and retracts from a point
on the sample surface (see Figure 3.5a, top). Force volume imaging associates each (X,Y) position
with a force curve in Z for some selected range. By plotting these values along X and Y
coordinates, you may view stratified layers of force at various Z-axis heights above the sample
surface. The value at a point (X,Y,Z) in the volume is the deflection (force) of the cantilever at that
position in space (see Figure 3.5a, bottom).

A force volume data set can be used to map in two or three dimensions the interaction forces
between a sample and the AFM probe tip. Possible applications include studies of elasticity,
adhesion, electrostatics and magnetics. Force volume imaging enables the measurement of forces at
various Z-positions and at thousands of (X,Y) positions during a single image scan.

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Figure 3.5a Force Curve with Both Extending and Retracting Traces (top)

Away from sample

Towards sample

Z
Y
X

Sample

Force Volume Array of (Identical in this Case) Force Curves (bottom)

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3.5.2 Varieties of Force Volume Imaging

The matrix below summarizes each of the major imaging types.

Signal Type Contact AFM TappingMode

Amplitude 5
Deflection 5 5
Friction 5
Phase 5

The type of force image captured from a surface depends on how the SPM is set up. For example:

• If an magnetic force microscopy (MFM) image is being captured, force volume imaging
(phase) allows the detection of long-range magnetic forces otherwise difficult to detect.

• For ordinary contact AFM, the use of force volume imaging (deflection) allows the user
to see otherwise invisible electrostatic forces.

CAUTION: It is the responsibility of the microscopist to carefully define all

force volume experiments. There are at least ten types of force
volume imaging, including numerous combinations of triggers,
drive frequency and amplitude, Z-axis direction, offset, etc. The
utility of each image is subject to the interpretations and controls of
the experimenter. This document does not cover all possible force
volume types; therefore, discussion is limited to a general
description of controls and an example in contact AFM.
Experimentation is encouraged.

3.5.3 A Force Volume Imaging “Jump Start”

This section provides an overview of force volume imaging for the casual reader or the experienced
experimenter eager to get started. Force volume images require preliminary use of the Force
Measurement function.

The basic procedure for generating a force volume image follows.

1. Create a height image of the surface of interest. This assigns values to image parameters,
including image size.

2. Switch to ramp mode and generate a standard force curve featuring both contact and non-
contact tip/sample interactions. Set SENSITIVITY as described in your SPM Instruction
Manual and set the DEFLECTION LIMIT to 24.58V. Set Z SCAN RATE, Z SCAN SIZE, and a

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RELATIVE TRIGGER with a TRIG THRESHOLD of approximately 40 nm. Ensure that

triggering is functioning properly before proceeding.

3. Switch back to Scan mode by clicking on the Scan node in the workspace bar.

4. Switch to Force Volume mode by selecting ACQUIRE > FORCE VOLUME or clicking the
Force Volume node in the workspace bar. Using the same method, add the Force Volume
Parameter window, shown in Figure 3.5c.

5. Verify the force plot parameters are still in effect in all control panels. Set the number of
SAMPLES PER LINE to 16, the number of samples per force plot (NUMBER OF SAMPLES =
512), and the number of force plots (FORCE PER LINE = 16) and start collecting data. Don't
forget to capture the image.

Force volume mode displays the data in three separate, but interdependent, regions (see Figure
3.5b). The left image displays height. The right portion of the screen displays the force volume
image. It is a horizontal (parallel to the sample surface) slice through the volume at a distance Z
DISPLAY above the piezo position at the deflection trigger. The girded region in the lower right
corner of the screen displays force curves as they are collected. The position of the cross hairs
determines the slice presented in the force volume region. The position of the horizontal cursor on
the deflection axis of the force curves determines the offset of the scale bar in the force volume
image. The position of the vertical cursor sets Z DISPLAY.

Figure 3.5b The Force Volume Interface

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Figure 3.5c Force Volume Parameter Window

While collecting data in this mode, it is possible to change the slice displayed and its offset without
affecting the raw data. This is helpful in determining whether or not the parameters have been set
correctly. Only data collected after the cursors are moved is displayed with the new DATA CENTER
and Z DISPLAY.

With NanoScope 7.30 and later software, you can turn Z Closed Loop ON and OFF without
withdrawing the probe from the sample. With this change, Z LIMIT and Z RANGE are no longer
coupled.

Force volume data can be evaluated offline like other images, and, additionally, with specialized
analysis options. Different slices can be chosen by sliding the vertical green line along the Z axis of

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the force plot region, clicking on and dragging the line with the mouse. Force curves can be
displayed by clicking on appropriate pixels in either the image or volume region. See Force
Volume Display and Interpretation, page 132 for more detail.

3.5.4 Sample Preparation

Samples intended for force volume imaging require no special preparation. Force volume imaging
can be done in both air and fluid environments.

CAUTION: Be careful not to allow liquid to leak onto the (expensive)

piezoelectric actuating scanner tube; it can be damaged in a high
voltage short circuit and require replacement.

Refer to Support Note 290, Fluid Operation: Overview for Contact and TappingMode with a
MultiMode Microscope or Electrochemical SPM (part number 004-125-000), Support Note 410,
Direct Drive Fluid Cantilever Holder, the Dimension V or MultiMode V Instruction Manuals for
fluid cell preparation details.

Interpretable force volume images depend on an appropriate probe selection. A stiff cantilever may
provide better control when measuring strong forces and is less prone to entrapment by surface
tension; however, a stiff cantilever does not respond to small forces. A flexible cantilever is more
sensitive to small forces and is less harmful to delicate samples. Too pliant a probe, in responding
to myriad small forces, generates noise, and may jump to contact if large attractive forces act. Refer
to the Veeco website, www.veeco.com, for an illustrated survey of probe options.

3.5.5 Force Volume Procedures

Tip Movement

The force volume data set height image is collected in a slightly different manner than one taken in
Image Mode. In Image Mode, the tip is scanned along a line in the XY plane, deflecting to and from
the surface as it encounters features. The heights of features are determined by the piezoelectric
actuator moving the probe to minimize the error between the setpoint and tip deflection. In Force
Volume Mode, the piezoelectric actuator closes the distance between sample and tip until a
(trigger) threshold tip deflection is reached. The piezo position at the deflection trigger is recorded
as the height of the feature. Tip deflection or another signal type during this approach is recorded as
the extending portion of a force curve. Once the height measurement has been made, the
piezoelectric actuator retracts one Z SCAN SIZE and the AFM records the retracting portion of the
force curve. The forces measured reflect the Z component of the sum of forces acting on the tip at
that location. This process is then repeated at the next XY position in the area.

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Force volume imaging always includes executing tip motions as follows:

• The tip is lowered and pressed against the sample surface until the cantilever is
deflected to the Trig[ger] threshold value. If the surface is not contacted within one Z
scan size distance, the tip is extended one additional Z scan size (for a total distance of
two times the Z scan size), then retracted one Z scan size. This means that the tip is
incrementally lowered (or “ratcheted”) one Z scan size for each extension-retraction
cycle until the surface is contacted, or the Z piezoelectric actuator reaches its maximum
extension at 220 volts.

• Once the tip contacts the surface and deflection attains the Trig[ger] threshold value,
sample height is recorded for that Z-axis threshold. A force curve is recorded for the
(X,Y) coordinates after the piezoelectric actuator retracts. The tip is lifted clear of the
surface and translated to the next sample (X,Y) coordinates. The entire process is then
repeated.

Note: In NanoScope version 7, the ramp data is collected in the trace direction and
the system then moves the tip rapidly back to the start of the line.

Note: In NanoScope version 5.xx and earlier, the time required to add one scan
line to the height image is twice that calculated by multiplying Z SCAN RATE
for the force curves by the number of pixels in the image. This is because the
microscope collects both trace and retrace curves along each line in the XY
plane. Only data from one or the other scan direction can be saved.

General Force Volume Procedure

The general sequence for obtaining a force volume image consists of the following:

1. Obtain a height, deflection, amplitude or phase image of the sample in Image Mode. On the
Channel panel, select the same Data type intended for force calibrating and for triggering.

Note: A trigger is required to obtain a height image during force volume imaging.

2. Obtain a Force Plot of the sample surface (any portion of the surface suffices). Using the
force plot, determine the sample’s general force characteristics and set the following
parameters: Setpoint, Z range, Z scan size, Z scan start, and Trigger mode.

Note: While not required, using Image and Force Plot Modes to set parameters can
quicken the set-up process. Making parameter adjustments in Force Volume
Mode can take longer since the SPM responds to the new settings only when
it begins scanning a new line.

3. Return to Image Mode.

4. Obtain a Force Volume image by selecting Acquire > Force Volume or the Force Volume
workspace. Set the following parameters in the Force Volume Parameters panel: Z scan
rate, FV scan rate, Number of samples, Force per line, Samples per line, Display mode,
Sample period.

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5. Fine tune Image Channel parameters to obtain a height image. Based upon the experimental
design, set parameters in the FV (Force Volume) Channel and Force Channel panels.

6. Capture the Force Volume image.

Note: This takes longer than a normal image capture—the force volume image may
consist of up to 512 samples taken 512 times per line at the Z scan rate.

7. Interpret the Force Volume image using Offline commands.

Detailed Force Volume Procedure

Contact AFM Mode produces the best understood force volume images. The forces encountered,
both attractive and repulsive, include electrostatic, van der Waals, surface tension, capillary, ligand/
receptor, and magnetic interactions. Alternative modes of force volume imaging (tapping, phase,
etc.) are harder to interpret and are not discussed here.

Refer to Support Note 228, Force Measurements, for detail on generating force curves. A force
volume procedure follows.

1. Mount a sample and obtain a contact AFM image.

Select a sample and mount it on the AFM. Initially, the sample should be familiar enough to obtain
a recognizable image easily (e.g. a silicon calibration reference). Ensure that Other >MICROSCOPE
MODE is set to CONTACT.

After engaging the surface, adjust the SETPOINT so the tip exerts minimal force on the sample.
Reduce the SETPOINT until the tip retracts, then raise it slowly until there is just enough tip-sample
contact to obtain an image. Optimize the Channel 1 parameters for a good image: set DATA TYPE
to HEIGHT and REALTIME PLANEFIT to LINE. The image collected by Channel 1 is displayed as the
height image in the force volume display.

If the sample is weakly adsorbed to the substrate or there is some other reason for minimal tip-
sample contact before collecting the volume (i.e.: to avoid contamination of or damage to the tip), it
is possible to collect force volume data skipping the contact image step. First, before engaging, set
Image > SCAN SIZE to 0. Then engage normally, or false engage if it is absolutely necessary not to
contact the surface. Once engaged, lower the Setpoint until the tip is retracted from the surface. The
rest of the procedure is essentially the same.

2. Create a force plot of the surface.

To obtain a force plot of the surface, click the RAMP node. Set the (Ramp) Scan Rate to the
recommended default of 4 HZ. (In fluid, higher rates can induce hydrodynamic forces on the tip.)

Using the data scale from your image, set the RAMP SIZE to a number larger than the roughness of
your sample.

Click the SINGLE RAMP icon on the NanoScope task bar.

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Set the SENSITIVITY parameter using the mouse to draw a line on the force curve parallel to its
slope in the contact region (see Figure 3.5d). This parameter must be well-determined for
quantitative force readings.

Figure 3.5d Calibrating Deflection as Displacement

• Click and hold on either side of the plot area to get a cursor line.

• Drag this cursor line onto the plot to mark one part of the contact portion of the force
curve.

• Get and drag a second cursor onto another part of the contact portion of the force curve.

• Right click to choose the trace or retrace curve (Active curve 1 or 2).

• Then under the FORCE tab, select UPDATE SENSITIVITY.

3. Adjust the Z Scan parameters until a good force curve is obtained, that is, one such that a
significant portion of the curve contains the transition from noncontact to contact. For
example, if measuring an interaction force with a decay length of 10 nm, have a Z SCAN SIZE
on the order of 50 NM.

Make sure the piezoelectric actuator is centered in the Z direction. This gives it ample room to
move in response to surface features.

4. Return to Image Mode by clicking on the SCAN node. (You cannot switch directly from
RAMP to FORCE VOLUME.)

Once a good force curve is obtained, return to Scan Mode.

5. Obtain a force volume image of the surface.

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To obtain a force volume image, click Acquire > Force Volume or the Force Volume workspace.

Note: The screen appears similar to the one shown in Figure 3.5e, except that most
of the image regions are blank at first. (A minimum of several minutes are
required to obtain complete images.)

Figure 3.5e A Force Volume Image

Figure 3.5e shows the following:

• Left Image: The large image on the left side of the screen is a height image similar to
the one shown in Real-time/Image mode; however, it may appear more pixelated.

• FV Image: The right plots force as a function of Z distance.

Note: The resolution of the force plot varies depending upon various parameter
settings.

• The force plot at the bottom-right corner of the panel displays a series of superimposed
force plots for each scan line.

There are six Force Volume panels in the Force Volume Parameters window, shown in Figure
3.5f, which control sampling and scanning for the force volume image and force curve. They are
organized by function:

• Image Scan - Real-time parameters for the height image shown in the upper-left corner
of the display monitor, such as Scan size, X- and Y offset, Scan angle, and Scan rate.

• Image Channel - more Real-time parameters affecting the height image.

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• Z Scan - parameters affecting vertical movement of the probe, including Z scan start, -
size and -rate.

• Feedback - parameters controlling Setpoint, and where probe travel is to be reversed

(triggered): Trigger mode, -threshold and -channel.

• FV Channel - force volume channel controls affecting the force volume image in the
upper-right corner of the window, including FV scale, Force per line, Z direction and -
display, and Data Center.

• Force Channel - parameters affecting the force plots.

Figure 3.5f Force Volume Parameters Window

6. Set Z Scan parameters.

The Z Scan Controls panel groups basic sampling and scanning parameters for the force volume
image and force curve.

The following parameters are often carried over from the force plot settings: Z SCAN START, RAMP
SIZE and SCAN RATE.

The DISPLAY MODE parameter in the Z Scan panel can be set to display in the force plots region the
EXTEND portion of the force curves, the RETRACT portion, or BOTH.

7. Set the resolution of the height, FV, and force plot images.

Remember that you are constructing a “map” of many separate force plots across the sample surface;
therefore, there is a lot of data to sort. Depending upon settings, capturing a detailed force volume
image can require hours.

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Note: While the size of the area imaged by the AFM is ultimately limited by the
characteristics of the piezoelectric actuator tube, the resolution of the data is
limited by the computer hardware and software. The total amount of data for
any given force volume image file is limited to a maximum of 128 megabytes
(MB). This places restrictions on the resolution of the force curves, and the
force volume image.

There are three parameters in three distinct control panels in Force Volume Mode which affect the
resolution of the data: NUMBER OF SAMPLES, FORCE PER LINE and SAMPLES PER LINE.

The NUMBER OF SAMPLES parameter in the Force Channel control panel sets the number of points
collected in each force curve. This is the number of slices in the force volume image, that is, the Z
resolution of the force volume image. This parameter does not affect the speed of the scan but does
affect file size. A good default setting is 32.

The FORCE PER LINE parameter in the FV Channel control panel sets the number of force curves
collected and stored along each scan line of the sample and significantly affects the scan speed.
This parameter is, effectively, the XY resolution of the force volume image. A setting that
sufficiently resolves force-defined features, yet minimizes collection time, is desirable. A good
default value is 64.

These two parameters are interdependent, due to the 128 MB limit:

(FORCE PER LINE)2 × (4 × NUMBER OF SAMPLES) < 128 MB

The above requirements restrict the maximum number of force curves per line in the volume to 64.

The SAMPLES PER LINE parameter in the Image Channel control panel sets the number of pixels in
each scan line of the height image.

Note: For each pixel in the height image, a force curve is collected. Increasing the
value of SAMPLES PER LINE, therefore, increases the scanning time needed
to collect the entire volume. This parameter directly affects the XY
resolution of the height image only. A setting of 128 provides sufficient
detail to resolve many small features while helping to reduce capture time.

When SAMPLES PER LINE is greater than FORCE PER LINE, at each XY position in the height
image, the NanoScope moves the probe toward the sample until the TRIG THRESHOLD is reached
and then retracts - the same motion as a force curve. However only one force curve, the first one
taken in a pixel’s area of the force volume image, is displayed in the force volume image. For
example, with 512 SAMPLES PER LINE and FORCE PER LINE set at 64, then there are 16 pixels
(4×4) in the height image that correspond to one pixel in the force volume image. While the
piezoelectric actuator and the tip go through the motions of a force curve at each of those sixteen
pixels, only the first force curve is used in the force volume pixel.

The size limit on the data file enforces a trade-off between XY resolution and Z resolution. To
know whether a tip sticks to the surface at different locations, low Z resolution (NUMBER OF
SAMPLES) in favor of high XY resolution (SAMPLES PER LINE and FORCE PER LINE) is sufficient.
If a detailed examination of the interaction forces between tip and sample is desired, then high Z

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resolution is needed. Saving the Scan Mode height image (step 1) can compensate for low XY
resolution in the force volume image.

Setting NUMBER OF SAMPLES, FORCE PER LINE, and SAMPLES PER LINE to 16, 16, 512,
respectively, are good starting values.

Resolution and scan speed are the major determinants of the time required to collect a complete
force volume image. Figure 3.5g illustrates the effect that SAMPLES PER LINE and Z SCAN RATE
parameters have on imaging time. The times were calculated assuming the maximum number of
force curves per line (FORCE PER LINE) for each SAMPLES PER LINE.

Figure 3.5g Image Scan Time versus Samples per line and Z scan rate.

Doubling the lateral resolution roughly quadruples the capture time, while doubling the scan rate
halves the capture time.

8. Adjust Feedback parameters.

Feedback panel parameters carry over from the force plot settings; however, changes may be
required to protect the tip and optimize the force volume image.

For silicon nitride tips, the SETPOINT may be adjusted to within plus or minus several volts of the
microscope noncontact free-deflection signal value. For crystalline silicon TappingMode tips, the
Setpoint should normally be increased no more than 1-3 volts below the RMS amplitude voltage;
this helps protect the tip.

In Force Volume imaging, triggers are used to set the direction reversal point of the Z-axis
piezoelectric actuator during both height and force measurements. The DATA TYPE parameter

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registers which data channel acts as the trigger. Usually, this is the same as the DATA TYPE located
on the Force Channel panel. The Trigger Mode determines the type of trigger to be employed,
RELATIVE, or ABSOLUTE. The trigger may also be turned OFF.

A relative trigger measures the trigger threshold relative to the non-contact voltage deflection value
and compensates for drift. An absolute trigger measures the trigger threshold relative to the
Setpoint. In most cases, a relative trigger is preferable, as it offers better protection to the tip and
sample by limiting the total force on the surface independent of setpoint and drift.

The TRIG THRESHOLD parameter limits forces on the sample and the tip by “clipping” the RAMP
SIZE. For example, when using a relative trigger of 25 NM and a RAMP SIZE of 500 NM, if the tip
were to come into contact with the surface after extending only 300 nm of the scan size, the tip
would halt its movement after 25 nm more extension (for a total of 325 nm) before retracting. Thus,
tip-sample forces are constrained, and the force curve is defined for a controlled interval of tip-
sample interaction.

During the execution of a force curve with a trigger on, the piezoelectric actuator extends
continuously, bringing the surface towards the tip until the tip is deflected to the TRIG THRESHOLD
value. Once deflecting to the TRIG THRESHOLD value, the piezoelectric actuator retracts one Z
SCAN SIZE distance - it does not retract to the position defined by Z SCAN START. Thus, the
collection of the next force curve begins at a piezo position one Z SCAN SIZE value lower than the
piezo position at the TRIG THRESHOLD value. Keep this in mind when setting the Z SCAN START
and Z SCAN SIZE parameters if a relative trigger is used.

Note: This discussion assumes that SENSITIVITY has been properly set and that the
detector range has not been exceeded. Otherwise, the TRIG THRESHOLD
value does not correspond to the true deflection value.

In Force Volume imaging, triggers are used to set the turnaround point of the Z-axis piezoelectric
actuator. The TRIGGER MODE determines the type of trigger to be employed. Two types are
offered: RELATIVE and ABSOLUTE, or the trigger may be turned OFF.

Note: If the TRIGGER MODE is turned OFF, no height image is displayed.

The DATA TYPE determines which data channel is to act as the trigger. (Normally, this is the same
as Force Channel/DATA TYPE.)

A relative trigger measures the trigger threshold with respect to the free-air deflection voltage value
and compensates for drift. An absolute trigger sets the threshold with respect to the SETPOINT.
Normally, a relative trigger is the preferable default, as it offers better protection to the tip and
sample, limiting the total force on the surface independent of setpoint.

Note: When using a relative trigger threshold, be certain RAMP SIZE (in the Z Scan
panel) is sufficiently large to deflect the cantilever to the TRIG[ger]
THRESHOLD value and lift the tip clear of the surface. This ensures the tip is
not ratcheted into the surface and dragged laterally through surface material
during XY indexing.

To limit forces on the sample and tip, RAMP SIZE may be clipped to within some TRIG
THRESHOLD value. For example, a tip which is being oscillated along the Z-axis with a Z SCAN
SIZE of 500 NM may have its TRIG THRESHOLD set to -25.0 NM. When using a RELATIVE type

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TRIGGER MODE, if the tip encounters the sample surface after extending 300 nm, it halts its Z-axis
extension at 325 nm, then reverses (retracts). Thus, tip-sample forces are limited and the force
curve is defined for a controlled interval of tip-sample interaction.

Note: This example assumes the SENSITIVITY parameter has been properly set (see
step #2 above) and that the detector’s range has not been exceeded.

9. Adjust Force Channel parameters.

The Force Channel panel features parameters for the force plots region at the bottom right of the
Force Volume display window. In most ways the force plots region is exactly like a Force Plot
graph.

The available settings for the DATA TYPE parameter depend on the type of imaging being done.
Also available are Amplitude, Deflection, Potential, and Thermal. Set the Data type
accordingly. For Contact Mode force volume imaging, select DEFLECTION, for instance.

When beginning a force volume scan, set Z DISPLAY to its maximum to locate the force plots. (The
force curves resemble a thin line.) Z DISPLAY is the range of deflection values plotted in the force
curves region. Slowly decrease Z DISPLAY until the force plot fills most of the graph area.

The CENTER PLOT parameter determines where the force plots are graphed relative to the current
SETPOINT. When CENTER PLOT is OFF, the center horizontal line of the graph is positioned at the
probe SETPOINT value and deflection is measured from there. When CENTER PLOT is ENABLED, the
central horizontal line is positioned at the tip noncontact voltage (i.e., the voltage when the tip is
just clear of the surface - in the noncontact portion of the curve) from which the deflection is
measured.

10. Adjust FV Channel parameters.

Parameters in the FV Channel panel control the type and range of forces viewed in the force
volume image. In addition, the FV SCALE parameter also affects the viewable range of data
captured during force volume imaging. These parameters affect the real-time display of the force
volume image only. The deflection at (X,Y), and Z-position data of each force curve (extending
and retracting) are saved to disk.

The Z DIRECTION parameter determines which portion of the Real-time force curve cycle, EXTEND
or RETRACT, is shown in the force volume image. For example, if the force of interest is material
elasticity, the Extend portion of the curve is selected. If adhesion forces are probed, then the Retract
portion is usually used.

The FV SCALE parameter sets the range of values represented by the force volume image. Because
the force volume image is generated line by line and the effects of changing FV SCALE are not
displayed until the next line of data is taken, several adjustments of this parameter may be needed
before it is optimized.

The DATA CENTER parameter adds (or subtracts) a constant value to (or from) the data signal
(DEFLECTION in the case of Contact Mode force volume imaging). This is used to center the force
volume data within the FV scale bar. For most applications, the value should coincide with a value
on one of the force curves. This is most easily accomplished by positioning the cursor on a force
curve. This centers the force volume image within the color bar of the specified Z DISPLAY. DATA

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CENTER can be set in two ways. The first is to simply enter the desired value in the control panel.
The second is to use the cursors. Drag a vertical cursor from the left or right side of the plot region.
Drag a horizontal cursor from the top or bottom of the plot region. Position the cursor vertically at
the desired offset and click the left mouse button (see Figure 3.5h). In a slice, the pixels are colored
based on their distribution within the range defined by FV SCALE and the DATA CENTER.
Modifying these parameters during data collection affects the display only. The raw deflection and
piezoelectric actuator position data are saved.

Figure 3.5h Data center and Z display are Controlled by Cross-hairs

The Z DISPLAY parameter determines which slice of the force volume is displayed in the force
volume image region. Like DATA CENTER, the Z DISPLAY can be set in two ways. The first is to
enter the desired Z value of the slice in the control panel. The second is to use the mouse to change
the horizontal position (that is, the Z position) of the cursor in the force plot region. For example, a
Z DISPLAY of 30 NM causes the force volume image region to depict forces on the tip when it is at a
Z position of 30 nm above the piezoelectric actuator position at the TRIG THRESHOLD. The Z
display parameter may be thought of as defining bands of force at fixed distances from the sample
surface.

The Z DISPLAY and DATA CENTER parameters work in unison to define which portion of the
superimposed force curves is plotted in the display monitor force volume image. These parameters
are also simultaneously represented as a green cursor on the force plot graph. Both Z DISPLAY and
DATA CENTER may be changed by positioning the cursor with the mouse, or vice versa (i.e., the
cursor is repositioned automatically whenever these parameters are changed.) The relationship of
each parameter to the cursor is shown in Figure 3.5i.

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Figure 3.5i Z Display and Data center in Relation to Cursor

: DISPLAY
3ETPOINT

&REE AIR
$EFLECTION
$ATA CENTER

11. Collect the force volume data set.

Once all parameters have been properly set, begin collecting force volume data by clicking the
CONTINUOUS RAMPING icon (shown). Use Frame/SCAN UP (DOWN) to start the scan at the
bottom (top) of the image and force volume image regions.

12. Capture the force volume data set.

Completed images are saved to disk by clicking the CAPTURE icon (shown).

Note: If parameters are changed during a scan, the capture is interrupted. To force
the capture, click the Capture icon a second time. The more recent parameter
value entries are saved with the image.

If you forgot to capture an image, and the next image is not yet complete, click CTRL-B to Back
Capture the image. You can also select REALTIME > CAPTURE LAST. Back capturing in Force
Volume Mode captures whatever image was collected before the last change of frame direction,
that is, in the slow-scan direction.

Use of CAPTURE LAST can reduce the time required to gather data when only a non-square,
rectangular subarea of the image is relevant (see Figure 3.5j; panels 1-4 show a scan in progress).
Begin scanning an image from the top, for example, of the image region. In panel one, a new frame
(dark) is scanned from top to bottom. When the strip of interest has been scanned, click on the
Frame/Down icon (the scan is finished in panel 2). When the new image is beginning, enter
CTRL-B to capture the strip. The slow-scan direction reverses in panel 3 and a new frame is begun
(dark speckled). In panel four, the upward scan from panel 3 is interrupted and a new upward scan
(light speckled) begins. The lower panels show what part of the scan is saved if the back capture is
pressed in step 3 versus in step 4, after the new upward scan begins.

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Figure 3.5j CAPTURE LAST Assists Collecting Non-Square Force Volume Data (see text for discussion)

Another trick to imaging only strips of interest is to set TRIG THRESHOLD to zero and the Z SCAN
RATE to a high value (i.e.: 20 HZ) and begin a scan. When the tip is positioned near the beginning
of the strip of interest, reset TRIG THRESHOLD and Z SCAN RATE to their appropriate values and
capture the image.

3.5.6 Force Volume Troubleshooting

Mechanical complications or poor choices of settings for both operational and display parameters
can frustrate force volume data acquisition. Some common situations and their resolution follow.

A Force Volume Image is Uniform

If a force volume image is uniform at all Z display values (that is, all slices), check the various
display parameters first. The settings may be too high or too low. For example, if FV SCALE is
much smaller (or larger) than the actual range of cantilever deflections at any Z position, then all
the pixels at the Z position will be to the low (or high) end of the scale. The same effect occurs if
DATA CENTER fails to bring the measured forces into the VOLUME SCALE range. Adjust FV
SCALE and DATA CENTER until the variation in forces is displayed.

If FV Channel/Z DISPLAY is set too high, force curves appear as flat lines; if it is too low, the
majority of force curves display flattened against one or the other extreme of Z position.

Check the color bar. If the contrast is too high, only the extremes of deflection show up in the force
volume image. Changing the Color Table in Image Mode can reduce contrast (different color tables
have different default contrast levels).

If SENSITIVITY was not set properly in Force Plot Mode, then force plot scaling is inaccurate.

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If a trigger is being used, make sure it is enabled, and vary TRIG THRESHOLD to assure that the
threshold deflection is large enough. If it is too low, only the noncontact portion of the curve is
measured. For example, a 320 µm cantilever with a spring constant of 0.01N/m oscillates with an
amplitude of roughly 3 nm at room temperature. These oscillations and a 2 nm TRIG THRESHOLD
initiate the trigger almost immediately after beginning a scan.

All the interesting forces may be mapped to a single pixel of Z data; that is, the Z resolution is too
low for the forces of interest. Trade off XY resolution (i.e., FORCE PER LINE or SAMPLES PER
LINE or both) for Z resolution (NUMBER OF SAMPLES) to alleviate the problem.

If no adjustment to display parameters creates a nonuniform image, perhaps there is no force

variability in the scan area. Adjust Z SCAN START and RAMP SIZE in the Z Scan panel to scan the
regions of interest within the force curves. It may be necessary to return to Force Plot Mode to do
this. If the probe cantilever is too stiff to respond to the forces present, replace it with a more pliant
cantilever or use a higher TRIG THRESHOLD.

Drift

Although drift is a symptom that has a number of causes, it appears in Force Volume in two
characteristic ways. The force curves, over time, can drift vertically or horizontally in the force
plots region. The shades of the force volume image drift to one end of the color bar, as do the pixel
values in the height image. Horizontal, or substrate, drift is due to the substrate or Z piezoelectric
actuator drifting. Vertical, or cantilever, drift can result from DC electrical drift in the probe,
thermal fluctuations, bubbles attached to the cantilever in fluid or slipping of the O-ring in a fluid
cell - to name a few sources. Even small rates of drift can distort a force volume image during the
hours needed to collect such a data set.

If the drift rate is low, it can be ignored during data collection and subtracted out offline by a
horizontal or vertical cursor and selecting X or Y TRANSLATE. A relative trigger keeps the
magnitude of probe deflections within a fixed range.

If the drift is slow to moderate (relative to the time scale of the entire collection process), adjust FV
Channel/Z DISPLAY upwards to keep the curves from drifting out of view. Reset the SETPOINT
and collect the image. Set Force Channel/CENTER PLOT to ENABLE to zero the force curves as
they are taken.

If the drift is fast, check the hardware for mechanical causes. Ensure that the probe is secure in its
holder. Thermal fluctuations near and within a probe can cause fast drift. Flexible cantilevers make
good thermometers and respond to the slight temperature increases due to laser heating. To
minimize thermal drift, bring sample, fluid (if any), probe and probe holder into thermal
equilibrium (i.e., the same temperature) at the start of imaging.

Note: NanoScope AFMs take 90 minutes from when the machine is turned on to
achieve thermal equilibrium.

If the force curves appear nonsensical, the extending and retracting portions reading maximum
force along their entire length, FV SCAN RATE may be set too low for the NanoScope DSP board. A
FV SCAN RATE of 6 HZ ensures smooth signal averaging. Too low a FV SCAN RATE and the force
curves will appear discretized.

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If imaging in fluid, bubbles in the fluid cell or adsorbed to the cantilever can result in fast drift rates.
Bubbles can be removed by injecting more solution into the fluid cell and forcing the bubbles out of
the cell through a tube. If the O-ring was subjected to torque in making a seal, it can relax and slide
across the sample surface. This is remedied by minimizing lateral movement of the O-ring during
set-up, or by not using an O-ring at all (though, then the probe is more sensitive to air currents and
thermal variation).

CAUTION: Not using an O-ring is not recommended by Veeco. Leaks are hard
to avoid and can quickly lead to expensive damage to the high
voltage piezoelectric scanner tube.

As a last resort, if fast drift cannot be removed from the system, reset the setpoint (Feedback >
SETPOINT) during data collection to keep the force curves “in bounds”. Capture must be forced
(click on the Capture icon twice in quick succession) to save the image. Another way to
compensate for fast drift during imaging is to track the drift with the photodetector adjustment
screws during the retrace portion of a line scan. The banding in the resulting height and force
volume images can be removed offline by setting CENTER PLOT to ENABLED.

Excessive Adhesion

Excessive adhesion of the tip to the sample results in the absence of the noncontact portion of the
force curves as well as, in some cases, a downward curvature in the extending portion of the curve
towards and meeting the retracting curve at the end of the noncontact region (see Figure 3.5k). This
is caused by the inability of the tip to leave the surface as it is retracted. This can damage the
sample during the repositioning of the tip to the next XY location. Adjust Z SCAN START and Z
SCAN SIZE in the Z Scan Controls panel to ensure that the tip is lifted clear of the surface during
retraction. Check that most piezoelectric actuator motion occurs near its center position. Adjust
TRIG THRESHOLD if the tip is being pushed so far into the sample that adhesive forces on the tip
are unnecessarily large.

Figure 3.5k Example of Excessive Adhesion

Hydrodynamic Drag

Occurring only in fluid cells, hydrodynamic drag appears as a vertical separation between the
noncontact portions of the extending and retracting curves on the force plot. The magnitude of the

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separation is dependent on the rate of the scan; reduce Z Scan Controls/SCAN RATE until the
curves are colinear in the noncontact region.

3.5.7 Force Volume Display and Interpretation

Display Options During Imaging

Perform analysis in real-time by adjusting display parameters during imaging. For instance, Z DISPLAY
chooses the slice of the volume to be displayed in the force volume image region. Lines scanned after
changing Z DISPLAY correspond to the new slice. Lines scanned before the change correspond to the
previous slice.

Adjusting FV SCALE and DATA CENTER allow the user to zoom in on particular features of a force
volume image. Set these parameters to mask all but the range of forces of interest. See Detailed
Force Volume Procedure, page 119, step 10.

Adjust the Image Controls/Z RANGE scale to modify the height image. Z DIRECTION determines
whether the trace or retrace scan line are collected.

If any of these parameters are modified while scanning, force image capture (by double-clicking
the Capture icon) to save the data, including the final parameter set.

Post-Data Collection Image Analysis

NanoScope Offline analysis software processes force volume images in much the same way as it
handles topographical images and force plots. There are also tools specific to the interpretation of
force volume images.

When a force volume image is selected from the Offline directory, it is displayed much as it
appears during data collection. The three regions - height image, force volume image, and force
plots - are in their respective corners. Both the topographic and the force volume images appear as
they did during collection.

Scales and Offsets

Scaling and offset options for each data type are available in the offline parameter list in the lower
left of the Force Volume view.

The first DATA SCALE parameter sets the scale of the height image. The Z SCALE sets the
deflection scale for the force curve.

FV SCALE defines the range of deflection values to be displayed in the force volume image.

Setting CENTER PLOT to ENABLE centers all the retracting force curves noncontact portions to the
center horizontal line in the force plots region, effectively subtracting out any DC drift from the
data. (The extending curves also are shifted, but they maintain their position relative to the

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retracting curve.) All deflection values are then measured relative to the center horizontal line. This
allows for clear comparisons to be made among force curves in the data set and is recommended
before further analysis.

Z DIRECTION toggles the force volume image between displays of the EXTEND (e.g., to study
elasticity) or RETRACT (e.g., to study adhesion) portions of force curves.

Viewing Slices

You may inspect each slice in a volume (see Figure 3.5l).

Figure 3.5l Force Volume Slices - Block Height Represents Deflection.

To display a force volume slice at a particular Z position, drag a cursor from the left or eight edge
of the force plot region. Clicking on consecutive pixels in the force plots region (with the
MULTIPLE radio button selected) displays consecutive slices in sequence (see Figure 3.5l, Figure
3.5n). Note that multiple force curves, measured at points A, B, and C in the height image, can be
displayed simultaneously offline.

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Figure 3.5m Force Volume: multi-layered polyethylene

Save images of slices for later use through the EXPORT menu. This saves (or exports) an image of
the display monitor screen to disk. The images can be modified in third party graphics software
(e.g., IDL, NIH image, Canvas, etc.). For example, the slices selected in Figure 3.5m are displayed
as a montage in Figure 3.5n.

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Figure 3.5n Retracting Slices: Adhesion vs. Z Positions 1-4 in Figure 3.5m

1 2

3 4

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Viewing Force Curves

Display individual force curves by first opening the file from the appropriate capture directory and
then selecting Force Curve Mode > SINGLE. Click the left mouse button on a specific pixel in
either the height image or the force volume image to display the associated force curve in the force
plots region (see Figure 3.5m). Note that the pixels in the height image and the force volume image
are marked with white crosses. The Z value of the slice is displayed in the force volume image as a
vertical cursor at that particular Z value.

Individual force curves can be analyzed separately from the height and volume data; select SAVE
CURVES and the standard force curve analysis view is saved and can be opened from the Browse
window. Once modified and analyzed, select File/SAVE to save the image and modified force
curve.

Selecting Force Curve Mode > MULTIPLE to display several force curves in the force plots
region. Click either the topography or the force volume image to display the associated force curve
in the force plots region. A white cross labels the (X,Y) position of the force curve in both the
topographic and force volume images. Superimpose multiple force curves by selecting many pixels
(see Figure 3.5m). Select Force Curve Mode > CLEAR ALL to erase the force plots region.

If multiple force curves are displayed, clicking SAVE CURVES saves each curve as its own standard
force curve file.

Selecting Images to Analyze

A height image can be analyzed independently of force data by selecting OPEN IMAGE from the
Force Volume window. The standard image analysis software loads. Once modified and analyzed,
select File > SAVE to save the image and modified force curve.

Constant Force Surfaces

NanoScope software displays force volume data as a distribution of forces at a given Z position. It
is also possible to consider the force volume data as a stack of constant force surfaces. Importing
the force volume image file into a third party software package with array processing and three-
dimensional graphical display capabilities, like IDL, can produce images of these iso-force
surfaces. Constant force surfaces can be measured directly with the AFM, but force volume data
facilitates generating many iso-force surfaces. For the bacteriorhodopsin (BR) membrane adsorbed
to mica shown in Figure 3.5o, the flat lower surface corresponds to a TRIG THRESHOLD of 20 NM.
All the Z positions are zero since they are measured relative to the piezo position at TRIG
THRESHOLD. The upper surface is a lower force just before tip contact with the membrane; it is
effectively a topographic image. The iso-force surfaces were calculated and displayed using IDL.

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Figure 3.5o Iso-Force Surfaces: Bacteriorhodopsin Adsorbed to Mica.

Interpretation

A two dimensional image is specific to a particular Z position of the base of the probe and is a
mapping from an area of the XY sample plane to the deflection values obtained at each sampled
point in the area. A three dimensional volume is a collection of images over the same XY area, each
at a different Z value in a range of probe/sample separations.

To convert deflection data to values of force, the spring constant of the cantilever must be
determined.

Tip charge density and shape, charge density of the sample, adsorbents on both tip and sample, and
the elasticity of the sample are among the contributors to tip/sample force. Where possible, include
reference control samples in your experiment to minimize unexplained variability in your
interpretation of force volume data.

3.5.8 Force Volume Glossary

Data type: occurs in Image and Force Volume Modes. In Image Mode, DATA TYPE identifies the
type of signal displayed in the image window. In Force Volume Mode, DATA TYPE identifies force
volume imaging type (in the Force Channel panel); the choices depend on SPM (e.g., a
MultiMode AFM has more options than a standard AFM). This note discusses force volume
imaging based on the deflection signal. Under the Feedback panel, the DATA TYPE of the FV
trigger is selectable.

Display mode: in the Z Scan control panel is set to display in the force plots region the EXTEND
portion of the force curves, the RETRACT portion, or BOTH.

Force per line: in the FV Channel control panel determines the number of force curves collected
and stored along each scan line and significantly affects the scan speed. This parameter is,
effectively, the XY resolution of the force volume image.

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Number of samples: in the Force Channel control panel sets the number of points collected in
each force curve. This is also the number of slices in the force volume image, that is, the Z
resolution of the force volume image. This parameter does not affect the speed of the scan but does
affect the file size.

Center plot: in the Force Channel control panel determines where the force plots are graphed
relative to the current setpoint. When Center plot is OFF, the center horizontal line of the graph is
positioned at the SETPOINT value and cantilever deflection is measured from this value. When
Center plot is ENABLED, the central horizontal line is positioned at the tip noncontact voltage (i.e.,
voltage when the tip is clear of the surface - the noncontact portion of the curve) from which the
deflection is measured.

Samples per line: in the Image Channel control panel sets the number of pixels in each scan line
of the height image. Total force volume data acquisition time is proportional to SAMPLES PER
LINE. This parameter directly affects the XY resolution of the height image only.

Sensitivity: in the Force Channel control panel relates cantilever deflection as measured in
photodetector output voltage to topographic height.

Data Type: in the Feedback panel determines the data channel to act as the trigger. Usually, this
has the same value as Force Channel/DATA TYPE.

Trig threshold: in the Feedback control panel is set to the tip deflection magnitude which causes
the piezoelectric actuator to begin retracting if a trigger is in use. TRIG THRESHOLD limits forces
on the sample and tip.

Trigger mode: in the Feedback panel determines the type of trigger to be employed: RELATIVE, or
ABSOLUTE. A relative trigger measures the trigger threshold relative to the noncontact deflection
voltage value, so compensates for drift. An absolute trigger measures the trigger threshold with
respect to SETPOINT.

Data Center: in the FV Channel control panel adds/subtracts a constant value to/from the data
signal (deflection in the case of contact mode force volume imaging). This is used to center the
force volume data within the FV scale bar.

FV scale: in the FV Channel control panel sets the range of values displayed by the force volume
image in RealTime. For offline viewing, use FV SCALE in the Offline Parameters panel in the
lower left of the FV view.

Z direction: in the FV Channel control panel determines which portion of the Real-time force
curve cycle, EXTEND or RETRACT, is shown in the force volume image region. Z direction is also
found in the Offline Parameters list of a captured force volume.

Z display: in the FV Channel control panel determines which slice of the force volume is
displayed in the force volume image region. Z display is also found in the Offline Parameters list
of a captured force volume.

Data Scale: in the Force Channel control panel sets the range of cantilever deflection values
plotted in the force curves region.

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Scan rate: in the Z Scan panel sets the rate at which the AFM collects a force curve, both
extending and retracting portions. SCAN RATE and SAMPLES PER LINE determine the time to
collect a force volume data set.

Ramp size: in the Z Scan panel sets the excursion size for the probe during the extend and retract
portions of a force curve. When the cantilever deflects an amount equal to TRIG THRESHOLD, the
piezoelectric actuator retracts one RAMP SIZE before beginning the next curve.

Z scan start: in the Z Scan panel sets the starting position of the piezoelectric actuator for the first
force curve only.

3.5.9 Force Volume Sample Parameter Settings

For imaging a relatively smooth (features less than 100 nm tall) surface:

Image Scan Controls:

Scan size: 2 µm
Scan angle: 90 deg.
Scan rate: 20 Hz
Slow scan: Enabled
Z limit: 440 V

Z Scan Controls:

Ramp size: 100 nm

Scan rate: 4 Hz
FV scan rate: 6 Hz

Feedback Controls:

Trigger mode: Relative

Trig threshold: 10 nm
Data type: Deflection

Image Channel:

Samples per line: 64, 32 or 16

Realtime Planefit: Line
Offline planefit: None

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Force Channel:

Number of samples: 64, 256 or 512

Data type: Deflection

FV Channel:

Force per line: 64, 32 or 16

3.5.10 Fluid Cell Preparation for Force Volume

If making force volume measurements in fluid, ensure that the fluid cell is clean. Wash the cell
with a mild detergent, rinse in de-ionized water, and blow dry with a few blasts of compressed air.

Place the cantilever (preferably UV cleaned) in the holder and gently seat the O-ring in its place in
the cell. Ultraviolet (UV) cleaning is achieved by irradiating the probe at 3-5mm distance from a
UV lamp.

Place a thin film of fluid/buffer (20-30µL) on the sample before placing it into the microscope.

Adjust the positioning screws so that, when the fluid cell is placed in the head of the microscope,
neither the O-ring nor the tip are in contact with the fluid.

Place the holder into the microscope and aim the laser at the tip of the cantilever and adjust the
photodetector so that the deflection is approximately zero.

Using the screws, slowly lower the tip towards the sample until the fluid meets the O-ring. Then,
watching the A+B (sum) signal for a large deflection, lower the tip until it is pulled by surface
tension into the fluid. Lower the stage carefully a little more to ensure that the entire fluid cell is
full of fluid.

If there are no air bubbles in the cell or on the cantilever, simply adjusting the mirror should bring
the laser spot back onto the photodetector.

If the laser spot cannot be found, gently inject (by syringe and/or through a tube) more fluid into the
cell to flush bubbles out (also through a tube).

CAUTION: Be careful; if the O-ring is not well-seated or the fluid cell

otherwise leaks, the piezoelectric actuating scanner tube may
suffer a high voltage short circuit and require replacement.

Once the signal is regained, lower the tip to the surface and begin imaging.

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Force Volume

3.5.11 Force Volume Image File Format

While the NanoScope analysis software includes many useful routines, sometimes one might wish
to import a force volume image into third party software - a spreadsheet program or an image
processing system. The following discussion explains how to extract data from a saved (captured)
force volume image.

Like all NanoScope image files, the force volume image file has two parts: a header, and one or
more images (see Figure 3.5p). The header contains a series of lists, each of which contains a
number of parameters. There is a list for the microscope, for the piezoelectric actuator, for the
images, and for the force curves. Basically, every parameter under operator control is written to
some line in a list in the header. This information, when combined with the data stored in the
images, can be used to reconstruct the original images.

Figure 3.5p Force Volume Data File Structure.

The end of the header is flagged with a CTRL-Z character (ASCII 26). Different types of files have
different length headers, but they all end with the CTRL-Z. There is a block of padding (random)
data between the header and the actual images. The height image (Channel 1) is first, followed by
the force volume image. All the image data is saved by the NanoScope with 16 bits per pixel, (i.e.,
in 2’s complement notation for negative numbers with the least significant byte (LSB) in “little
endian” form).

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The height image data begins at byte 8192. It is a two dimensional array of data. The NanoScope
Manual explains how to reconstruct the image from information in the header.

The force volume data is stored as a series of force curves. Depending on the resolution of the
height image, the starting byte will vary. The start position of the force volume data can be found in
the Data offset line of the Ciao Force List, designated as:

\*Ciao Force List

..

..

\Data offset:

Regardless of which is displayed during data collection, both the retract and extend portions of the
force curve are written to disk. The force curve data set is a linear array of deflection values. The
first half of the array is the retracting portion of the curve; the second half is the extending portion.
Both Z position and deflection values need to be scaled based on header values.

The force curves which make up the force volume image are saved in column major format. For
example, if NUMBER OF SAMPLES is 256 and FORCE PER LINE is 32, then there are 32 x 32 =
1024 force curves, each with 512 (retract and extend) deflection values. The force curves are
ordered such that the first 32 form the first row of the image, the second 32 the next row, etcetera.

Only the deflection values of the force curves are saved to the file. The corresponding Z-position
values are calculated from information in the header:

z = index *440.0 * zsens * zscansize / (65536.0 * samples)

where index = the index in the Z direction, 0-511, of a deflection value

zsens = \Z sensitivity

zscansize = \*Force image list\Scan Size

samples = \*Force image list\Samps/line

Deflection values are scaled according to the following formula:

deflscaled = deflraw* (20.0 /dsens) / 65536.0

where deflraw = the raw, integer values from the file.

dsens = \Detect sens.

Once the force volume data has been extracted from the file, it can be processed and analyzed by
third party software such as RSI’s IDL, NIH Image, or Adobe Photoshop.

Third party graphics software is needed to construct a composite figure of several slices or
representative force curves pictured along with the height image, for example. The images (heights

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Piezoresponse Force Microscopy

or slices) and force curves need to be saved/exported individually and then loaded into the third
party software.

3.6 Piezoresponse Force Microscopy

Piezoresponse force microscopy is a Contact Mode technique to measure sample displacement out
of the sample plane in response to an applied AC bias. The method is most directly applicable to
piezoelectric samples such as lead zirconia titanate, but can also work for electrostrictive samples
such as lead magnesium niobate, and has been used on ferroelectric materials such as barium
titanium oxide.

With the SPM in Piezoresponse Mode, the tip is engaged with the sample and an AC voltage is
applied between tip and sample during scanning. A responsive sample expands and contracts in
synchronization with the applied voltage. By feeding the photodetected cantilever deflection signal
into a lock-in amplifier whose reference signal is the applied AC bias frequency, background
topography is suppressed from the resulting image which features only the sample surface height
changes induced by the applied field.

Piezoresponse imaging does not require any dedicated hardware and works with both fixed tip/
rastered sample (MultiMode) and fixed sample/rastered tip (Dimension) SPMs. There are several
consequences of the need to form a circuit to bias the sample:

• The sample must be electrically connected to the sample platform (e.g., with silver
paint; see Figure 3.7j).

• Though a light imaging force best preserves samples, the tip must stay in contact with
the sample to maintain the applied tip/sample voltage. A particularly rough sample may
require a higher load force, higher gains or slower scan speeds to ensure a continuous
electrical connection.

Note: Internal current limiting protects the NSV Controller and the probe tip when
using the NanoScope V Controller to apply the bias voltage.

• A conductive cantilever (such as MESP [Magnetic, Etched Silicon Probe], NPG [silicon
Nitride Probe, Gold-coated], PIC [Platinum Iridium, Contact], or PIT [Platinum
Iridium, Tapping]) is required.

Note: Active tip cantilevers are not conductive, so PR is not operable with FastScan
or dual scan, but only by normal scan using the tube scanner exclusively.

• Piezoresponse imaging may be performed in a nonconducting fluid. In a conductive

fluid, a conductive cantilever must be insulated from the fluid, except at the tip; this is
difficult to accomplish.

Piezoresponse imaging is set up in the following procedure:

1. Select PIEZO RESPONSE for MICROSCOPE MODE in the Other panel. See Figure 3.6a.

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Figure 3.6a Select PIEZO RESPONSE for MICROSCOPE MODE

2. In the Main submenu of the Feedback panel, set DEFLECTION SETPOINT to 0.2V initially.
Decrease this later while looking at an image to lower the force applied to the sample, or
increase it to ensure contact on a rough, but robust sample. The low value, 0.2V, assumes a
stiff cantilever (such as MESP, PIC or PIT).

Note: For an NPG probe, set DEFLECTION SETPOINT to 2.0V instead.

Note: Most of the Piezo Response controls parameters start with PR for Piezo
Response (see Figure 3.6b).

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Figure 3.6b Scan Parameter List including Piezoresponse variables

3. Engage the tip on the sample and optimize scan parameters while watching the displayed
image with Channel 1/DATA TYPE set to HEIGHT.

The following steps provide initial settings for the Piezo Response control parameters.

4. Select TIP (or SAMPLE, but not DISABLED) in the AC BIAS drop-down menu.

Note: Voltage is applied to the tip if selected and the sample is connected to ground.
If SAMPLE is selected, voltage is applied there and the tip is grounded.

5. Set PR LOCK-IN BW to 15000HZ for best resolution. Reduce PR LOCK-IN BW if the

resultant image is noisy or exhibits artifacts from failure of the amplifier to lock.

6. Set PR DRIVE AMPLITUDE to 750MV initially. Adjust this control of AC bias amplitude to
optimize contrast in your PR image.

7. Set PR DRIVE FREQUENCY.

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CAUTION: AC bias frequency is set to excite piezoresponse in the chosen sample.

Typical values are between 2 and 5KHZ, though 60KHZ PR imaging
has also been successful. The bias frequency should be well above the
scan rate so at least one full bias cycle is performed at each pixel in a
piezoresponse image. Check TappingMode Cantilever Tune (see the
Q Control chapter in the NanoScope 5 Controller Manual) to
determine the cantilever resonant frequency if there is a possibility it
is close to the AC bias frequency desired. PIC cantilevers have
resonant frequencies of approximately 10kHz; PIT probes resonate
between 60 and 90kHz. Do not set PR DRIVE FREQUENCY near the
cantilever resonant frequency because the probe could begin
mechanically oscillating, compromise tip/sample contact and
confound cantilever deflection due to energy absorbed at resonance
from the desired deflection due only to piezoresponse of the sample.
A 2nm cantilever deflection amplitude is typical both of a
piezoresponsive material and of a cantilever being driven in
TappingMode.

8. Set PR DRIVE PHASE to 0° initially. This may be adjusted to shift the location of high
contrast regions in the piezoresponse image.

9. Set PR AMPL LIMIT to 20V (unlimited) initially to see if the piezoresponse deflection
amplitude fills the available range (view with a Channel DATA TYPE set to PR AMPLITUDE).
Lower the limit to improve resolution on signals smaller than the amplitude range.

10. Set PR PHASE LIMIT to 360° (unlimited) initially to see if the piezoresponse deflection
phase fills the available range (view with a Channel DATA TYPE set to PR PHASE). Lower the
limit to improve resolution on signals smaller than the phase range.

Note: SPM systems operating with a Generation II SCM Application Module include
four additional parameters in the Piezo Response controls submenu of the
Feedback Controls panel: PR X LIMIT, PR Y LIMIT, PR X INPUT GAIN and
PR Y INPUT GAIN.

11. Select PR AMPLITUDE or PR PHASE for DATA TYPE in Channel 2.

Additional information about the piezoresponse mode can be found in Piezoresponse Atomic Force
Microscopy Using a NanoScope V Controller, Veeco p/n 013-444-000.

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Surface Potential Detection

3.7 Surface Potential Detection

3.7.1 Surface Potential Detection Overview

Surface potential detection measures the effective surface voltage of the sample by adjusting the
voltage on the tip to match that of the surface, thereby minimizing the electric force from the
sample. Samples for surface potential measurements must have a surface voltage in the range
[-10,+10 volts], and operation is easiest for voltages in the range of [-5,+5V]. The noise level with
this technique is typically 10mV. Samples may include both conducting and nonconducting
regions. Samples with regions of different metals will also show contrast due to contact potential
differences. Quantitative voltage measurements are made of the relative voltages within a single
image.

3.7.2 Surface Potential Detection—Theory

Theory Overview

Surface potential detection is a two-pass procedure where the surface topography is obtained by
standard TappingMode in the first pass and the surface potential is measured on the second pass
(see Figure 3.7a). The two measurements are interleaved: that is, they are each measured one line at
a time with both images displayed on the screen simultaneously. A block diagram of the Surface
Potential measurement system is shown in Figure 3.7b. On the first pass, in TappingMode, the
cantilever is mechanically vibrated near its resonant frequency by a small piezoelectric element. On
the second pass, the tapping drive piezo is turned off and an oscillating voltage VAC sin ωt is
applied directly to the probe tip. If there is a DC voltage difference between the tip and sample, then
there will be an oscillating electric force on the cantilever at the frequency ω. This causes the
cantilever to vibrate, and an amplitude can be detected.

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Figure 3.7a LiftMode Principles Used in Surface Potential Detection

¨
Surface Potential Scope Data
‘ (Interleave scan)

1521
Topographic Scope Data
(Main scan)
Electric Field Sources

1. Cantilever measures surface topography on the first (main) scan.

2. Cantilever ascends to lift scan height.
3. Cantilever follows stored surface topography at the lift height above sample
while responding to electric field influences on the second (interleave) scan.

If the tip and sample are at the same DC voltage, there is no force on the cantilever at ω and the
cantilever amplitude will go to zero. Local surface potential is determined by adjusting the DC
voltage on the tip, Vtip, until the oscillation amplitude becomes zero and the tip voltage is the same
as the surface potential. The voltage applied to the probe tip is recorded by the NanoScope
Controller to construct a voltage map of the surface.

Figure 3.7b Simplified Block Diagram of Surface Potential Detection

Cantilever Deflection Signal
Photodiode Signal
Amplitude Signal
Lock-in
Amplifier Amplitude * sign(phase)
Data Channels

Reference
Laser Signal Servo Controller
Beam (Feedback loop
To DC Voltage adjusts DC tip
Photo- Tip voltage to zero lock-in
detector Sum
signal)
AC

Potential Signal
Sample
GND
High Resolution
Oscillator Signal Oscillator

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Theory Details

A good way to understand the response of the cantilever during Surface Potential operation is to
1 2
start with the energy in a parallel plate capacitor, U = --- C ( ΔV ) , where C is the local capacitance
2
between the AFM tip and the sample and ΔV is the voltage difference between the two. The force
on the tip and sample is the rate of change of the energy with separation distance:
dU- = – 1--- ------
F = – ------ dC- ( ΔV ) 2
dZ 2 dZ

Figure 3.7c Force as a Function of Voltage

2
F ~ (ΔV) F (attractive)

ΔVDC = -2V ΔVDC = 2V

ΔV
VAC

5716
VAC

In the operation of Surface Potential the voltage difference ΔV consists of both a DC and an AC
component. The AC component is applied from the oscillator, VACsinωt; where ω is the resonant
frequency of the cantilever.
ΔV = ΔVDC + VAC sin ωt

ΔVDC includes applied DC voltages (from the feedback loop), work function differences, surface
2
charge effects, etc. Squaring ΔV and using the relation 2sin x = 1 – cos ( 2x ) produces:

F = – 1--- dC dC- ΔV V sin ωt + 1--- dC

2 + --1- V 2 ) – ------
------- ( ΔV DC ------- V 2 cos ( 2ωt )
2 dZ 2 AC dZ DC AC 4 dZ AC
⎬
⎬
⎫
⎬
⎫
⎫
⎭

⎭
⎭

DC term ω term 2ω term

The oscillating electric force at ω acts as a sinusoidal driving force that can excite motion in the
cantilever. The cantilever responds only to forces at or very near its resonance, so the DC and 2ω
terms do not cause any significant oscillation of the cantilever. In regular TappingMode, the
cantilever response (RMS amplitude) is directly proportional to the drive amplitude of the tapping
piezo. Here the response is directly proportional to the amplitude of the Fω drive term:

amplitude of F ω = dC
------- ΔV DC V AC
dZ

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The goal of the Surface Potential feedback loop is to adjust the voltage on the tip until it equals the
voltage of the sample (ΔVDC=0), at which point the cantilever amplitude should be zero (Fω=0).

The larger the DC voltage difference between the tip and sample, the larger the driving force and
resulting amplitude will be. But the Fω amplitude alone is not enough information to adjust the
voltage on the tip. The driving force generated from a 2V difference between the tip and sample is
the same as from a -2V difference (see Figure 3.7c).

What differentiates these states is the phase. The phase relationship between the AC voltage and
the force it generates is different for positive and negative DC voltages (see Figure 3.7d through
Figure 3.7g).

In the case where ΔVDC = 2V, the force is in phase with VAC. When ΔVDC = -2V, the force is out of
phase with VAC. Thus, the cantilever oscillation will have a different phase, relative to the reference
signal VAC, depending on whether the tip voltage is larger or smaller than the sample voltage. Both
the cantilever amplitude and phase are needed for the feedback loop to correctly adjust the tip
voltage. The input signal to the Surface Potential feedback loop is the cantilever amplitude
multiplied by the sign of its phase (i.e., amplitude for phase ≥0 degrees, -amplitude for phase <0
degrees). This signal can be accessed in the software by selecting POTENTIAL INPUT (interleave
scan line) in one of the channel panels.

If ΔVDC = 0, the electric drive force is at the frequency 2ω. The component of the force at ω is zero
so the cantilever does not oscillate (see Figure 3.7h and Figure 3.7i). The Surface Potential
feedback loop adjusts the applied DC potential on the tip, Vtip, until the cantilever’s response is
zero. Vtip is the Potential data that is used to generate a voltage map of the surface.

Figure 3.7d VAC at ω, ΔVDC = 2V

ΔV

2V VAC

7908
Time (arbitrary units)

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Figure 3.7e Major Force Component in Phase with VAC at Frequency ω, ΔVDC = 2V
Force

Time (arbitrary units) 7909

Figure 3.7f VAC at ω, ΔVDC = −2V

Time (arbitrary units)
ΔV

-2V VAC

7910

Figure 3.7g Major Force Component 180° Out of Phase with VAC at Frequency ω, ΔVDC = −2V
Force

7911
Time (arbitrary units)

Figure 3.7h VAC at ω, ΔVDC= 0V

ΔV

VAC
0V

7912
Time (arbitrary units)

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Figure 3.7i Force at frequency of 2ω, ΔVDC = 0V

Force

7913
Time (arbitrary units)

3.7.3 Surface Potential Detection — Voltage Application

If the sample does not require voltage to be applied (as in measuring work function difference on a
sample made up of several metals), skip to Surface Potential Detection — Procedure: Section
3.7.4.

It is often desirable to apply a voltage to the probe tip and/or to the sample. The NSV Controller
provides a dedicated programmable power supply for each option through parameters TIP BIAS
CONTROL and SAMPLE BIAS CONTROL, respectively.

To bias the sample using an NSV Controller, ensure the sample is electrically connected to a
standard steel sample puck using conductive epoxy or silver paint, as shown in Figure 3.7j.

Note: Painted samples are easier to remove from the puck than epoxied samples.

Figure 3.7j Electrically Connecting a Sample to the Piezo Cap (MultiMode) or Chuck (Dimension)
Conductive Epoxy
or Paint

Sample Steel Sample Puck

Piezo Cap/Sample Chuck

Note: With an NSV Controller, it is often unnecessary to insulate a sample from the
conductive sample platform (the MultiMode piezo cap or the Dimension
sample chuck) to bias the sample using an external power supply. Instead,
electrically connect the sample to its platform (see Figure 3.7j) and bias the
platform. To apply a custom waveform or a voltage >|12V| directly to the
sample, isolate (insulate) the sample from the platform (with Kapton tape, see
Figure 3.7k).

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Figure 3.7k Electrically Isolating a Sample from the Piezo Cap (MultiMode) or Chuck (Dimension)
>10 MΩ

External
Voltage
Sample Source
Electrical Insulator

Piezo Cap

To electrically bias the tip during scanning, set Other tab/TIP BIAS CONTROL to TIP BIAS.
Similarly, to electrically bias the sample platform, set Other tab/SAMPLE BIAS CONTROL to
SAMPLE BIAS as shown in Figure 3.7l. With the NSV Controller, the TIP BIAS signal is dedicated
to applying a voltage to the tip, while the SAMPLE BIAS signal is dedicated to sample biasing. The
TIP BIAS power supply may be set anywhere in the range [-12, +12V] while the SAMPLE BIAS
power supply range is [-10, +10V]. Therefore, the tip/sample voltage difference may be made as
large as 22V.

Figure 3.7lSample Bias

Note: TIP BIAS and Sample BIAS parameter names do not appear in the Feedback
Tab and Interleave Controls panel until selected for either TIP BIAS
CONTROL or SAMPLE BIAS CONTROL.

In the Feedback panel, set the desired voltage levels for the two parameters for the main scan lines
(for Surface Potential, setting to zero or ground is recommended). In the Interleave Controls panel
set TIP BIAS and SAMPLE BIAS separately for the interleave scan lines.

Alternatively, each of these two parameters may be assigned the value GROUND instead. The GROUND
setting is used to force the tip or sample to ground. Selecting GROUND for TIP BIAS CONTROL
overrides the current value of TIP BIAS in setting the voltage of the tip. Similarly, selecting GROUND
for SAMPLE BIAS CONTROL overrides the current value of SAMPLE BIAS in setting the voltage of
the sample platform.

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Note: Tip and sample biasing as just described are not limited to Surface Potential
Detection, but work as well with other SPM applications using the NSV
Controller.

Note: We recommend biasing the tip for Surface Potential detection.

3.7.4 Surface Potential Detection — Procedure

1. Mount a sample onto the sample platform. Ensure electrical connectivity between sample
and platform if bias will be applied to the sample (see Figure 3.7j).

2. Mount a metal-coated cantilever into the probe holder (i.e., an MMEFCH probe holder for
MultiMode SPMs). MESP- or SCM-PIT model cantilevers (metal coated, 225 µm long, with
resonant frequencies around 70 kHz) usually work well.

Note: The MMEFCH probe holder for MultiMode SPMs is a special probe holder
used for both EFM and Surface Potential that can be recognized by the white
Teflon washer beneath the screw at the base of the cantilever clip.

3. Set up the AFM for TappingMode operation. Click RealTime > CANTILEVER TUNE or the
CANTILEVER TUNE icon (shown). Set START FREQUENCY, END FREQUENCY and TARGET
AMPLITUDE appropriately then click AUTOTUNE to locate the cantilever resonant peak.

4. Engage the AFM and make the necessary adjustments for a good TappingMode image while
displaying height data in Channel 1.

5. Under the Scan Parameter List set the Interleave/DRIVE FREQUENCY, AMPLITUDE
SETPOINT, and SPM FEEDBACK (and any other unmentioned interleave parameters) to the
main feedback values (i.e., set parameters gray).

Note: When an Interleave parameter is green, the value shown is used during the
interleave scan. To fix any parameter so that it is the same on the main and
interleave scans, click on that parameter. The parameter changes color to gray
(“off”) and the main Feedback value for that parameter is used.

6. The Interleave/DRIVE AMPLITUDE is the AC voltage that is applied to the AFM tip, VAC.
To start, choose a DRIVE AMPLITUDE of 6V and set the corresponding button green.

7. Set Interleave/LOCK-IN PHASE. For MESP, SCM-PIT, or FESP cantilevers (resonant

frequency ~60-80khz) enter a LOCK-IN PHASE of -90 DEGREES. Ensure that the
corresponding button is green.

Note: The NSV Controller records phase in standard degrees with the convention that
cantilever phase is zero at resonance.

8. Choose a LIFT START HEIGHT of 0NM (i.e., the parameter is ignored because there is no
need for additional initial retraction to break free of the surface in TappingMode) and a LIFT
SCAN HEIGHT of 100NM. The LIFT SCAN HEIGHT can be readjusted later (i.e., in step 12).

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9. In the Interleave panel set INPUT FEEDBACK to POTENTIAL (set parameter green). Set
INTERLEAVE MODE to LIFT. Set SCAN LINE to INTERLEAVE, then Channel 2 image DATA
TYPE to POTENTIAL. For both data channels (height and potential) set the SCAN LINE
direction to RETRACE. The retrace direction should be chosen because the lift step occurs on
the trace scan.

10. Set SAMPLE BIAS CONTROL and TIP BIAS as appropriate.

Note: If the Feedback/AMPLITUDE LIMIT parameter is set to 2.5V to clip larger

photodetector signals while INPUT FEEDBACK is set to POTENTIAL, then the AC
voltage applied in surface potential detection is correspondingly restricted.
Such use of a limit improves resolution for signals that fall within the
acceptance range. The unrestricted setting for AMPLITUDE LIMIT is 20V.

11. Adjust the input gains. In the Other panel set INPUT IGAIN to 0.1 and INPUT PGAIN to 1.0
as a starting point. As with the topography gains, the scan can be optimized by increasing the
gains to maximize feedback response, but not so high that oscillation sets in. More
information on tuning the feedback loop is given in Section 3.7.5.

12. Optimize the LIFT SCAN HEIGHT. The best resolution is achieved with LIFT SCAN HEIGHT
at the smallest value possible that does not make the tip crash into the sample surface (see
Optimizing LIFT SCAN HEIGHT, page 156 ).

3.7.5 Surface Potential Detection Pointers

Troubleshooting

Potential signal is oscillating

1. Select the SCOPE mode and look at the Potential signal. If oscillation noise is evident in the
signal, reduce the input gains. If oscillations persist even at very low input gains, try
increasing the LIFT SCAN HEIGHT and/or reducing the Interleave/DRIVE AMPLITUDE until
oscillation stops. If the tip crashes into the surface during the Potential measurement, dark or
light streaks or dots appear in the Potential image, and the signal becomes unstable and can
cause the feedback loop to malfunction. Increasing the LIFT SCAN HEIGHT and reducing the
DRIVE AMPLITUDE can prevent this problem.

Note: An electrically “floating” sample is a common cause of oscillation. Make sure

there is a low impedance ground connection.

2. Lower Other/INPUT IGAIN and INPUT PGAIN.

Potential signal is stuck at an extreme (i.e., railed), at either +12V or -12V

1. If the Potential signal is perfectly flat and shows no noise even with a small data scale, the
feedback loop is probably railed at ±12V. Verify this by changing the value of REALTIME

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PLANEFIT to NONE in the Channel 2 panel and increasing the DATA SCALE to the maximum
value, 20V. Select SCOPE in the Scan window and check if the data is railed at one of the
limits. Common reasons for this include:

• A regular probe holder is being used instead of the EFM probe holder.

• An inappropriate DRIVE PHASE is being used. For MESP or SCM-PIT probes make
sure the Interleave LOCK-IN PHASE is set near -90 DEGREES. For more details on
optimizing drive phase, see Lock-In Phase, page 157 .

• An incorrect electrical connection is being made. Verify that the sample is connected
properly to the sample platform. Verify that the jumpers in the base of the MultiMode or
on the backplane of the Dimension are in their factory configuration.

Signal contrast is poor, but the Potential signal is not railed

1. Verify there is an electric field at the sample surface. If applying bias voltage to the sample to
generate an electric field, set the potential channel REALTIME PLANE FIT to NONE. While in
SCOPE mode, vary the interleave BIAS value and verify that the potential signal shifts
accordingly.

Optimizing LIFT SCAN HEIGHT

1. Fine tune LIFT SCAN HEIGHT to as small a value as possible without hitting the surface.
Lateral resolution of surface potential detection improves with decreased tip/sample
separation. The minimum LIFT SCAN HEIGHT depends on the roughness of the sample, the
difference between the AMPLITUDE SETPOINT and free air amplitude, and the quality of the
height image. Hitting the surface usually produces phase data with extremely high contrast
(i.e., either black or white pixels).

Because the tip is not oscillating during the Potential measurement (the feedback loop works
to keep the amplitude zero), the LIFT SCAN HEIGHT is generally smaller than with other
LiftMode techniques. LIFT SCAN HEIGHTs down to –5NM are possible on smooth samples.
This lower limit to the LIFT SCAN HEIGHT is affected by sample roughness, scan speed, and
target amplitude used during tuning, etc. Once oscillation stops, you can increase the input
gains for improved performance.

Tip Choices

It is possible to deposit custom coatings on model FESP silicon TappingMode cantilevers. Verify
that all deposited metal adheres strongly to the silicon cantilever.

It is also possible in some cases to use uncoated tips. The metallic coating and low spring
constant/resonance frequency of MESP and SCM-PIT tips make them well suited for sensitive
electrical measurements. However, the coating increases the tip radius, and wear of the coating can
cause significant changes in the detection of the electric field in the immediate vicinity of the tip. It
has been suggested (Jacobs, H.O., Knapp, H.F., Stemmer, A., “Practical Aspects of Kelvin Probe
Force Microscopy,” Rev. Sci. Instrum. 70 (1999) 1756.) that these changes in tip shape account for

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many of the DC shifts observed in Surface Potential images. Standard TappingMode probes
(Models TESP) and the Force Modulation probes (Model FESP) are highly n-doped silicon that are
often conductive enough for surface potential detection. The advantage to using the uncoated
silicon tips is the small tip radius improves lateral resolution in topographic imaging and the
absence of changes in the metallic coating during surface potential detection. FESP tips have a
lower spring constant and should be more sensitive to smaller forces than TESP tips. There is a
reduction in sensitivity to small electric fields with the decreased conductivity of an uncoated tip.

If tips with higher resonant frequency are used, such as TESP (~300kHz), a different drive phase
must be used, see Lock-In Phase, page 157 .

Tuning

Two curves should appear in the Cantilever Tune box—the amplitude curve in blue and the lock-in
curve in red. In Surface Potential it is more important than usual that the resonant peak is
symmetric. If the peak is unsatisfactory, its shape can often be changed by readjusting the position
of the probe in the probe holder. The laser and photodiode usually require readjustment after the
probe is moved.

Drive Amplitude

Higher interleave DRIVE AMPLITUDEs produce larger electric forces on the cantilever, and this
makes for more sensitive potential measurements. Conversely, the maximum total voltage (AC +
DC) that may be applied to the tip is ±12V. So a large DRIVE AMPLITUDE reduces the range of the
DC voltage that can be applied to the tip (Potential signal). If the potentials to be measured are very
large, it is necessary to choose a small DRIVE AMPLITUDE (it is not recommended to use less than
2V), while small surface potentials can be imaged more successfully with large DRIVE
AMPLITUDEs. To start, choose a DRIVE AMPLITUDE of 6V.

Lock-In Phase

LOCK-IN PHASE adjusts the phase of the reference signal to the lock-in amplifier. The correct
phase relationship must exist between the reference and the input signal to the lock-in for the
Potential feedback loop to perform correctly. For cantilevers with resonant frequencies from 60-
80kHz (such as MESP, SCM-PIT, and FESP), use an interleave LOCK-IN PHASE of -90 DEGREES.
For cantilevers with higher resonant frequencies there is an increased lag in the electronics that
must be compensated for. For cantilevers around 300khz (such as TESP) an interleave LOCK-IN
PHASE near -70 DEGREES often works well.

Open Loop Operation

Sometimes it is useful to run Surface Potential in the “open-loop” configuration. This means that
the Potential feedback loop is disabled and the data is only qualitative. The AC voltage is applied to
the tip as in the standard Potential operation; the tapping piezo used for mechanical driving of the
cantilever is disabled. Because the feedback is disabled, there is no adjustment of the DC voltage on
the tip, so the oscillating electrical force drives the cantilever into motion. This motion can be
monitored by observing the amplitude signal (the input to the potential feedback loop), called

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Surface Potential Detection

“potential input.” Set up the system as described above with the following changes: Set the INPUT
IGAIN and INPUT PGAIN to zero. Select AMPLITUDE or POTENTIAL INPUT as the DATA TYPE.

Note: Turning the input gains to zero stops further changes to the DC voltage on the
tip but does not set the tip voltage back to zero.

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NanoScope V Controller Lock-In

3.8 NanoScope V Controller Lock-In

The Generic Lock-In GUI, brings together all of the controls associated with the use of the three
internal lock-in amplifiers of the NanoScope V Controller into a single panel, shown in Figure 3.8a.
The tabs along the top of the main panel are used to access the interface for individual lock-ins.

Figure 3.8a The Generic Lock-In, shown configured for TappingMode imaging. The DDS 1 output is routed to
the Tapping Piezo and the lock-in input is set to monitor the vertical photodetector signal.

3.8.1 Mode-specific behavior

TappingMode

When calling the lock-in panel with the microscope set to TAPPINGMode, the primary lock-in
selection tab is labelled Feedback. In addition the parameters DRIVE ROUTING, LOCK-IN1
SOURCE and Lock-in ENABLE/DISABLE are disabled and greyed out. This prevents the user from
inadvertently mode switching while scanning and using the primary lock-in for feedback.

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NanoScope V Controller Lock-In

Contact Mode

When calling the lock-in panel with the microscope set to CONTACT mode the primary lock-in
selection tab is labelled Lock-In 1. All of the lock-in parameters including those disabled for
tapping mode are enabled for user selection. Lock-in changes are unable to change the microscope
mode while scanning in Contact mode.

Other Modes

STM, Tapping/TR, TR/Tapping, Dynamic Friction and Piezo Response modes are not yet
supported by the Generic Lock-In.

3.8.2 Generic Sweep Window

Below the lock-in selection tabs are controls, shown in Figure 3.8b, that enable the lock-in enable
setting parameters for both main and interleave modes. Each of the three lock-in panels has all of
the controls necessary to use that lock-in independent of the state of the other lock-ins. Each panel
also has a button that allows the user to rapidly access the NanoScope Generic Sweep function,
shown in Figure 3.8c.

Figure 3.8b Buttons to enable/disable the lock-in and to set parameters for main and interleave modes.

Generic Sweep

The GENERIC SWEEP button takes the user to the Generic Sweep window and populates fields
based on values in the calling lock-in panel. Clicking the MORE button of the Generic Sweep
window allows the user to toggle between the enabled lock-ins without leaving the Generic Sweep
window.

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NanoScope V Controller Lock-In

Figure 3.8c The Generic Sweep window may be accessed from the lock-in panel.

3.8.3 Drive Output Panel

The Drive Output panel, shown in Figure 3.8d, contains all of the controls to configure the output
waveform of the DDS including frequency, amplitude, DC offset and the signal routing.

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NanoScope V Controller Lock-In

Figure 3.8d The Drive Output panel

Harmonic

The HARMONIC Drive Output option, available for Lock-In 2, locks in on a user-selected
harmonic (1-25) of the drive (DDS 1) signal. This enables you to lock in on higher (than the
fundamental) frequency modes of the cantilever. You must set Lock-In 1 (Feedback) to ENABLED
and select set Lock-In 2 to HARMONIC.

Drive Frequency

Sets the frequency of the corresponding DDS output and the reference for the lock-in input.

Drive Amplitude

Sets the zero-to-peak amplitude of the DDS output.

Drive DC Offset

Applies a DC shift to the AC bias.

Note: The maximum output voltage of the DAC is +/-10 Volts. Ensure that the DC
offset plus the AC DRIVE AMPLITUDE is less than 10V to avoid clipping the
output waveform.

Drive Routing

Sets the output destination for the drive signal. Options are TAPPING PIEZO, TIP, SAMPLE, X
DRIVE, Y DRIVE, Z DRIVE, FRONT PANEL (Lock-In 2)and NULL. When the output is selected as
FRONT PANEL, the output is routed to the DDS 2 BNC on the front panel of the NanoScope V
Controller. When the output is selected as NULL, the output is not routed but allows a reference
signal to be generated and the lock-in used for inputs.

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NanoScope V Controller Lock-In

3.8.4 Lock-Input Panel

The Lock-In Input panel, shown in Figure 3.8e, contains all of the controls to configure the inputs
to the lock-in.

Figure 3.8e The Lock-In Input panel.

Reference Frequency

Duplicates the frequency from the Drive Output panel.

Lock-In Source

Selects the input source to the lock-in amplifier. Options are VERTICAL Photo-detector,
HORIZONTAL Photo-detector, APPLICATION MODULE and FRONT PANEL.

Lock-In Phase

Sets the phase offset between the detected signal and the reference. Three buttons below the
parameter display add/subtract 90° or Zero the current phase.

Lock-In BW

Sets the lock-in bandwidth for the lock-in input.

Time Constant

Calculated from the lock-in bandwidth as (1/lock-in BW).

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High Speed Data Capture

3.9 High Speed Data Capture

The High Speed Data Capture window, shown in Figure 3.9a, allows you to capture and store
many signals. To open the High Speed Data Capture window, click REALTIME > HIGH SPEED
DATA CAPTURE...

Figure 3.9a High Speed Data Capture window

Status panel

3.9.1 Channel Selection Panel

Channels A and B can capture data at 6.25MHz and 50MHz while channels C and D capture data at
500kHz. Channels A and B capture VERTICAL and LATERAL DEFLECTION respectively. Data
capture of those channels may also be turned OFF.

The following data types are available for capture at 500kHz by the C and D channels:

• Height

• Signal Sum

• X sensor

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High Speed Data Capture

• Y sensor

• Z sensor

• Amplitude

• Phase

• TM Deflection

• Deflection Error

• Friction

• Z Feedback Output

• Input 1

• Input 2

• Input 3

• X Scan

• Y scan

3.9.2 Trigger Controls Panel

The following trigger controls are available:

Arm Trigger

ARM TRIGGER begins monitoring for the trigger conditions to be met and starts data acquisition
into the FIFO buffer. This button toggles to DISARM TRIGGER when the trigger is armed.

Disarm Trigger

DISARM TRIGGER stops data acquisition and stops monitoring for a trigger event.

Auto Re-Arm

The AUTO RE-ARM check box causes the trigger to be re-armed after the data acquisition is
completed. If AUTO RE-ARM is not checked, the trigger will be disarmed after the data acquisition
has been completed.

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High Speed Data Capture

Force Trigger

The FORCE TRIGGER button triggers data collection.

Event

The trigger EVENT drop-box allows you to trigger on an EDGE, EOL (End of Line), EOF (End of
Frame) or NONE. When the trigger is armed and a trigger EVENT occurs (or, if the trigger is forced),
an ABORT box, shown in Figure 3.9b, giving you the ability to abort the data acquisition appears.

Note: If EVENT = NONE, you must FORCE TRIGGER to begin data acquisition.

Figure 3.9b Abort box

Channel

The Channel drop-box allows the following data types to be used as a trigger:

• Signal Sum

• X sensor

• Y sensor

• Z sensor

• Deflection Error

• Friction

• Z Feedback Output

• Input 1

• Input 2

• Input 3

• X Scan

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High Speed Data Capture

• Y Scan

Level

Select the trigger LEVEL at which you wish to begin acquiring data.

Slope

You may trigger on either a POSITIVE or NEGATIVE SLOPE.

Delay

Trigger DELAY, if POSITIVE, specifies the amount of time between when the trigger conditions are
met and when data capture begins. If NEGATIVE, DELAY specifies the amount before the trigger
conditions are met that data capture begins.

Duration

The time DURATION of data that is saved.

3.9.3 Status Panel

The high speed data capture status is displayed in the status panel at the bottom of the HSDC
window. Captured file names have a suffix of .hsdc

3.9.4 Point And Shoot

The High Speed Data Capture (HSDC) function in the Point and Shoot view, shown in Figure 3.9c,
allows you to mark a spot for data collection. This can be operated in two modes:

1. WHILE SCANNING: triggers a capture when the tip passes the marker point.

2. WHILE SCAN IDLE: stops the scan, moves to the marked point and captures data there.

In either mode, you must set the capture conditions in the High Speed Data Capture window
before acquiring data.

FORCE TRIGGER: forces a trigger at the marked point regardless of the preset trigger conditions.

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High Speed Data Capture

Figure 3.9c Point and Shoot - High Speed Data Capture

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Pulse Counting

3.10 Pulse Counting

Counting of TTL-compatible pulses input through the DIGITAL 1 IN 1 and DIGITAL 2 IN 2 inputs is
enabled by setting the CHANNEL DATA TYPE to either COUNTER 1, COUNTER 2, FREQ.1 or
FREQ.2 shown in Figure 3.10a. COUNTER 1/2 DATA TYPES display results in counts/pixel while
FREQ.1/2 DATA TYPES display results in counts/second (Hz). I.e. each pixel represents a
frequency. This result is a function of SCAN RATE and number of SAMPLES/LINE.

Figure 3.10a Pulse Counter Enabled

Set OFFLINE PLANE FIT to NONE. If OFFLINE PLANE FIT is not set to NONE, the frequency data will
be offset. REALTIME PLANE FIT applies only to image view mode, not data, but typically should
be set to LINE to enable visibility of data over all ranges.

The counter range is 0 to 32767 counts/pixel.

The sensitivity of pulse counter is user-adjustable but should generally be left unchanged at 1.0.

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Pulse Counting

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Chapter 4 File Navigation and Browsing

The Browse and File Navigation commands allow you to select, display and export NanoScope
images.

Refer to the following commands available in the NanoScope software:

• The Browse Window: Section 4.1

• Image Display: Section 4.1.1

• Exporting Images: Section 4.1.2

• Image Processing Add View Commands: Section 4.1.3

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The Browse Window

4.1 The Browse Window

Open the Browse window by clicking VIEW > BROWSE, shown in Figure 4.1a, on the toolbar.
Directory icons appear in the browse window. Double-click a folder icon to browse that directory
(see Figure 4.1b).

Figure 4.1a Select VIEW > BROWSE to Open the Browse Window.

Figure 4.1b Browse Window

Capture Directory Icon

Directory Folder Icon

Selecting the first icon in the upper left of the file browsing window initiates a List View of file
information, shown in Figure 4.1c. Right-clicking the HEADERID button allows you to view and
sort for many SPM parameters. See Figure 4.1d.

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The Browse Window

Figure 4.1c Browse for Folder Window Open Upon Clicking Directory

HEADERID

Figure 4.1d Browse Column Configuration

The second icon in the upper left of the file browsing window causes thumbnail presentation of
image files, illustrated in Figure 4.1e. If no images are selected, right-clicking in the image browse
window (but not on an image icon) allows you to sort the image icons in the browse window. See
Figure 4.1f. Double- click on a thumbnail to open the image for further analysis. The Capture

Directory icon in the upper left of the file browsing window displays file information, in
either text or thumbnail presentations, of the capture directory (default is D:\capture).

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The Browse Window

Figure 4.1e Thumbnail Images in the Browse Window

Figure 4.1f Sorting Thumbnails

You can change the current capture directory in the Capture File dialog box by selecting
REALTIME > CAPTURE FILENAME..., shown in Figure 4.1g.

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 File Navigation and Browsing
The Browse Window

Figure 4.1g Capture File Dialog Box

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File Navigation and Browsing
The Browse Window

4.1.1 Image Display

If no images are selected, right-clicking in the image browse window (but not on an image icon)
allows you to select a display channel and a color table for the image icons in the browse window.
See Figure 4.1h.

Figure 4.1h Selecting the Display Channel and Color Table for the Icons

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The Browse Window

4.1.2 Exporting Images

You may export images, in either bitmap, JPEG or tiff formats from the image browse window by
right-clicking single or multiple images, shown in Figure 4.1i. You may select the channel and a
color table.

Figure 4.1i Exporting Multiple Images from the Image Browse Window

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File Navigation and Browsing
The Browse Window

4.1.3 Image Processing Add View Commands

The Offline Add View menu for image processing, available by right-clicking the offline icon of an
image in the workspace window, differs from the RealTime Add View commands. The commands
include display, measurement, analysis and modification commands (see Figure 4.1j).

Figure 4.1j Image Processing Functions Menu

display commands

measurement/analysis commands

modification commands

You can also add Offline views by clicking OFFLINE in the toolbar and selecting the desired
function (see Figure 4.1k).

Figure 4.1k Adding Offline Functions

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The Browse Window

Selecting OFFLINE > ADD OFFLINE VIEWS... opens the Add Views window, shown in Figure 4.1l,
to the file that you have selected.

Figure 4.1l Add Offline Views Window

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The Browse Window

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Chapter 5 Display Commands

The Display commands relate to the display of images captured in Realtime mode. These
commands are known as image processing.

Refer to the following analysis commands available in Offline menu of the NanoScope software:

• Image: Section 5.1

• Multiple Channel Analysis: Section 5.2

• 3D Surface Plot: Section 5.3

• Zoom: Section 5.4

• High Speed Data Capture Display: Section 5.5

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Image

5.1 Image
The term Image refers to the data captured in RealTime mode. The current image processing
capabilities include data analysis, modification, presentation and storage of the images. The source
of the image includes:

• Data captured in RealTime scanning mode

• New image files created using modification or analysis commands

For general information on the interface and basic functions in image processing, see Using the
Image Interface: Section 5.1.1.

5.1.1 Using the Image Interface

To process an image, you must open an image file. This can be done by:

• Clicking File > Open. When the Open Nanoscope File dialog box opens (see Figure
5.1a), select Captured Data File (*.*) and click the Ok button.

Figure 5.1a Open NanoScope File Dialog Box

• Double-click an image in the Browse window. The new image appears in the client
window (see Figure 5.1b).

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Image

Figure 5.1b Image for Processing

Right-Clicking in the Image Window

By right-clicking in the Image window, but not on the image (see Right-Clicking on the Image on
page 184), shown in Figure 5.1b, that allows you to perform the following tasks:

• Note—Adds notes to an image file.

• All Channels—When checked, the All Channels button displays all captured data
channels.

• Export View—Exports the current view as a jpeg image.

• Copy View—Copies the current view to the clipboard.

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Display Commands
Image

Right-Clicking on the Image

By right-clicking on the image, you will get a menu, shown in Figure 5.1c, that allows you to
perform the following tasks:

Figure 5.1c Image Click

• Rotating Line—Left-click, hold, and drag out a line. Release the mouse button to end
the line.

• Box (for some analyses)—Left-click, hold, and drag out a box and release the mouse
button.

Note: Left-clicking in the center of the box allows you to translate. Left-clicking on
edges allows you to change the box size.

• Copy Clipboard—Copies the image to the Microsoft clipboard.

• Tooltip Info Level:

• Basic

• Medium

• Advanced

• None

• Export—Exports the image as a bitmap.

• Channel—Selects which channel is displayed.

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Image

Image Buttons

Clicking the Image buttons above the captured image (see Figure 5.1d) performs the following
functions:

• Measure—Left-click, hold, and drag out a line. Length of line appears in a box near the
line any time cursor is on the line.

• Pan—From a zoomed image, the user can pan around to other areas of the original
image.

• Data Zoom—Left-click, hold, and drag out a box. Release the mouse button and the
image will automatically zoom in to the area of the box. The zoomed region will be
centered about the point originally selected.

• Forward/backward arrows —Toggles between zoomed and original views.

Right-Clicking on the Color Bar

Right-clicking on the color bar along the right side of the image (see Figure 5.1d) will produce a
Color Scale button. Clicking on this Color Scale button will open the Color Scale dialog box,
where you can perform the following image adjustments:

• Contrast—Number (-10 to +10) designates contrast of colors in displayed image (e.g.,

-10 shows little change, while 10 shows highest contrast).

• Offset—Number (-128 to +128) designates offset of colors in displayed image (e.g.,

120 shows illuminated background on image). Offset effectively changes the color
value around which the color scale is mapped.

• Data Scale—Designates the vertical range of the displayed data, corresponding to the
full extent of the color table.

• Table—Designates the Color Table number. There are 25 available color scales. For
instance color Table 0 is grayscale, color Table 1 features blue...

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Image

Figure 5.1d Image Adjustment Controls

Image
Buttons

Color
Scale
Dialog Box

Color Bar

Color Scale
Menu

Using the Mouse Within a Captured Image

Left-Click anywhere in image Creates a line of X length, at θo angle in the image window
window, drag line out, and
release

Place cursor on line Displays length and angle values of line in the image window

Place cursor on line, click Allows you to drag the line anywhere in the image window
and hold left button, and
drag

Click and hold on either end Changes length and/or the angle of the line
of line and drag

Right-Click Clicking the right mouse button when the cursor is on the line
accesses the Image Cursor menu (see Figure 5.1e)
• Delete—deletes the line.
• Flip Direction—switches the line end to end.
• Show Direction—Adds small arrowhead to the line to
indicate direction.
• Set Color—Allows you to change the color of the line.
• Clear All—Deletes all lines.

Figure 5.1e Image Cursor Menu

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Image

5.1.2 Dual-Scan Image

When you open a dual-scan image, the Channel 1 and Channel 2 images will appear side by side,
with Channel 1 on the left and Channel 2 on the right, and the channel data will typically be
shown below the left image. Click on the desired image to select the channel and the corresponding
channel data will appear (see Figure 5.1f).

Note: The location of the Channel data may vary depending on window proportions.

Figure 5.1f Captured Dual-Scan Image

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Display Commands
Image

5.1.3 Triple-Scan Image

When you open a triple-scan image, the Channel 1 and Channel 2 images will typically appear
side by side, with Channel 1 on the left and Channel 2 on the right, and the Channel 3 image will
typically appear below the Channel 1 image. Channel data is now shown to the right of the
Channel 3 image. Click on the desired image to select the channel and the corresponding channel
data will appear (see Figure 5.1g).

Note: The location of the Channel data may vary depending on window proportions.

Figure 5.1g Captured Triple-Scan Image

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Multiple Channel Analysis

5.2 Multiple Channel Analysis

It is often advantageous to analyze more than one channel of data from the same scan
simultaneously. The Multiple Channel Analysis feature allows you to view up to eight channels of
data simultaneously with one channel enlarged.

5.2.1 Eight Channel Image

Open the Multi-Channel offline view by double-clicking an image file containing more than three
channels in the image browse window. See Figure 5.2a. Change the displayed channel by clicking
either a thumbnail on the left or the previous/next buttons below the image window.

Figure 5.2a Multi-Channel offline view

5.2.2 Analyzing Captured Multichannel Images

When performing any analysis of a multichannel scan, you may only analyze one channel at a time.
Highlight the appropriate channel image by clicking on it, then select the desired Analysis View by
any one of the following:

• Right-clicking on the image file name in the Workspace, selecting Add View, and
clicking on the desired view.

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Multiple Channel Analysis

• Selecting Offline from the menu bar and clicking on the desired view.

• Clicking on the appropriate button in the button bar.

Once you select the desired channel, and the appropriate view, a new window will open with only
the image of the selected channel and you may start your analysis in accordance with the
instructions in Section 5.1 through Section 5.4. If the image display in the view is not the desired
channel, you can right-click on the image, go to Channel, and select the appropriate channel from
the pop-up menu.

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 Display Commands
3D Surface Plot

5.3 3D Surface Plot

The 3D Surface Plot View displays the selected image with color-coded height information in a
three-dimensional, oblique perspective. You can select the viewing angle and illumination angle for
a modeled light source.

You can view the 3D Surface Plot view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > 3D Surface
Plot from the popup menu.

Or

• Select Offline > 3D Surface Plot from the menu bar.

Or

• Click the 3D Surface Plot icon in the upper toolbar.

The Surface Plot panel appears and allows formatting of image data on the Display Monitor (see
Figure 5.3a).

Figure 5.3a 3D Surface Plot Window

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3D Surface Plot

5.3.1 Parameters in the 3D Surface Plot Inputs

The Projection Type, Plot Type, and Label Type 3D Surface Plot parameters can be changed by
clicking on the related window and selecting from the drop-down menus. The remaining
parameters may be changed by typing the desired information in the related window or by use of
the keyboard and mouse keys.

• To zoom in or out on the image, hold the control key down and slide the mouse up and
down on the image while holding the left mouse button.

• To pan, hold the shift key down and move the mouse up, down, left, or right on the
image while holding the left mouse button.

• Clicking and holding the right mouse button down while moving the mouse left and
right changes the light rotation on the image. This is only available when Plot Type is
set to Mixed.

• Clicking and holding the right button while moving the mouse up down changes the
light pitch. This is only available when Plot Type is set to Mixed.

The function of the Input parameters are:

Projection Select either Parallel or Perspective

• In Parallel mode, the viewing volume does not
change, which has the effect keeping objects the
same size as they are projected. This is useful for
maintaining the size and angle of objects between
the front and back of the view.
• In Perspective mode, objects appear to get smaller
the further away they are from the eye. This is how
the objects are perceived in the real world.

Plot Type Select Height, Wire, or Mixed

• Height displays the image with height values
encoded according to the color table.
• Wire displays the image as a line representation of
the scanned data.
• Mixed displays a combination of height and
illumination encoding.

Rotation The Rotation parameter in the Surface Plot Inputs

changes as the viewing angle is changed by rotating the
displayed image about the Z axis relative to its captured
orientation.

Pitch The Pitch parameter in the Surface Plot Inputs changes

as the viewing angle by manually changing the pitch of the
Y axis in the three-dimensional Surface Plot image.

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3D Surface Plot

Light Rotation The Light Rotation parameter in the Surface Plot Inputs
rotates the light source in the horizontal plane (xy plane).
This is only available when the Plot Type is set to Mixed.

Light Pitch The Light Pitch parameter in the Surface Plot Inputs
changes the viewing angle by selecting the pitch of the Z
axis in the three-dimensional Surface Plot image. This is
only available when the Plot Type is set to Mixed.

Light Intensity Selects the percentage of the imaginary light source mixed
with the color-encoded height information when the Plot
Type is set to Mixed.

Label Type The Label Type parameter in the Surface Plot Inputs
selects whether labels and/or axes are displayed with the
image.
• All displays the axes with labels.
• Axis displays the axes without labels.
• None displays the image without labels.

Channel Displays the current channel of multichannel scan dis-

plays.

The Export button allows the operator to export the image in the window to either JPEG or bitmap
format.

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Display Commands
Zoom

5.4 Zoom
The Zoom function has been replaced by the Crop and Split function. See Crop and Split:
Section 7.3.

5.5 High Speed Data Capture Display

Files created using the High Speed Data Capture on page 164 feature can be displayed by double-
clicking the file icon (.hsdc file type) in the NanoScope browse window. This opens a window,
shown in Figure 5.5a, that displays the captured data for multiple channels.

Figure 5.5a HSDC Offline Display Window

You may zoom in on the plotted data by using CTRL plus the left mouse button. Revert to the
original plot scale by clicking the magnifying glass in the lower left corner of the plot area.

In addition to displaying the captured data plotted vs. time, you may also perform a Fast Fourier
Transform of the data by changing the DISPLAY TYPE to AMPLITUDE VS FREQUENCY.

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High Speed Data Capture Display

The function of the Channel Data parameters are:

Channel Number Selects the CHANNEL (1-4) to display

Points/Pixel This parameter is used to speed plotting of large data files in a small (~355
pixels horizontally) display area. If your file has 100,000 data points and you
select 100 points/pixel (the default) ~35,500 data points will be plotted—
every third point. As you zoom in, the number of skipped points will decrease.
Alaising may occur if there are many skipped points.
The total number of points in the file and plot increment is shown in the status
bar at the lower left of the NanoScope window.

Display Type Determines the type of plot:

• CHANNEL VS TIME
• AMPLITUDE VS FREQUENCY computes and displays a FFT of the
data between the markers. If you do not have markers, the FFT will be
performed on all the input data1.
The plot is updated only when the DISPLAY TYPE is changed.

Frequency Bin Width The approximate width of the histogram bin used in for the FFT calculation.
Because a FFT algorithm is employed, this user input is updated so that 2n
points are used.

Number of Time Segments (sample data time)/(1./frequency bin width). [1] A portion of the last segment
may be truncated to accommodate the FFT 2n points requirement. You may
wish to increase the FREQUENCY BIN WIDTH if the NUMBER OF TIME
SEGMENTS is small.

X Scale Determines the scaling of the X Axis:

• LINEAR
• LOG base 10

Y Scale Determines the scaling of the Y Axis:

• LINEAR
• LOG base 10

High Speed Data Type Displays the DATA TYPE of the selected channel.

Units Determines the Y axis units:

• VOLTS
• METRIC

Fit Type Determines the type of fit between the markers:

• NONE
• LINE

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Chapter 6 Analysis Commands

The Analysis commands relate to analyzing the surface behavior of materials on images captured
in Realtime mode. These commands are known as image processing or analysis commands. The
commands contain views, options and configurations for analysis, modification, and storage of the
collected data. The analysis may be automated (i.e., in autoprograms) or completed manually. In
general, the analysis commands provide methods for quantifying the surface properties of samples.

Refer to the following analysis commands available in Offline menu of the NanoScope software:

• Depth: Section 6.1

• Power Spectral Density: Section 6.2

• Roughness: Section 6.3

• Section: Section 6.4

• Step: Section 6.5

• Width: Section 6.6

• XY Drift: Section 6.7

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6.1 Depth
To analyze the depth of features you have numerous choices which measure the height difference
between two dominant features that occur at distinct heights. Depth was primarily designed for
automatically comparing feature depths at two similar sample sites (e.g., when analyzing etch
depths on large numbers of identical silicon wafers).

Refer to the following sections on Depth analysis:

• Depth Theory: Section 6.1.1

• Depth Procedures: Section 6.1.2

• Depth Interface: Section 6.1.3

6.1.1 Depth Theory

The Depth command accumulates depth data within a specified area, applies a Gaussian low-pass
filter to the data to remove noise, then obtains depth comparisons between two dominant features.
Although this method of depth analysis does not substitute for direct, cross-sectioning of the
sample, it affords a means for comparing feature depth between two similar sites in a consistent,
statistical manner.

The display screen includes a top view image and a histogram; depth data is displayed in the results
window and in the histogram. The mouse is used to resize and position the box cursor over the area
to be analyzed. The histogram displays both the raw and an overlaid, Gaussian-filtered version of
the data, distributed proportional to its occurrence within the defined bounding box.

Histogram

Raw Data

Figure 6.1a (bottom graph) displays a histogram from raw depth data. Data points A and B are the
two most dominant features, and therefore would be compared in Depth analysis. Depending upon
the range and size of depth data, the curve may appear jagged in profile, with noticeable levels of
noise.

Note: Color of cursor, data, and grid may change if user has changed the settings.
Right-click on the graph and go to Color if you want to change the default
settings.

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Depth

Figure 6.1a Depth Histogram

A
3 B

2
1
0 30 60 90 120
Depth (nm)

Correlation Curve

The Correlation Curve is a filtered version of the Raw Data Histogram and is located on the
Raw Data Histogram represented by a red line. Filtering is done using the Histogram filter cutoff
parameter in the Input parameters box.The larger the filter cutoff, the more data is filtered into a
Gaussian (bell-shaped) curve. Large filter cutoffs average so much of the data curve that peaks
corresponding to specific features are unrecognizable. On the other hand, if the filter cutoff is too
small, the filtered curve may appear noisy.

The Correlation Curve portion of the histogram presents a lowpass, Gaussian-filtered version of
the raw data. The low-pass Gaussian filter removes noise from the data curve and averages the
curve’s profile. Peaks which are visible in the curve correspond to features in the image at differing
depths.

Peaks do not show on the correlation curve as discrete, isolated spikes; instead, peaks are
contiguous with lower and higher regions of the sample, and with other peaks. This reflects the
reality that features do not all start and end at discrete depths.

When using the Depth view for analysis, each peak on the filtered histogram is measured from its
statistical centroid (i.e., its statistical center of mass).

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6.1.2 Depth Procedures

1. If no workspace is present, open a new workspace (File > New Workspace).

2. Open the image you wish to analyze (File > Open > Captured Data File) or double click on
the browse view image.

3. In the workspace, position the cursor on the file name and right-click to access a functions
pop-up menu.

Figure 6.1b Functions Menu

4. In the pop-up menu, select Add View > Depth.

5. You can view the Depth view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Depth from
the popup menu.

Or

• Select Offline > Depth from the menu bar.

Or

• Click the Depth icon in the upper toolbar.

6. Using the mouse, left-click and drag a box on the area of the image to analyze.
The Histogram displays the depth correlation on this specified area.

Note: If no box is drawn, by default, the entire image is selected.

7. Adjust the Minimum Peak to Peak to exclude non relevant depths.

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8. Adjust the Histogram Filter Cutoff parameter to filter noise in the histogram as desired.

9. Note the results.

Note: To save or print the data, run the analysis in an Auto Program
(see Chapter 8).

Figure 6.1c Depth Interface

6.1.3 Depth Interface

The Depth interface includes a captured image, Input parameters, Results parameters and a
correlation histogram (see Figure 6.1d).

Figure 6.1d Depth Histogram

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Depth

Depth Input Parameters

The depth input parameters below define the slider cursor placement for determining the exact
depth of a feature.

Number of Histogram Bins The number of data points which result from the filtering calculation. Note:
Having more histogram bins than pixels is unnecessary.

Histogram Filter Cutoff Lowpass filter which smooths out the data by removing wavelength com-
ponents below the cutoff. Use to reduce noise in the Correlation histogram.

Minimum Peak To Peak Sets the minimum distance between the maximum peak and the second
peak marked by a cursor. The second peak is the next largest peak to meet
this distance criteria.

Left Peak Cutoff The left (smaller in depth value) of the two peaks chosen by the cursors.
Value used to define how much of the left peak is included when calculat-
ing the centroid. At 0 percent, only the maximum point on the curve is
included. At 25 percent, only the maximum 25 percent of the peak is
included in the calculation of the centroid.

Right Peak Cutoff The right (larger in depth value) of the two peaks marked by the cursors.
Value used to define how much of the right peak is included when calculat-
ing the centroid. At 0 percent, only the maximum point on the curve is
included. At 25 percent, only the maximum 25 percent of the peak is
included in the calculation of the centroid.

Data Range Pad Creates a buffer region at either end of the histogram.

Results Parameters:

Peak to Peak Distance Depth between the two data peak centroids as selected using the line cur-
sors.

Minimum Peak Depth The depth of the deeper of the two features.

Maximum Peak Depth The depth of the shallower of the two features.

Depth at Histogram Maximum Depth at the maximum peak on the histogram.

Number of Peaks Found Total number of peaks included within the data histogram.

Using the Grid Display

Measurement cursors for the histogram are automatically positioned based on the numerical values
selected in the Input fields. Right-clicking on the grid will bring up the Grid Parameters menu
(see Figure 6.1e) and allow you to make the following changes:

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Depth

Color Allows operator to change the color of the:

• Curve (data)
• Text
• Background
• Grid
• Minor Grid
• Markers
Filter Typically used for a Profiler Scan.
• Type—Select None, Mean (default), Maximum, or Minimum
• Points—Select 4k, 8k (default), 16k, or 32k
Minor Grid Places a minor grid in the background of the Graph window.
Scale Allows user to auto scale, set a curve mean, or set their own data
range
Line Style For each curve, the operator can choose a connect, fill down, or point
line.
User Preferences Restore—Reverts to initial software settings
Save—Saves all changes operator has made during this session. This
becomes the new default settings.
Copy Clipboard Copies the grid image to the Microsoft Clipboard
Print Prints out the current screen view to a printer
Export Exports data in bitmap, JPEG or XZ data format
Active Curve Determines which curve you are analyzing

Figure 6.1e Grid Parameters Menu

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Power Spectral Density

6.2 Power Spectral Density

The Power Spectral Density (PSD) function is useful in analyzing surface roughness. This
function provides a representation of the amplitude of a surface’s roughness as a function of the
spatial frequency of the roughness. Spatial frequency is the inverse of the wavelength of the
roughness features.

The PSD function reveals periodic surface features that might otherwise appear random and
provides a graphic representation of how such features are distributed. On turned surfaces, this is
helpful in determining speed and feed data, sources of noise, etc. On ground surfaces, this may
reveal some inherent characteristic of the material itself such as grain or fibrousness. At higher
magnifications, PSD is also useful for determining atomic periodicity or lattice.

Refer to the following Power Spectral Density sections:

• PSD and Surface Features: Section 6.2.1

• PSD and Flatness: Section 6.2.2

• Performing a Spectral Density Analysis: Section 6.2.3

• Changing Parameters of the Spectrum Plot: Section 6.2.4

6.2.1 PSD and Surface Features

Consider the image in Figure 6.2a.

Figure 6.2a Waveform Surfaces

X
Y

2D Spectrum

This synthetic surface consists of essentially two dominant wave forms: a long period waveform
along the X-axis, and a shorter period waveform along the Y-axis. A 2 dimensional power spectral
density plot consists of two dominant spikes (one for each dominant wavelength), plus some

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number of extra wavelengths inherent within the image. (These extra wavelengths may appear due
to fine surface features and/or side bands of the dominant wave forms.) Because of the sinusoidal
nature of the composite wave form, a relatively small set of spectral frequencies suffices to describe
the entire surface. By contrast, an image comprised of angular (saw-toothed or square) waveform
contains more spatial frequency components.

Over a given range of spatial frequencies the total power of the surface equals the RMS roughness
of the sample squared.

The frequency distribution for a digitized profile of length L, consisting of N points sampled at
intervals of do is approximated by:
N i---------
2π- 2
2d o (n – 1)(m – 1) m–1
PSD(f) = --------
N ∑ e N z( n) for f = -------------
Nd o
n=1

N⁄2
Where i = √-1, and frequencies, f, range from --1- to ----------- . Practically speaking, the algorithm used
L L
to obtain the PSD depends upon squaring the FFT of the image to derive the power. Once the
power, P, is obtained, it may be used to derive various PSD-like values as follows:
P
1D PSD = ------
Δf
P
1D isotropic PSD = ---------
2πf
P
2D isotropic PSD = --------------------
2πf ( Δf )

The terms used in the denominators above are derived by progressively sampling data from the
image’s two-dimensional FFT center (see Figure 6.2b).

Figure 6.2b Progressive Data Sampling

Δf

f = 1 pixel f = 2 pix els f = 3 pix els f = 4 pix els

Each sampling swings a “data bucket” of given frequency f. Since samples are taken from the
N⁄2
image center, the sampling frequency, f, is limited to ----------- , where N is the scan size in pixels. This
L
forms the upper bandwidth limit (i.e., the highest frequency or Nyquist frequency) of the PSD plot.
The lower bandwidth limit is defined at 1/L.

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6.2.2 PSD and Flatness

PSD is used increasingly as a metrology tool for evaluating extremely flat surfaces, such as
polished or epitaxial silicon. Generally, the desired surface is expected to adhere to certain PSD
thresholds, signifying it meets a specified flatness criterion.

The main advantage gained over traditional RMS specifications is that PSD flatness is qualified
through the full spectral range of interest. For example, one may specify spectral thresholds at
frequencies measured on the atomic scale, thus ensuring surfaces consist largely of uniform lattices.
Setting the precise thresholds for various materials remains a matter of debate.

Consider the image of epitaxial gallium arsenide in Figure 6.2c.

Figure 6.2c Epitaxial Gallium Arsenide Image

This surface is comprised of “terraces” formed from the material’s natural lattice structure; each
terrace is one atomic monolayer thick and is spaced at fairly regular intervals. This degree of
flatness is handily evaluated with PSD, as the terraces produces a spectral spike corresponding to
their spacing wavelength. A PSD plot for this type of surface generally takes the form shown in
Figure 6.2d.

Figure 6.2d PSD Plot for Terraced Sample

Special spike corresponding to “terrace” spacings on surface

3D Isotropic PSD
104

P
S
D

10-1
101 10-2
Wavelength (mm/cycle)

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Power Spectral Density

This tapered PSD plot is characteristic of flat, isotropic surfaces. Longer wavelengths are present
up to the scan width, and are accompanied by uniformly decreasing powers of shorter wavelengths
down to 2 pixels. On the plot shown above a spike stands out, corresponding to the wavelength
spacing of the terraced features. Depending upon the qualitative standards of the person evaluating
such a plot, this spike may exceed a threshold standard of flatness.

6.2.3 Performing a Spectral Density Analysis

To use the PSD Analysis function, perform the following procedures:

1. Select View > Browse from the menu bar, then open the image you wish to analyze by
double-clicking it.

2. You can view the PSD Analysis view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > PSD from the
popup menu.

Or

• Select Offline > PSD from the menu bar.

Or

• Click the PSD icon in the upper toolbar.

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The PSD window opens to allow spectral density plotting on the Display Monitor (see Figure
6.2e).

Figure 6.2e PSD Analysis

Compute PSD Buttons

Once the PSD analysis window is opened, select the type of spectral density analysis you wish to
perform by clicking the appropriate button above the Results window.

2D Isotropic—Executes a two-dimensional Power Spectral Density analysis.

Horizontal Axis—Executes a one-dimensional Power Spectral Density analysis along the X-axis.

Vertical Axis—Executes a one-dimensional Power Spectral Density analysis along the Y-axis.

The calculation begins as soon as the button is selected. The PSD and a table of values from the
graph are shown in the Results window. Completion of the analysis will also result in a
topographical histogram in the spectrum plot window (see Figure 6.2f).

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Power Spectral Density

Figure 6.2f Power Spectral Density Histogram

Results Display

The Results window displays the Name and Value of the procedures performed during a PSD
analysis. The teal shaded area in the display window corresponds to the area designated by the teal
cursor on the Power Spectral Density histogram, and the purple shaded area corresponds to the
purple cursor. You can generate a report by right-clicking in the Results window, selecting COPY
TEXT and pasting the clipboard into another application (e.g. Notepad, Word...).

Select Displayed Parameters

The operator can select which Results will or will not be displayed in the Results window by
Right-clicking in the Results window, selecting Show All from the popup menu, and checking or
unchecking the appropriate boxes (see Figure 6.2g).

Figure 6.2g Select Show All On/Off Check Boxes

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Exporting Text

Selecting COPY TEXT from the popup menu will copy the text from the Results window, in tab-
delimited text format, to the Windows clipboard. You may then paste it into a text or word
processing program.

6.2.4 Changing Parameters of the Spectrum Plot

The Spectrum Plot window displays results of the PSD analysis (see Figure 6.2h). The window
has two cursors whose color corresponds to the shaded areas in the Results window. You can move
either of these cursors within the Spectrum Plot window by placing the cross hair cursor directly
over the cursor, clicking and holding the left mouse button, and dragging the mouse to the left or
right. You can also move both cursors simultaneously by left-clicking the mouse with the cross hair
cursor anywhere between the two cursors and dragging to the left or right.

To change the parameters of the Spectrum Plot, right-click in the Spectrum Plot window at the
bottom of the display and choose from the popup menu.

Figure 6.2h Spectrum Plot Parameter Menu

Teal Cursor Popup Menu Purple Cursor Spectrum Plot

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Spectrum Plot Popup Menu Items

Color—Changes the colors of the curves, text, background, grid lines, minor grid lines (if
selected), and the marker pairs (see Figure 6.2i).

Filter—Selects Filter type and points (see Figure 6.2j).

Minor Grid—Shows/hides minor grid lines

Figure 6.2i Color Menu Items

Figure 6.2j Filter Menu Items

Scale—Sets the vertical axis range, the center of the range, or allow the software to autoscale (see
Figure 6.2k).

Line Style—Changes the line style of the Spectrum Plot graphical display (see Figure 6.2l).

User Preferences—You can either save all changes made to the graphical display, or restore
previously saved settings (see Figure 6.2m). Save will result in all graphical displays maintaining
any design changes made to this display.

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Copy Clipboard—Copies the graphical display only to the Windows clipboard, allowing it to be
pasted into any compatible Windows program.

Print—Prints the graphical display only to a printer.

Export—Saves the graphical display as a JPEG graphic, a Bitmap graphic, or as an XZ Data file
text, which can be read in a database program (e.g. Excel).

Active Curve—Changes the curve displayed when more than one curve has been plotted. (Does
not occur in PSD).

Figure 6.2k Scale Settings Dialog Box

Figure 6.2l Line Style Display

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Roughness

Figure 6.2m User Preferences Menu

6.3 Roughness
The Roughness command generates a variety of statistics on surfaces, including classical
roughness values and peak and zero crossing data. “Image” statistics are reported for the entire
image. “Box” statistics are reported only for the region you define within a cursor box. In addition,
the data can be augmented with stopbands, (excluding features) to isolate desired analysis.

Refer to the following sections on Roughness:

• Roughness Theory: Section 6.3.1

• Roughness Procedures: Section 6.3.2

• Roughness Interface: Section 6.3.3

Most industrial standards for roughness measurement call for planefitting data before calculating
values. Planefitting applies a temporary first-order planefit before calculating statistics. On many
surfaces, especially those which are tilted, this yields different values from those seen in raw
(unplanefitted) data. Moreover, peripheral features included within the analyzed region may
produce cumulative results uncharacteristic of the feature(s) of interest. To ensure the best results,
you should observe the following rules when using Roughness analysis:

• If the image shows signs of second- or third-order distortion (e.g., bow due to large
scans on large scanners), apply a second- or third-order Flatten and Planefit to the
image before using Roughness analysis.

• Isolate your analysis to specific areas of the image. This may be accomplished by using
the box cursor in Roughness to analyze only select portions of the image.

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Roughness

6.3.1 Roughness Theory

Regarding the effects of Planefitting on Roughness statistics—When Roughness analysis is

applied to an image, statistical values are calculated according to the relative heights of each pixel
in the image. Planefitting (used to correct images for tilt and bow) reorients these pixels in a
manner which can affect roughness statistics dramatically on some surfaces. This is especially true
of surfaces having broad, coplanar features. Planefitting can be applied at the time of file capture
using Offline planefit from a Channel panel, or via the Offline > Plane Fit function.

When Roughness analysis is applied to an image, the image data is automatically planefit
beforehand. This is done to accord with ASME and ISO metrological standards. (Only the Raw
mean parameter is exempt from this operation, being calculated from raw data only.) To avoid
unexpected results due to planefitting, be certain to apply Roughness analysis only to the
surface(s) of interest by utilizing a cursor box, or by scanning just the specific site of interest.
Including peripheral features within an analyzed area may produce cumulative results
uncharacteristic of the feature(s) of interest.

The relationship between the zero plane and the data also changes according to the setting of the
Offline planefit parameter. If the Offline planefit parameter is set to None the offset is not
removed from the data and it is very possible that the zero plane does not intersect the data. The
other settings (see Data Type Range or Settings on page 66) of the parameter subtract the average Z
value from every point in the image so the data varies around the zero plane.

Regarding Basic Roughness Measurements—Average roughness (Ra) is one of the most commonly
used roughness statistics. Figure 6.3a represents two surfaces having the same average roughness.

Similarly, a number of other roughness values are based upon least-squares calculations (e.g., RMS
roughness, or Rq), and their algorithms are more concerned with a best fit of all height points than
with the spatial frequency of features.

The surface of image A is represented as having a high frequency profile of features. Image B
represents a separate surface having the same average feature height, but distributed at wider
(lower-frequency) intervals. In terms of average and RMS roughness, both surfaces are equally
rough. If you are interested in differentiating between the two, you must rely upon other statistical
parameters such as Power Spectral Density.

Figure 6.3a Basic Roughness Measurements

A B

Best-fit plane

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Roughness

6.3.2 Roughness Procedures

Example of Using Roughness Analysis

For general Roughness Analysis, complete the following procedures:

1. Select an image file from the file browsing window at the right of the main window. Double
click the thumbnail image to select and open the image.

2. You can view the Roughness view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Roughness
from the popup menu.

Or

• Select Offline > Roughness from the menu bar.

Or

• Click the Roughness icon in the upper toolbar.

3. The Roughness View appears showing results for the entire image.

4. To perform Roughness measurements within an area, left-click and move the mouse to draw
a measurement box. Click on the Execute button to calculate the Roughness inside the box.

5. To exclude an area, right-click in the image to access a pop-up menu and select Stop band.
Using the mouse, draw a box around the area to be excluded by the stop band command.
Click on the Execute button to calculate the Roughness outside the box.

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6.3.3 Roughness Interface

The Roughness View shows the image along with Input parameters and a Results window.

Note: Some parameters are reported only when certain subroutines are turned on.

Figure 6.3b Roughness Display

Results
PARAMETERS

Input
Parameters

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Roughness

Input Parameters

Peak

The Peak feature, when switched On, isolates specified height portions of the image (peaks) from
background data. Peaks are specified using the Peak Threshold parameters, either in terms of their
absolute height or their deviation from the RMS value of all surface data, and relative to either the
highest data point (Peak) or the mean (Zero). When Peak is turned On, portions of the image
contained within the box cursor and falling within the specified boundaries are retained; all other
data is removed.

Range or Settings—When Peak is turned On, the following subcommands are activated (see
Figure 6.3c):

Peak Threshold The Reference buttons select whether the threshold is defined relative to
Reference the Zero (lowest) value, or the tallest Peak in the selected region.
Peak Threshold The Value Type determines whether the threshold is defined as an abso-
Value Type lute distance from the reference point in nanometers (Absolute value) or
a percentage of the root-mean-square (Rms %) of the Z values.
Peak Threshold The Value is an absolute distance from the reference point in nanometers
Value (Absolute value) or a percentage of the root-mean-square (Rms %) of the
Z values.

When Peak is turned On, the following statistical parameters are turned on. All Peak parameters
are calculated from the thresholds you define with the Peak subcommands.

• Rz

• Rz count

• Peak Count

• Valley Count

• Max peak ht (Rp)

• Av. Max ht (Rpm)

• Max depth (Rv)

• Av. max depth (Rvm)

When Peak is turned Off, statistics are not calculated.

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Figure 6.3c Input On Parameters

Peak Input Parameter ON

Zero Crossing

Zero Crossing

A zero crossing is a point where the Z values go through zero regardless of slope. This value is the
total number of zero crossings along both the X and Y center lines divided by the sum of the box
dimensions.

Range or Settings—When Zero crossing is turned On and you click the Execute button, the
number of zero crossings along the X and Y center lines of the box cursor is determined (see Figure
6.3c). The number of zero crossings is divided by the sum of the lengths of the X and Y center lines
and reported as the Line density.

When Zero crossing is turned Off, the zero crossing determination is not performed.

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Results Parameters

Statistics used by the Roughness routine are defined in this section. The terms are listed
alphabetically. Most are derived from ASME B46.12 (“Surface Texture: Surface Roughness,
Waviness and Lay”) available from the American Society of Mechanical Engineers.

Av max Depth (Rvm) Average distance between the (VALLEY COUNT value) lowest profile
points and the mean data plane.
Av max ht (Rpm) Average distance between the (PEAK COUNT value) highest profile
points and the mean data plane.
Box x Dimension The width of the Lx box cursor you define.

Box y Dimension The length of the Ly box cursor you define.

Image Mean Mean value of data contained within the image.

Image Projected surface Area of the image rectangle (X x Y).
area
Image Ra Arithmetic average of the absolute values of the surface height deviations
measured from the mean plane.
N
1
R a = ---- ∑ Z j
N
j=1

Image Raw mean Mean value of image data without application of plane fitting.
Image Rmax Maximum vertical distance between the highest and lowest data points in
the image following the planefit.
Image Rq Root mean square average of height deviations taken from the mean
image data plane, expressed as:
2
∑ Zi
---------------
N

Image Surface area The three-dimensional area of the entire image. This value is the sum of
the area of all of the triangles formed by three adjacent data points.
Image Surface Area Difference between the image’s three-dimensional Surface area and two-
Difference dimensional projected surface area.
Image Z range Maximum vertical distance between the highest and lowest data points in
the image prior to the planefit.
Kurtosis This is a non-dimensional quantity used to evaluate the shape of data
about a central mean. It is calculated as
N
1 1 4
Kurtosis = --------4- ---- ∑ Z j
Rq N
j=1

Graphically, kurtosis indicates whether data are arranged flatly or sharply

about the mean.

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Line Density The number of zero crossings per unit length on the X and Y center lines
of the box cursor. A zero crossing is a point where the Z values go through
zero regardless of slope. This value is the total number of zero crossings
along both the X and Y center lines divided by the sum of the box dimen-
sions.
Maximum Depth (Rv) Lowest data point in examined region.

Max Height (Rmax) Maximum vertical distance between the highest and lowest data points
within the cursor box.
Max Peak ht (Rp) Maximum peak height within the analyzed area with respect to the mean
data plane.
Mean The average of all the Z values within the enclosed area. The mean can
have a negative value because the Z values are measured relative to the Z
value when the microscope is engaged. This value is not corrected for tilt
in the plane of the data; therefore, plane fitting or flattening the data
changes this value.
Mean Roughness (Ra) Arithmetic average of the absolute values of the surface height deviations
measured from the mean plane within the box cursor:
N
1
R a = ---- ∑ Z j
N
j=1

Peak Count The number of peaks taller than the THRESHOLD VALUE.
Projected Surface Area Area of the selected data.
Raw Mean Mean value of image data within the cursor box you define without appli-
cation of plane fitting.
Rms (Rq) This is the standard deviation of the Z values within the box cursor and is
calculated as:

Rq =
∑ ( Zi )
-------------------
N

where Zi is the current Z value, and N is the number of points within the
box cursor. This value is not corrected for tilt in the plane of the data;
therefore, plane fitting or flattening the data changes this value.
Rz This is the average difference in height between the (RZ COUNT value)
highest peaks and valleys relative to the Mean Plane.
Rz Count Number of peak/valley pairs that are used to calculate the value Rz.

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Skewness Measures the symmetry of surface data about a mean data profile,
expressed as:
N
1 1 3
Skewness = --------3- ---- ∑ Z j
Rq N
j=1

where Rq is the Rms roughness. Skewness is a non dimensional quantity

which is typically evaluated in terms of positive or negative. Where
Skewness is zero, an even distribution of data around the mean data plane
is suggested. Where Skewness is strongly non-zero, an asymmetric, one-
tailed distribution is suggested, such as a flat plane having a small, sharp
spike (> 0), or a small, deep pit (< 0).
Surface Area The three-dimensional area of the region enclosed by the cursor box. This
value is the sum of the area of all of the triangles formed by three adjacent
data points.
Surface Area Diff Difference between the analyzed region’s three-dimensional Surface area
and its two-dimensional, footprint area.
Valley Count The number of valleys shorter than the THRESHOLD VALUE.
Z Range Peak-to-valley difference in height values within the analyzed region.

6.4 Section

The Section command displays a top view image, upon which one, two or three reference lines may
be drawn. The cross-sectional profiles and fast Fourier transform (FFT) of the data along the
reference lines are shown in separate windows. Roughness measurements are made of the surface
along the reference lines you define.

Section is probably the most commonly used Offline command; it is also one of the easiest
commands to use. To obtain consistently accurate results, ensure your image data is corrected for
tilt, noise, etc. before analyzing with Section.

• Sectioning of Surfaces: Overview: Section 6.4.1

• Section Procedures: Section 6.4.2

• Section Interface: Section 6.4.3

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6.4.1 Sectioning of Surfaces: Overview

Samples are sectioned to learn about their surface profiles. The Section command does not reveal
what is below the surface—only the profile of the surface itself. When sectioning samples, you
should first ascertain surface topology. Depending upon the topology and orientation of the sample,
the results of Section analysis may vary tremendously.

Figure 6.4a Section Analysis Orientation

1
2

1
2

In Figure 6.4a, the sample surface (a diffraction grating) is sectioned along three axes. Sections 1
and 2 are made perpendicular to the grating’s rules, revealing their blaze and spacings. (Sections 1
and 2 may be compared simultaneously using two fixed cursor lines, or checked individually with a
moving cursor.) Section 3 is made parallel to the rules, and reveals a much flatter profile because of
its orientation.

The Section command produces a profile of the surface, then presents it in the Section grid (see
Figure 6.4b).

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Section

Figure 6.4b Section Command Profile

Generally, Section analysis proves most useful for making direct depth measurements of surface
features. By selecting the type of cursor (Rotating Line, Rotating Box, or Horizontal Line), and
its orientation to features, you may obtain:

• Vertical distance (depth), horizontal distance and angle between two or more points.

• Roughness along section line: RMS, Ra, Rmax, Rz.

• FFT spectrum along section line.

Features are discussed below. Refer to Roughness: Section 6.3 for additional information
regarding roughness calculations.

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6.4.2 Section Procedures

1. Select an image file from the file browsing window at the right of the main window. Double
click the thumbnail image to select and open the image.

2. You can view the Section View using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Section from
the popup menu.

Or

• Select Offline > Section from the menu bar.

Or

• Click the Section icon in the upper toolbar.

3. Before doing a section analysis, ensure that the image is properly oriented by removing any
tilt or bow. This is especially important if a high level of precision is to be employed in
measuring the blaze angle.

4. To remove any tilt which might be present, select Offline > Plane Fit. Set the Planefit
Order parameter in the panel to 1st, then click the Execute button. The image is fitted to a
plane (“leveled”) by fitting each scan line to a first-order equation, then fitting each scan line
to others in the image. At this point, the image has not been appreciably altered, it has only
been reoriented slightly.

5. In Section Analysis, to make a single-line section of the image, use the mouse to draw a line
through the image, as in Figure 6.4c, and note the results.

6. Move the grid cursors along the section to make measurements.

Figure 6.4c Mouse Drawing Line

Use the mouse to drag a line

cursor across the image.

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6.4.3 Section Interface

When a line is drawn on the image, the cross-sectional profile is displayed in the upper right
window, and the FFT spectrum along the line is displayed directly below it (see Figure 6.4d). More
detail about the FFT algorithm used may be found at http://www.fftw.org.

The markers may be positioned in the profile and FFT spectrum. The results window at the bottom
of the display lists roughness information based on the position of the presently selected reference
markers. Each marker pair is color coordinated with the data in the results window.

Figure 6.4d Section View

Grid Markers:

A pair of markers in the section grid and a single marker in the spectrum grid will automatically be
drawn. Place the mouse cursor on the desired marker and left-click to move.

Marker pair 0 Default display color is blue. Slide the markers into the grid from the left or right side by
clicking and holding the left mouse button. Data between the two markers will be dis-
played in the results window at the bottom of the display screen in blue.
Marker pair 1 Default display color is red. Slide the markers into the grid from the left or right side by
clicking and holding the left mouse button. Data between the two markers will be dis-
played in the results window at the bottom of the display screen in red.

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Marker pair 2 Default display color is green. Slide the markers into the grid from the left or right side
by clicking and holding the left mouse button. Data between the two markers will be
displayed in the results window at the bottom of the display screen in green.
Spectrum Marker Displays a slider cursor along the spectral data (e.g., FFT Spectrum).

Results Parameters:

The standard deviation RMS (Rq), mean roughness (Ra), the maximum height (Rmax), and the
10-point roughness (Rz) for the segment between the reference markers are also listed in the
Results window.

Results Parameters:

Length Length of the roughness curve.

RMS (Standard Devia- Standard deviation of the Z values between the reference markers, calcu-
tion) lated as:
2

RMS = σ =
∑ ( Zi – Zave )
-------------------------------------
N

where Zi is the current Z value, Zave is the average of the Z values

between the reference markers, and N is the number of points between the
reference markers.

Ra (Mean Roughness) Mean value of the roughness curve relative to the center line, calculated
as:
L
1
R a = --- ∫ f ( x ) dx
L
0

where L is the length of the roughness curve and f(x) is the roughness
curve relative to the center line.

Rmax (Maximum Height) Difference in height between the highest and lowest points on the cross-
sectional profile relative to the center line (not the roughness curve) over
the length of the profile, L.

Rz (Ten-Point Mean Average difference in height between the five highest peaks and five low-
Roughness) est valleys relative to the center line over the length of the profile, L. In
cases where five pairs of peaks and valleys do not exist, this is based on
fewer points.

Freq. Cutoff (μm) Frequency Cutoff measured in terms of a percentage of the root mean
square.

Changing the cursor on the FFT changes lc, the cutoff length of the high-pass filter applied to the
data. The filter is applied before the roughness data is calculated; therefore, the position of the
cutoff affects the calculated roughness values.

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• Rz Count—number of peaks used for Rz computation

• Radius—radius of circle fitted to the data between the cursors

• Radius Sigma—mean square error of radius calculation

• Surface Distance—distance measured along the surface between the cursors

• Horizontal Distance—horizontal distance between the cursors

• Vertical Distance—vertical distance between the cursors

• Angle—angle of the imaginary line drawn from the first cursor intercept to the second
cursor intercept

• Spectral Period—spectral period at the cursor position

• Spectral Frequency—spectral frequency at the cursor position

• Spectral RMS Ampl.—amplitude at the cursor position

Right-clicking in the bottom results window opens allows you to open a Configure Columns
window, shown in Figure 6.4e, which lets you select which parameters will be computed and
displayed.

Figure 6.4e Configure Columns Window

Mouse Operations for a Rotating Line Cursor:

• Mouse down, drag—Anchors the origin of a line segment and expands from the selected
position, allowing a line segment to be drawn in any direction.

• Mouse up—Anchors the terminal point of the first (dashed) line segment and draws a
moving reference line perpendicular to the fixed-line segment. The cross-sectional

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profile and the FFT along the reference line are displayed at this time. The position of
the moving reference line tracks the movements of the mouse. When the mouse is
stationary, the cross-sectional profile and the FFT of the data along the moving
reference line is updated.

• Clicking on the center of the line and dragging moves the line on the image.

• Clicking on either end of the line rotates the line.

Mouse Operations for Rotating Box Cursor (Right-Click Selection):

• 1st click—Anchors the origin of a box and “rubber bands” out from the center of the
selected position.

• As a reference, the cursor positions show up on the center line in the box.

• Clicking on the box—Allows the box to be moved (cursor inside box), or resized (cursor
on edge of box). Clicking on the corner allows the box to be resized in two directions.

• Holding the Shift button down while clicking on the box and dragging in a circular
direction rotates the box.

Mouse Operations for a Horizontal Line Cursor:

• Mouse down—Draws a horizontal line segment at that location.

• Clicking on the line and dragging moves the line on the image.

Using the Grid Display

Measurement cursors for histogram and cross section views in Depth and Section are provided to
the left and right of the Grid Display. You can bring the cursors into the grid by placing the mouse
cursor onto the measurement cursors, clicking and holding the left mouse button, and dragging
them onto the grid. When you place the mouse cursor onto a measurement cursor, the cursor will
change to a horizontal or vertical double-arrow cursor , which indicates you can grab and drag
this cursor.

Right-clicking on the grid will bring up the Grid Parameters menu (see Figure 6.1e) and allow
you to make the following changes:

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Color Allows operator to change the color of the

• Curve (data)
• Text
• Background
• Grid
• Minor
• Marker
Filter Typically used for a Profiler Scan.
• Type—Select None, Mean (default), Maximum, or Minimum
• Points—Select 4k, 8k (default), 16k, or 32k
Minor Grid Places a minor grid in the background of the Graph Window.
Scale Allows user to auto scale, set a curve mean, or set their own data
range
Line Style For each curve, the operator can choose a connect, fill down, or point
line.
User Preferences Restore—Reverts to initial software settings
Save—Saves all changes operator has made during this session. This
becomes the new default settings.
Copy Clipboard Copies the grid image to the Microsoft Clipboard
Print Prints out the current screen view to a printer
Export Exports data in bitmap, JPEG or XZ data format
Active Curve Determines which curve you are analyzing

Figure 6.4f Grid Parameters Menu

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Step

6.5 Step
The Step command makes relative height measurements between two regions (steps) on sample
surfaces. Typical applications include measuring film thickness and etch depths. Step works
similarly to a Section command with an averaging box cursor, but its operation is simplified.

Step displays a top view of the image, then the user draws a reference line across the regions to be
measured. A height profile is generated from averaged data on either side of the reference line in
the box. Cursors—which are moved along the profile—define specific regions (steps). These may
be measured (Measure button) relative to each other, with or without data leveling (Level button).

6.5.1 Step Interface

The Step interface, shown in Figure 6.5a, includes a captured image and a graph of averaged height
within a selected box. Two pairs of cursors (one black and one red) can be moved across this profile
to define the steps to be measured. The region between each cursor defines a “step.” The marker
position is shown below the height graph.

Figure 6.5a Step Interface

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Step

Step Display Menu Commands

Level

Reorients the profile so that the average height of each step region (between cursor pairs) is equal.

Figure 6.5b Level Option Profile

Measure

Displays the relative height between steps.

Restore

Returns the profile to its original, unleveled form. (Deselects the Level option.)

Results

Vertical Distance

Displays the difference between the average height of each region (between cursor pairs). If the
height of the region between the second pair of cursors is lower than the first’s, this will be a
negative value.

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Using the Grid Display

Measurement cursors for the graph are automatically positioned based on the numerical values
selected in the Input fields. Right-clicking on the grid will bring up the Grid Parameters menu
(see Figure 6.5c) and allow you to make the following changes:

Color Allows operator to change the color of the:

• Curve (data)
• Text
• Background
• Grid
• Minor Grid
• Markers
Filter Typically used for a Profiler Scan.
• Type—Select None, Mean (default), Maximum, or Minimum
• Points—Select 4k, 8k (default), 16k, or 32k
Minor Grid Places a minor grid in the background of the Vision window.
Scale Allows user to auto scale, set a curve mean, or set their own data
range
Line Style For each curve, the operator can choose a connect, fill down, or point
line.
User Preferences Restore—Reverts to initial software settings
Save—Saves all changes operator has made during this session. This
becomes the new default settings.
Copy Clipboard Copies the grid image to the Microsoft Clipboard
Print Prints out the current screen view to a printer
Export Exports data in bitmap, JPEG or XZ data format
Active Curve Determines which curve you are analyzing

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Width

Figure 6.5c Grid Parameters Menu

6.6 Width
To analyze the width of features you have numerous choices which measure the height difference
between two dominant features that occur at distinct heights. Width was primarily designed for
automatically comparing feature widths at two similar sample sites (e.g., when analyzing etch
depths on large numbers of identical silicon wafers).

The Width command is designed to automatically measure width between features distinguished
by height, such as trenches and raised features.

The Width command is best applied when comparing similar features on similar sites. Width
measurement on dissimilar sites is better performed using the Section command.

Refer to the following sections on Width analysis:

• Width Theory: Section 6.6.1

• Width Procedures: Section 6.6.2

• Width Interface: Section 6.6.3

6.6.1 Width Theory

The Width algorithm utilizes many of the same functions found in Depth analysis by accumulating
height data within a specified area, applying a Gaussian low-pass filter to the data (to remove
noise), then rapidly obtaining height comparisons between two dominant features. For example, 1)
the depth of a single feature and its surroundings; or, 2) depth differences between two or more
dominant features. Although this method of width measurement does not substitute for direct,
cross-sectioning of the sample, it does afford a means for comparing feature widths between two or
more similar sites in a consistent, statistical manner.

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Width

The Width window includes a top view image and a histogram; depth data is displayed in the
results window and in the histogram. The mouse is used to resize and position the box cursor over
the area to be analyzed. The histogram displays both the raw and an overlaid, Gaussian-filtered
version of the data, distributed proportional to its occurrence within the defined bounding box.

Histogram

Raw Data

Histograms for depth data are presented on the bottom of the Width window. The histogram peaks
correspond to the distribution of depths of analyzed regions of the image (see Figure 6.6a).

Figure 6.6a Depth Histogram Analysis

0

Analyzed area
40

1
Depth [nm]

Surface
80

2
Pit
120
160

0 0.50 1.0
Correlation

Note: Color of cursor, data, and grid may change if user has changed the settings.
Right-click on the graph and go to Color if you want to change the default
settings.

Correlation Curve

The Correlation Curve is a filtered version of the Raw Data Histogram and is located on the
Depth Histogram represented by a red line. Filtering is done using the Histogram filter cutoff
parameter in the Inputs parameter box.The larger the filter cutoff, the more data is filtered into a
Gaussian (bell-shaped) curve. Large filter cutoffs average so much of the data curve that peaks
corresponding to specific features are unrecognizable. On the other hand, if the filter cutoff is too
small, the filtered curve may appear noisy.

The Correlation Curve portion of the histogram presents a lowpass, Gaussian-filtered version of
the raw data. The low-pass Gaussian filter removes noise from the data curve and averages the
curve’s profile. Peaks which are visible in the curve correspond to features in the image at differing
widths.

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Width

Peaks do not show on the correlation curve as discrete, isolated spikes; instead, peaks are
contiguous with lower and higher regions of the sample, and with other peaks. This reflects the
reality that features do not all start and end at discrete depths.

When using the Width View for analysis, each peak on the filtered histogram is measured from its
statistical centroid (i.e., its statistical center of mass).

6.6.2 Width Procedures

Brief instructions can be found in the Width Analysis Guidelines window below the Inputs
window.

Note: The maximum recommended input file size is 512 lines by 512 samples/line.

1. If no workspace is present, open a new workspace (File > New Workspace).

2. Open the image you wish to analyze (File > Open > Captured Data File) or double click on
the browse view image.

3. You can access the Width view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Width from
the popup menu.

Or

• Select Offline > Width from the menu bar.

Or

• Click the Width icon in the upper toolbar.

4. Using the mouse, left-click and drag a box on the area of the image to analyze.
The Histogram displays the depth correlation on this specified area.

Note: If no box is drawn, by default, the entire image is selected.

5. Adjust the Minimum Peak to Peak to exclude non relevant depths.

6. Adjust the Histogram Filter Cutoff parameter to filter noise in the histogram as desired.

7. Adjust the threshold cursor along the histogram to set the level of the cutoff plane. The
features above or below (depending on Feature Direction) this plane are a single shade in
the selected area.

8. Right-click on the image in a region outside the box and click Select Feature.

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9. Click on various regions inside of the box. Statistics in the table will be generated for each
distinct (as defined by the Input parameters) feature.

Note: To save or print the data, either copy, by right-clicking on the results table, and
paste the text and export the Graphic or XZ Data or run the analysis in an Auto
Program (see Chapter 8).

Figure 6.6b Width Interface

6.6.3 Width Interface

The Width interface includes a captured image, Input parameters and Grid Markers display,
Results table, Guidelines and a depth histogram with grid markers, shown in Figure 6.6c.

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Width

Figure 6.6c Depth Histogram

Width Input Parameters

The depth input parameters below define the slider cursor placement for determining the exact
depth of a feature.

Feature Direction Select above or below to indicate if features above or below the reference
plane are to be analyzed.

Threshold Plane The z height which is used as a minimum for the higher peak. This can be
adjusted by moving the cyan Threshold Depth cursor in the depth histo-
gram.

Number of Histogram Bins The number of data points, ranging from 4 to 512, which result from the fil-
tering calculation.

Reference You may specify a reference point for the cursor. This feature is useful for
repeated, identical measurements on similar samples. After moving the cur-
sor to a specific point on the correlation histogram, that point is saved as a
distance from whatever reference peak you choose. These reference peaks
include: HIGHEST PEAK, LOWEST PEAK.

Histogram Filter Cutoff Lowpass filter which smooths out the data by removing wavelength com-
ponents below the cutoff. Use to reduce noise in the Correlation histogram.

Minimum Peak To Peak Sets the minimum distance between the maximum peak and the second
peak marked by a cursor. The second peak is the next largest peak to meet
this distance criteria.

Distance From Peak % DISTANCE, ABSOLUTE DISTANCE

Distance From Peak Cursor distance from the REFERENCE peak

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Width

Grid Markers

Three user-adjustable markers are placed on the depth histogram:

Threshold Depth Cyan. Distance from peak and distance from peak type.

Lowest Peak Magenta. The right (larger in depth value) of the two peaks marked by the
cursors.

Highest Peak Gold. The left (smaller in depth value) of the two peaks chosen by the cur-
sors. You can adjust min and max peaks by adjusting the MINIMUM
PEAK TO PEAK.

Results Parameters:

X location X location

Y location Y location

X mean The average of the highlighted X values within the enclosed area.

X sigma The standard deviation of the measured X values.

Y mean The average of the highlighted Y values within the enclosed area.

Y sigma The standard deviation of the measured Y values.

Area The area below the threshold in the selected region.

Threshold to Local Minimum The distance from the Threshold Plane to a local minimum.

Threshold to Local Maximum The distance from the Threshold Plane to a local maximum.

Using the Grid Display

Measurement cursors for the histogram are automatically positioned based on the numerical values
selected in the Input fields. Right-clicking on the grid will bring up the Grid Parameters menu
(see Figure 6.6d) and allow you to make the following changes:

Color Allows operator to change the color of the:

• Curve (data)
• Text
• Background
• Grid
• Minor Grid
• Markers

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Width

Filter Typically used for a Profiler Scan.

• Type—Select None, Mean (default), Maximum, or Minimum
• Points—Select 4k, 8k (default), 16k, or 32k
Minor Grid Places a minor grid in the background of the Vision window.
Scale Allows user to auto scale, set a curve mean, or set their own data
range
Line Style For each curve, the operator can choose a connect, fill down, or point
line.
User Preferences Restore—Reverts to initial software settings
Save—Saves all changes operator has made during this session. This
becomes the new default settings.
Copy Clipboard Copies the grid image to the Microsoft Clipboard
Print Prints out the current screen view to a printer
Export Exports data in bitmap, JPEG or XZ data format
Active Curve Determines which curve you are analyzing

Figure 6.6d Grid Parameters Menu

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XY Drift

6.7 XY Drift
Due to temperature differences, thermal lateral drift can occur between two successive images
while scanning. Using Offline XY Drift analysis, the software can calculate the lateral shift
between two images. You can also manually enter the drift.

6.7.1 Offline XY Drift Analysis

Requirements

Two images captured within 1 day of each other are required. The capture direction must be the
same for both images (up or down), and the images must have the same microscope configuration
and scanner calibration properties.

Procedure

To calculate XY Drift using the software:

1. Start with the earlier image and use one of the following methods to open the XY Drift
Analysis view (see Figure 6.7a).

• Right-click on the image name in the Workspace and select Add View > XY Drift
from the popup menu.

Or

• Select Offline > XY Drift from the menu bar.

Or

• Click the XY Drift icon in the upper toolbar.

XY drift corrections calculated from other than the two most recently captured images may not
reflect current environmental conditions.

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Figure 6.7a XY Drift View

2. Use the Load Image button to browse for the subsequent image.

3. Click the Calculate Shift button. The software will calculate the shift of the second image
relative to the first image.

4. The results display in the Results box.

a. To apply the corrections in the Inputs box, click the Apply Correction button.

Or

b. You can also manually enter the correction values in the Inputs box. Click the Apply
Correction button.

Note: Apply Correction effects RealTime by applying a drift correction to the

RealTime images. Do not use Apply Correction if this is not your intent.

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Input Parameters

Statistics used by the XY Drift analysis are defined in this section.

Number of scan lines Specifies the number of lines to calculate.

Flatten Flattens both images before the shift is calculated. (Use the Undo Flatten
button to reverse the flatten).

X Correction Specifies the amount of correction to apply to the X-axis of the scanner.

Y Correction Specifies the amount of correction to apply to the Y-axis of the scanner.

Second Image Defines the location of the second image used in the analysis.

Image resize factor Speeds up the shift calculation by averaging for images larger than 512
pixels

Results Parameters

Results of the XY Drift analysis are presented in this section.

X Shift Specifies the amount of calculated shift along the X-axis of the second
image relative to the first.

Y Shift Specifies the amount of calculated shift along the Y-axis of the second
image relative to the first.

Tested Correlation Reports the correlation coefficient after correcting for the detected shift. A
Coefficient perfect correlation is 1.0. If the tested correlation coefficient is too low,
then the calculation is not valid and should not be applied. You may need
features that have more distinct contrast.

Raw Correlation Reports the correlation coefficient between the two images prior to pro-
Coefficient cessing.

XY Drift Buttons

Load Image Browse to open the second image in the right box.

Calculate Shift Compares left image to right image, and reports the shift statistics in the
Results box.

Apply Correction Applies the correction in the Inputs box to the second image.

Undo Flatten Undo Flatten restores the image to its original form.

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Chapter 7 Modify Commands

The Modify commands are in the lower portion of the Offline menu. Offline appears in the menu
bar once an image is open/active. Modify commands are also available in the Add View submenu
and are accessible with a right-click on the image name in the workspace. Modify commands are
used to eliminate noise and correct for bow and tilt. These operations process the captured/stored
image, then produce another (modified) version of the image

Refer to the following analysis commands available on the NanoScope software:

• Image Filtering using Data Matrix (Kernel) Operations: Section 7.1

• Clean Image: Section 7.2

• Crop and Split: Section 7.3

• Erase: Section 7.4

• Flatten: Section 7.5

• Gaussian: Section 7.6

• Lowpass: Section 7.7

• Median: Section 7.8

• Plane Fit: Section 7.9

• Spectrum 2D: Section 7.10

• Subtract Image: Section 7.11

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Image Filtering using Data Matrix (Kernel) Operations

7.1 Image Filtering using Data Matrix (Kernel) Operations

A number of Offline/Modify image filters use matrix operations to achieve their effects. The
matrix operations include:

• Clean Image

• Gaussian

• Lowpass

• Median

In each of these commands, data is analyzed in kernels (matrices), with every pixel individually
recalculated based upon its neighboring values. For example, data which is undergoing a Median
filter applies a 3 x 3 or 5 x 5 matrix operation to each image pixel. (Most filters utilize 3 x 3
matrices.)

Figure 7.1a Median Filter Example

Pixel a2a3 (height datum) Pixel a2a4

Shift neighborhood
one column right

Image data

Neighborhood A Neighborhood B

In the example in Figure 7.1a, each pixel is individually evaluated within its own local, 5 x 5
“neighborhood.” Neighborhood A has pixel a2a3 at its center. For a Median filter, the 25 pixels in
neighborhood A are evaluated to locate the median value pixel. The median value of neighborhood
A is then mapped to a new pixel a2a3 in a separate data set.

The matrix is shifted over one column to define a new neighborhood (“B”) with pixel a2a4 at its
center. The median value for neighborhood “B” is found, then mapped to pixel a2a4 in the separate
data set. The filtering process is repeated until all pixels have been remapped.

Note: In this and all other matrix operations, pixels are mapped to the new, separate
data set without changing pixel values in the original image data until saved.
(Matrices do not operate cumulatively on previously filtered data.) Filters
include averaging (e.g., Lowpass filter) and non-averaging (e.g., Highpass)
types.

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Image Filtering using Data Matrix (Kernel) Operations

Most filters utilize 3 x 3 pixel matrixes (see Figure 7.1b), which tend to confine averaging effects to
smaller areas. They process image data in a manner similar to the 5 x 5 matrix example in Figure
7.1a.

Figure 7.1b 3 x 3 Pixel Matrix

Pixel a2a2

 
Gaussian filters utilize a 1 x N matrix, where N is determined by the Filter size parameter. In this
instance, image data is analyzed in two-dimensional matrices which are shaped to a Gaussian curve
where the sigma value (σ) is determined by the Filter size parameter. (see Gaussian: Section 7.6.)

Figure 7.1c Gaussian Filter Example

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Clean Image

7.2 Clean Image

The Clean Image command is used to smooth noisy image data within the cursor box you specify.
The Spike cut off and Streak cut off commands define sigma cutoffs for spikes and streaks,
respectively. Data points lying beyond the mean ± designated sigma values (σ) are replaced with
the mean data value.

Figure 7.2a Clean Image Diagram

User-specified
cut off values

−σ
−3σ +σ
+3σ

Affected data Affected data

−2σ μ +2σ

1. Select an image file from the file browsing window at the right of the main window. Double
click the thumbnail image to select and open the image.

2. Open the Clean Image view using one of the following methods:

• From the menu bar, click Offline > Clean Image.

Or

• Right-click on the Image file name in the Workspace and select Add View > Clean
Image from the menu.

Or

• Click the Clean Image icon in the upper toolbar.

3. A separate window opens, also displaying the image. Right-click in the image to display the
Clean Image options menu (see Figure 7.2b).

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Clean Image

Figure 7.2b Clean Image Window

4. Click and drag in the image to define a box.

5. Configure the Input parameters.

6. Click EXECUTE to perform the operation.

7. To restore the unprocessed image, click the RELOAD button.

Figure 7.2c shows the image of Figure 7.2b after a clean operation with Spike and Streak cutoff
both set to 1σ.

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Figure 7.2c Image of Figure 7.2b after 1 clean operation

Clean Image Input Parameters

Remove Spikes Settings:

• ON—Enables the Spike cut off value and applies it to
data within the cursor box you specify.
• Off—Disables the Spike cut off value.
Remove Streaks Settings:
• ON—Enables the Streak cut off value and applies it to
data within the cursor box you specify.
• Off—Disables the Streak cut off value.
Spike Cutoff Number of sigma values to use as the cut off point for spike data. Data
points lying outside the mean ± Spike cut off sigma value(s) are
replaced by the mean data value.
Range:
• 0 to 10
Streak Cutoff Number of sigma values to use as the cut off point for streak data.
Data points lying outside the mean ± Streak cut off sigma value(s) are
replaced by the mean data value.
Range:
• 0 to 10
Output File Name Select the path of the extracted image file. Leave blank for immediate
view/use without saving the altered image file

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Buttons on the Clean Image Panel

Execute Initiates the Clean Image command.

Reload Restores the image to its original form by reloading the original file.

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Crop and Split

7.3 Crop and Split

The Crop and Split function replaces and expands the Zoom function used in version 7.0 and
earlier releases of NanoScope software. Use the Crop and Split function to extract an image from
a large Version 7 image for Version 5 analysis or to inspect only part of an image. NanoScope
Version 5 software features a number of Analysis functions currently not available in Version 7
software. Crop and Split will produce the largest Version 5 image size possible within the bounded
region (128 x 128, 256 x 256 or 512 x 512).

Note: The image produced by this analysis is Version 5 compatible, however, if the
image is later processed by a Version 7 analysis, the image may no longer be
Version 5 compatible.

7.3.1 Crop and Split Procedure

Use the Crop and Split function to isolate a portion of a high resolution image.

1. Open a large Version 7 image (larger than 512 x 512).

2. You can view the Crop and Split view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Crop and
Split from the popup menu.

Or

• Select Offline > Crop and Split from the menu bar.

Or

• Click the Crop and Split icon in the upper toolbar.

3. The selected image opens in the Crop and Split dialog box (see Figure 7.3a).

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Crop and Split

Figure 7.3a Initial Crop and Split Window

Bounding
Box

4. Create a bounding box by dragging the mouse in the image (see Figure 7.3a). Place the
cursor inside the box, and while holding the mouse button, move the box to the location of
interest. If CROP V5 COMPATIBLE is selected, the box is restricted to the largest possible
Version 5-compatible image size (usually 512 x 512).

5. Select the OUTPUT FILE NAME by clicking on the file name and then clicking the box to the
right of the file name. Select a location and name for the new image.

6. Select the CREATE FILE(S) button.

7. Use this new image for further (Version 5 or other) analysis.

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7.3.2 Crop and Split Interface

Input Parameters

Crop V5 Compatible Settings:

• YES—A V5 compatible file (128 x 128, 256 x 256 or 512 x
512) is created from the image.
• No—Crops to arbitrary sizes.
Method Available with CROP V5 COMPATIBLE set to YES.
Settings:
• INTERPOLATE—Data points will be interpolated to create
new image.
• Replicate—Data points will be used as is to create a new
image.
V5 Number of Samples Available with CROP V5 COMPATIBLE set to YES.
Settings:
• 128, 256, 512.
Save Channels Separately Settings:
• Yes— Individual files, named OriginalFileName_crop and
splitN.f07, where N is the channel number (1 through 8), are
created.
• No—One file with all selected channels will be created.
Save Subset File Settings:
• Yes—One file with all selected channels will be created.
• Yes— Individual files, named OriginalFileName_crop and
splitN.f07, where N is the channel number (1 through 8), are
created.

Note: You must select Yes for either the Save

Channels Separately or the Save Subset File
commands.
Output File Name Select the path of the extracted image file.
Include Channels Settings:
• Yes— This channel is included in the output file(s).
• No—This channel is not included in the output file(s).

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Results Parameters

Number of x Points Number of x points in the new image.

Number of y Points Number of y points in the new image.
Aspect Ratio Aspect ratio of the new image.
Scan Size Scan size of the new image. The units of this parameter are volts if the
Units parameter (Other Controls panel) is set to Volts. The units are
linear distance (nm or µm) if the Units parameter is set to Metric.
Error Possible errors:
• No Error—(Default)
• Not Enough X Points—Original image has less than 512
points/line.
• Invalid Aspect Ratio—Zoomed image results in an aspect
ratio greater than 256:1.
• File Write—A disk error occurred.
• Unknown—An unknown error has occurred.

Crop and Split Buttons

Create File(s) An image is created from the portion of the high resolution image that
is contained in the bounding box.

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Erase

7.4 Erase

The Erase modify command is a retouching function for editing images. This function allows
horizontal lines or areas to be replaced with an interpolation from the adjacent lines.

1. Select an image file from the file browsing window at the right of the main window. Double
click the thumbnail image to select and open the image.

2. Open the Erase view using one of the following methods:

• From the menu bar, click Offline > Erase.

Or

• Right-click on the Image file name in the Workspace and select Add View > Erase
from the menu.

Or

• Click the Erase icon in the upper toolbar.

3. A separate window opens, also displaying the image. Right-click in the image to display the
Erase options menu (see Figure 7.4a). Select either Horizontal Line or Area and a check
mark will appear. The option chosen will remain checked until another selection is made.

4. Click anywhere within the image to define a horizontal line, or click and drag in the image to
define a box to be replaced.

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Figure 7.4a Erase Options Menu

5. Click the Execute button to perform the interpolation.

Figure 7.4b Effect of the Erase Interpolation on a Rectangular Area

Before After

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6. Right-click on an Erase feature of a modified image (either line or box) for options to
complete the operation. Click Delete to erase the dashed construction lines from the display
of the selected feature. Click Clear All to eliminate all construction lines from the display,
while retaining the modifications to the image.

7. To eliminate all trace of Erase activity to an image, click the Reload button while the image
is still open in the Erase panel.

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Flatten

7.5 Flatten

The Flatten command eliminates unwanted features from scan lines (e.g., noise, bow and tilt). It
uses all unmasked portions of scan lines to calculate individual least-square fit polynomials for
each line.

Flatten is useful prior to image analysis commands (e.g., Depth, Roughness, Section, etc.) where
the image displays a tilt, bow or low frequency noise, which appear as horizontal shifts or stripes in
the image.

Figure 7.5a Image Flattened

Bow Removed

Bow in Image

Refer to the following sections on Flatten analysis:

• Flatten Theory: Section 7.5.1

• Flatten Procedures: Section 7.5.2

• Flatten View Interface: Section 7.5.3

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7.5.1 Flatten Theory

The Flatten command is a filter that modifies the data to delete low frequency noise and remove
tilt from an image. Each line is fit individually to center data (0th order) and remove tilt (1st order),
or 2nd or 3rd order bow. A best fit polynomial of the specified order is calculated from each data
line and then subtracted out. In some cases, the stopband (box cursor to exclude features) can be
used to remove regions of the image from the data set used for the polynomial fits. Click on the
image to start drawing a stopband box. Right-click on a box to delete it or change its color.

Flatten Polynomials

The polynomial equations calculate the offset and slope, and higher order bow of each line for the
data (see Table 7.5a).

Table 7.5a Flatten Polynomials

Order Polynomial Explanation

0 z=a Centers data along each line.
1 z = a + bx Centers data and removes tilt on each
line [i.e., calculates and removes off-
set (a) and slope (b).
2 z = a + bx + cx2 Centers data and removes the tilt and
bow in each scan line, by calculating
a second order, least-squares fit for
the selected segment then subtracting
it from the scan line.
3 z = a + bx + cx2 + dx3 Centers data and removes the tilt and
bow in each scan line, by calculating
a third order, least-squares fit for the
selected segment then subtracting it
from the scan line.

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7.5.2 Flatten Procedures

For an image that contains a number of noisy scan lines, use the Flatten command to correct the
problem.

1. Open the image. Note disjointed scan lines which are misaligned along the Z-axis (some are
high and some are low). This effect somewhat resembles an unshuffled deck of cards when
viewed on-edge or appears as horizontal streaks or bands. The image may have bow along its
Y-axis.

Figure 7.5b shows an image file in its original, raw form as an example for the Flatten command.
Many of the image’s scan lines are disjointed along the Z-axis.

Figure 7.5b Raw Image of Syndiatatic Polystyrene (500nm)

Top View of Image to Flatten Surface Plot of Image showing Bow

2. You can view the Flatten view using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Flatten from
the popup menu.

Or

• Select Offline > Flatten from the menu bar.

Or

• Click the Flatten icon in the upper toolbar.

3. Set the Flatten Order value to 0TH. This removes the scan line misalignment.

4. Click Execute to initiate the Flatten command. The flattened image appears on the display
screen.

Note: Figure 7.5c shows the same image file after using a zero-order Flatten (Flatten
Order = 0TH). The scan lines are now aligned.

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Figure 7.5c Flattened Image of Syndiatatic Polystyrene (500 nm)

Top View of Flattened Image Surface Plot View of Flattened Image

5. To see a variety of effects using the Flatten command, enter different Flatten order values.
Each new change may be undone by clicking on the Reload button.

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7.5.3 Flatten View Interface

Click Offline in the menu bar and select Flatten, or click on the Flatten icon in the tool bar. A
series of parameters appear in the Flatten View, allowing the order of the flatten polynomial to be
selected and display parameters to be adjusted to your preference.

Figure 7.5d Flatten View

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Input Parameters:

Range and Settings:

Flatten Order Flatten Order selects the order of the polynomial calculated and sub-
tracted from each scan line.
Settings:
• Zero Order (0th)—Removes the Z offset between scan lines
by subtracting the average Z value for the unmasked segment
from every point in the scan line.
• First Order (1th)—Removes the Z offset between scan lines,
and the tilt in each scan line, by calculating a first order, least-
squares fit for the unmasked segment then subtracting it from
the scan line.
• Second order (2nd)—Removes the Z offset between scan
lines, and the tilt and bow in each scan line, by calculating a
second order, least-squares fit for the unmasked segment then
subtracting it from the scan line.
• Third order (3rd)—Removes the Z offset between scan lines,
and the tilt and bow in each scan line, by calculating a third
order, least-squares fit for the unmasked segment then
subtracting it from the scan line.

Flatten Z Thresholding Specifies the range of data to be used for the polynomial calculation
Direction based on the distribution of the data in Z:
Range or Settings:
• Use Z >= —Uses the data whose Z values are greater than or
equal to the value specified by the Z thresholding %.
• Use Z <—Uses the data whose Z values are less than the value
specified by the Z thresholding %.
• No thresholding—Disables all thresholding parameters.
Flatten Threshold for Applies the Thresholding values for the whole image or each line inde-
pendently.
Range or Settings:
• The whole image
• Each line
Flatten Z Threshold % Defines a Z value as a percentage of the entire Z range in the image (or
data set) relative to the lowest data point.
Output File Name Specifies the name of the file to be created. Leave blank for immediate
view/use without saving the altered image file.

Buttons on the Flatten Panel

Execute Initiates the command, based on the order selected.

Reload Restores the image to its original form by reloading the original file.

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Gaussian

7.6 Gaussian

The single axis GAUSSIAN Filter permits analysis of images along either the X or Y axis with a 1-
by-X kernel you define specified in Gaussian terms. The FILTER SIZE value corresponds to the
sigma (σ) value of the Gaussian curve, encompassing approximately 68 percent of the data with the
symmetric Gaussian curve centered over the operated-upon pixel.

Larger Filter size values distribute the curve broadly (see Figure 7.6a). During LOWPASS filtering,
this lends greater weight to values farther away from the pixel and increases the Gaussian filter’s
averaging effects upon the image. During HIGHPASS filtering, this subtracts a decreased average
from each pixel, lessening the filter’s impact.

Figure 7.6a Larger Filter Size

S M S

/DUJHU)LOWHUVL]H

Smaller Filter size values concentrate curve data around the center value (see Figure 7.6b).

Figure 7.6b Smaller Filter Size

S M S

6PDOOHU)LOWHUVL]H

During Lowpass filtering, this lends less weight to pixels distant from the center, decreasing the
Gaussian filter’s ability to average local pixels with distant ones—the filter’s impact is lessened.
During Highpass filtering, the larger and more localized pixel average being subtracted from the
operated-upon pixel value yields an enhanced impact upon the image.

Note: Filter size is specified in units of Distance, Spatial Frequency, Time,

Temporal Frequency, and #pixels.

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7.6.1 Gaussian Filter Panel

The Gaussian Filter panel is shown in Figure 7.6c.

Figure 7.6c Gaussian Filter Panel

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Parameters in the Gaussian Filter Panel

Filter size Size of the scan line to be operated upon by the Gaussian filter kernel.
This value is expressed in the Cutoff Units specified below.
Range and Settings:
• Minimum = 3 pixels
• Maximum = one-half scan size
Filter Axis Settings:
• HORIZONTAL—Applies the one dimensional Gaussian filter
along the X axis.
• Vertical—Applies the one dimensional Gaussian filter
along the Y axis.
Cutoff Units Selected units are applied simultaneously to the Filter size. (The #pix-
els field displays the pixel equivalent of the current Filter size value.)
Range and Settings:
• DISTANCE
• SPATIAL FREQUENCY
• TIME
• TEMPORAL FREQUENCY
Filter Type Range and Settings:
• LOWPASS filtering allows longer wavelength features
through while filtering out shorter wavelength features. The
net effect is to remove noise in the form of spikes and fuzz on
the image.
• HIGHPASS filtering allows shorter wavelength features
through while filtering out longer wavelength features.
#pixels The current FILTER SIZE in pixel units. This value may be used to
both enter and monitor the FILTER SIZE.
Range and Settings:
• Minimum = 3 pixels
• Maximum = one-half scan size
Output File Name Select the path of the extracted image file. Leave blank for immediate
view/use without saving the altered image file

Buttons on the Gaussian Panel

Execute Applies the Gaussian Filter to the currently loaded image.

Reload Restores the image to its original form by reloading the original file.

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7.6.2 Gaussian Kernel Algorithm

The general equation used to generate a 1-by-(N+1) Gaussian kernel is:

1 i 2
– --- ⎛ ---⎞
1 2 ⎝ σ⎠
f i = -------------- e
σ 2π

Where i is in units of pixels, and σ is set by the Filter size value. Using this kernel, the filter output
is:
⎛N ---- ⎞
⎜ 2 ⎟
Lowpass pixel value a 0' = ⎜ ∑ a i f i⎟
⎜ ⎟
⎜ –N ⎟
⎝ ------
2
- ⎠

N-
⎛ --- ⎞
⎜ 2 ⎟
Highpass pixel value a 0' = a 0 – ⎜⎜ ∑ a i f i⎟⎟
⎜ –N ⎟
⎝ ------
2
- ⎠

The actual impact of filtering on an image is best demonstrated by reviewing examples of images
before and after filtering. In the following example, both Lowpass and Highpass Gaussian filter
capabilities are demonstrated.

7.6.3 Lowpass Gaussian Filtering

During LOWPASS filtering, the Gaussian Filter has a unique ability to average features oriented
orthogonally to the scan frame. For example, the Gaussian filter can average features running
parallel to an image’s Y scan axis while leaving features relatively unchanged along the X axis, or
vice versa. This is a similar capability to the Spectrum 2D (see Section 7.10) function; however, it
is more unidirectional (i.e., strictly operating along the X or Y axis). One such example is provided
in the three views of a diffraction grating in Figure 7.6d.

The grating image Scan size is 1.872 microns. Applying a Gaussian Filter with Filter size of 250
nm along the Y Filter axis results in view B. Notice that rulings running parallel to the Y axis are
smoothed along their length by the filter, while features oriented orthogonal to the Y axis remain
relatively unchanged. This results in an idealized (averaged) profile of the X axis.

In view C, the Filter size values is unchanged; however, the Filter axis has been rotated 90° to the
X axis. The filter’s impact upon the image here is very dramatic, destroying the ruling features in
the image by averaging across their profile. The result is an almost flat surface.

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Figure 7.6d Views of Diffraction Grating

A. Original image.

B. Filter axis = Y.

C. Filter axis = X.

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7.6.4 Highpass Gaussian Filtering

Applications for HIGHPASS filtering are limited to detecting smaller features. Generally, higher
frequency (shorter wavelength) features are enhanced, while sacrificing lower frequency (longer
wavelength) features and height data.

One example of applying a Gaussian Highpass filter is provided in Figure 7.6e.

This 27.41-micron, MFM image reveals magnetic domains in a permalloy specimen. Although
magnetic domains are visible on the original image, you may apply a Gaussian highpass filter to
highlight boundaries between domains.

Figure 7.6e Magnetic Domains in a Permalloy Specimen

Figure 7.6e shows the magnetic force microscopy (MFM) image in its original form. This is an
early MFM image of a permalloy specimen, and contains artifacts which are significantly reduced
in phase analyzed images. Magnetic force is represented in the image as height data. Suppose the
microscopist wanted to highlight the magnetic boundaries without regard to magnetic force (height
data). A Gaussian Highpass filter would be appropriate.

7.6.5 Procedure for the Gaussian Command

1. Select an image file from the file browsing window at the right of the main window. Double
click the thumbnail image to select and open the image.

2. Open the Gaussian view using one of the following methods:

• From the menu bar, click Offline > Gaussian.

Or

• Right-click on the Image file name in the Workspace and select Add View > Gaussian
from the menu.

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Or

• Click the Gaussian icon in the upper toolbar.

3. A separate window opens, also displaying the image.

4. Configure the Input parameters.

5. Complete the Output File Name field to save the result.

6. Click EXECUTE to perform the Gaussian filtering operation.

7. To restore the unprocessed image, click the RELOAD button.

Highpass Gaussian Filter Example

Example Explanation. First, the image is filtered along the X-axis by setting the Filter axis to
HORIZONTAL. Clicking Execute activates the Gaussian filter,—the result is shown in Figure 7.6f,
View A. Notice that features running parallel to the X-axis (e.g., the tips of each oval area) are
washed out, while features running perpendicular to the X-axis are enhanced. Enter an OUTPUT
FILE NAME to save the results for additional processing.

Figure 7.6f Gaussian Highpass-Filtered Images

X Filter Axis Y Filter Axis Composite Image

- =

A B C

Next, reload the image and filter along the Y-axis by setting the Filter Axis to VERTICAL. Clicking
Execute activates the Gaussian filter—the result is shown in Figure 7.6f, View B. Notice that
features running parallel to the Y-axis (e.g., the sides of each oval area) are washed out, while
features running perpendicular to the Y-axis are enhanced. Enter an OUTPUT FILE NAME to save
the results for additional processing.

To construct a composite image of the two Gaussian-filtered images, add them together. (This can
be accomplished by subtracting an inverted image from another image.) A composite of the two
filtered images is shown in Figure 7.6f, View C. This shows the domain boundaries clearly;
however, all Highpass filtered images have lost their height data, including the composite.

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7.7 Lowpass

The Lowpass modify command applies spatial filtering to a captured image, suppressing high
spatial frequency components. Each pixel in an image is replaced with the average value of the
3 × 3 pixels centered on it.

1. Select an image file from the file browsing window at the right of the main window. Double-
click the thumbnail image to select and open the image.

2. Open the Lowpass view (see Figure 7.7a) using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Lowpass
from the popup menu.

Or

• Select Offline > Lowpass from the menu bar.

Or

• Click the Lowpass icon in the upper toolbar.

Figure 7.7a Lowpass Image Display

3. Select the OUTPUT FILE NAME.

4. Click the Execute button in the Lowpass window to apply the low pass function to the copy
of the image in both windows.

5. To restore the unprocessed image, click the Reload button.

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Note: There are no parameter controls for the Lowpass modify command.

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Median

7.8 Median

The Median modify command is similar to Lowpass; it reduces the contributions of high spatial
frequency, reducing contrast in regions of high contrast. For each pixel in an image, Median
substitutes the median pixel value of the n×n array of pixels centered around that pixel. The size of
the filter’s sliding window pixel array is set under Inputs > Median Order. Figure 7.8a illustrates
the effect of three different size pixel arrays applied to the same image.

Figure 7.8a # Different Pixel Arrays of the Same Image

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1. Select an image file from the file browsing window at the right of the main window. Double-
click the thumbnail image to select and open the image.

2. Open the Median view using one of the following methods to open a separate window which
also displays the image (see Figure 7.8b):

• From the menu bar, click Offline > Median.

Or

• Right-click on the Image file name in the Workspace and select Add View > Median
from the menu.

Or

• Select the Median icon.

3. Select the Median Order from the Inputs menu: 3×3, 5×5, 7×7, 9x9, or 11×11.

4. Choose an Output File Name.

5. Click Execute to apply the Median filter.

6. Click Reload to start over.

Figure 7.8b Median View

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Plane Fit

7.9 Plane Fit

The Plane Fit command computes a single polynomial of a selectable order for an image and
subtracts it from the image. The Plane Fit operation can be applied to either or both of the XY
directions.

Box cursors or passbands allow specific points to be used in the calculation of the polynomial.
Click on the image to start drawing a passband box. Right-click on a box to delete it or change its
color.

Figure 7.9a illustrates an image with tilt and bow which could affect the analysis of the surface
data.

Figure 7.9a Visual Representation of Plane Fit

Tilt of Sample Surface 3rd Order Plane Fit

Refer to the following sections on Plane Fit analysis:

• Fitted Polynomials: Section 7.9.1

• Plane Fit Procedures: Section 7.9.2

• Plane Fit Interface: Section 7.9.3

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7.9.1 Fitted Polynomials

Refer to Table 7.9a to view the polynomials that calculate the best plane fit for the images in the
Plane Fit Auto function.

Table 7.9a Plane Fit Auto Equations

Order Variable Polynomial Equation

0 X z=a
Y z=a
XY (Add Higher Order Cross z=a
Terms for XY OFF)
XY (Add Higher Order Cross z=a
Terms for XY ON)
1 X z = a + bx
Y z = a + by
XY (Add Higher Order Cross z = a + bx + cy
Terms for XY OFF)
XY (Add Higher Order Cross z = a + bx + cy + dxy
Terms for XY ON)
2 X z = a + bx + cx2
Y z = a + by + cy2
XY (Add Higher Order Cross z = a + bx + cy + dxy + ex2 + fy2
Terms for XY OFF)
XY (Add Higher Order Cross z = a + bx + cy + dxy + ex2 + fy2+ gxy2 + hx2y +
Terms for XY ON)
ix2y2
3 X z = a + bx + cx2 + dx3
Y z = a + by + cy2 + dy3
XY (Add Higher Order Cross z = a+ bx + cy + dxy + ex2 + fy2 + gxy2 + hx2y +
Terms for XY OFF)
jx3 + ky3
XY (Add Higher Order Cross z = a + bx + cy + dxy + ex2 + fy2+ gxy2 + hx2y +
Terms for XY ON)
ix2y2 + jx3 + ky3 + lxy3 + mx2y3 +nx3y3 +ox3y +
px3y2

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7.9.2 Plane Fit Procedures

Use Plane Fit to correct the image distortion as follows:

1. Open an image file from the menu bar (File > Open > Image) or through Browse (View >
Browse), then double click on the image.

2. You can view the Plane Fit View using one of the following methods:

• Right-click on the image name in the Workspace and select Add View > Plane Fit
from the popup menu.

Or

• Select Offline > Plane Fit from the menu bar.

Or

• Click the Plane Fit icon in the upper toolbar.

Note: The Plane Fit input parameters appear along with the top view image.

3. Select X, Y, or XY as the Plane Fit Mode.

4. Select the Plane Fit Order as 0TH, 1ST, 2ND or 3RD.

5. Click Execute.

6. Notice that the image distortion is removed, reflecting a flat, planar profile.

Figure 7.9b Saddle Image Before Plane Fit

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Figure 7.9c Plane Fit View

Figure 7.9d Plane Fit Image

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Now, experiment with this image to explore the range of Plane Fit capabilities. Try the following:

• Change the Plane Fit Order value to see its effects. Notice that there is a vast
difference between a value of 1, 2 or 3.

• Try plane fitting in one axis (for example, X), but not the other. This generally keeps
whatever distortions are presently oriented along the unused axis. For example, the
image can be straightened along its Y axis, while leaving the X axis strongly bowed.

• Try using a different Plane Fit Order for the X and Y axis (for example, a setting of 3
for X, but a setting of 1 for Y.) This is similar to using one axis, but not the other.

• Compare the effect of Plane Fit with Flatten. Notice that each command has a
significantly different impact; although, the difference is less noticeable for some types
of images.

7.9.3 Plane Fit Interface

The Plane Fit dialog box, shown in Figure 7.9e, allows the display parameters and the Plane Fit
Order to be adjusted to your preferences.

Figure 7.9e Plane Fit Inputs Dialog Box

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Input Parameters:

Plane Fit Mode X, Y, XY

Plane Fit Order Selects the order of the plane calculated and subtracted from the image.
Settings:
• 0th—centers data.
• 1st—removes tilt.
• 2nd—removes 2nd order bow.
• 3rd—removes 3rd order bow.

Z Thresholding direc- Specifies the range of data to be used for the polynomial calculation based on
tion the distribution of the data in Z:
Range or Settings:
• Use Z > = —Uses the data whose Z values are greater than or equal to
the value specified by the Z thresholding %.
• Use Z <—Uses the data whose Z values are less than or equal to the
value specified by the Z thresholding %.
• No Thresholding—Disables all thresholding parameters.

Z Thresholding Per- Defines a Z value as a percentage of the entire Z range in the image (or data
cent set) relative to the lowest data point.

Add Higher Order Turning this on adds higher order cross terms to the polynomial fit when XY
is chosen (see Table 7.9a).

Output File Name Select the path of the extracted image file. Leave blank for immediate view/
use without saving the altered image file.

Buttons on the Plane Fit Window:

Execute Initiates the plane fit operation.

Reload Restores the image to its original form.

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Spectrum 2D

7.10 Spectrum 2D

The Spectrum 2D (two-dimensional) function transforms images into the frequency domain via a
2D fast Fourier transform (FFT), then allows you to selectively pass or remove specific frequencies
from the image. After selected frequencies are passed or removed, the image is reconstructed,
yielding an improved version. The Spectrum 2D function is extremely useful in removing
electrical and acoustic noise from images, and may also be used to isolate certain surface features
(e.g., lathe lines on turned surfaces, load marks on ground or polished surfaces, etc.).

Noise removable using the Spectrum 2D function generally consists of two types: 1) high
frequency electrical noise (most visible at atomic resolution); 2) lower-frequency acoustic noise
from floor vibrations, air blowers, etc. The 2D spectral display is scaled according to the scan size
of the original image

7.10.1 Spectrum 2D Procedures

Before beginning, it is advisable to make a backup copy of the original image file. The Spectrum
2D function is capable of making major changes to the image which, if saved, can destroy the
original data.

The Spectrum 2D command allows filtering of images in the frequency domain through the 2-
dimensional fast Fourier transform (FFT). The 2-D FFT (power spectrum) of the image is
calculated and displayed. As the cursor is moved through the 2D plot, instantaneous results are
displayed. Rectangular boxes representing either frequencies to pass (multiply by 1.0), passband, or
frequencies to stop (multiply by 0.0), stopband, can then be selected. Finally, the inverse transform
is performed on the filtered transform data to reconstruct a new filtered image.

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7.10.2 Spectrum 2D View

The Spectrum 2D view, shown in Figure 7.10a, allows display parameters to be adjusted to your
preferences.

Figure 7.10a The Spectrum 2D View

Input Parameters in the Spectrum 2D Panel

Output File Name Select the path of the modified image file.

Buttons in the Spectrum 2D Panel

FFT Initiates the two-dimensional FFT calculation.

INVERSE FFT Computes the modified image using the filter parameters
defined in the FFT step.
RELOAD Reloads the original image.

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Controls in Spectrum 2D

Right-clicking an image in a Spectrum 2D, shown in Figure 7.10b, window:

BOX Puts the mouse in the passband mode. This allows placement
of passband boxes which set the frequency data outside the
boxes to zero. Data inside the boxes is passed.
STOP BAND Puts the mouse in the stopband mode. This allows placement
of stopband boxes which set the frequency data within the
boxes to zero. The data outside of the boxes is passed. Stop-
bands appear on the top view image as “X-ed” rectangles.

Figure 7.10b Select BOX or STOPBAND

Stop Band

Box

Right-clicking inside a BOX or STOP BAND box in an (Fourier transformed) image, shown in
Figure 7.10c, window:

DELETE Erases the passband Box or Stopband box that enclose the cur-
sor.
CLEAR ALL Deletes all passband Box and Stopband boxes.
SET COLOR Allows you to set the cursor and/or box colors.

Figure 7.10c DELETE, SET COLOR and CLEAR ALL buttons are active inside a passband or STOPBAND
window.

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Results Parameters in Spectrum 2D

X PERIOD Spatial frequency in the x direction. The lowest frequency is at

the center of the plot.
Y PERIOD Spatial frequency in the y direction. The lowest frequency is at
the center of the plot.
R PERIOD Spatial frequency in the radial direction.
ANGLE Arctangent of (y/x).

MAX AMP The maximum amplitude (0-peak) of the transformed image.

MAX RMS AMP The maximum of the RMS amplitude of the transformed image.

MAX POWER The maximum power of the transformed image.

MAX PSD The maximum power spectral density of the transformed image.

AMP The amplitude of the 2D FFT at that spatial frequency.

RMS AMP Amp/(sqrt(2))

POWER Amplitude2 = (2D FFT)2

PSD Normalized power spectrum per number of points = (2DFFT * #
x_points * # y_points)2/(# x_points * # y_points)
REL AMP Amplitude/(Max Amplitude)

REL PSD PSD/(Max PSD)

Hints for Optimizing the Spectrum 2D Command

• If any passband boxes exist on the display, then data outside the passband boxes is
deleted. Thus, it is superfluous to have a stopband box completely outside the confines
of a passband box.

• Due to the symmetry of the transformed data about the line f x = – f y , all stopband and
passband boxes drawn actually produce two boxes on the display.

See also: Offline/Modify menu: Lowpass: Section 7.7 command.

7.10.3 Example 1—Simplifying an Image

Regarding data contained within an image, more data is not always better. Sometimes it is desirable
to eliminate components of an image to better isolate and accentuate another component of direct
interest. The following example demonstrates how to utilize the Spectrum 2D function to simplify
an image for analysis. The image utilized here is of lathed plastic used in the manufacture of
contact lenses.

1. Load an image from the IMAGES DIRECTORY (or in the IMAGES folder on your installed
system). Examine the image using the 3D Surface Plot function.

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Supposing you want to make a general, cross-sectional inspection of the sample’s lathe lines, it
may prove helpful to remove spikes and smaller, jagged features on the surface. Notice the surface
topology may be analyzed in terms of two dominant influences: 1) lathe lines running parallel to
the image’s Y-axis; 2) a contiguous, jagged aspect to each lathe line (i.e., the lines themselves are
not smooth streaks, but present a jagged profile along their length). Because the parallel lathe lines
occur at longer wavelengths than the short-wavelength, jagged bumps and spikes, it is possible to
separate these components using 2D spectral analysis.

2. With the image selected, click on Spectrum 2D. The Spectrum 2D panel appears as does
the image. Click the FFT button.

The 2D spectrum of the image appears in the Spectrum 2D image window as a clustering of data
having a narrow, horizontal band. This horizontal band reveals the prominence of the parallel lathe
lines, and the fact that they are distributed uniformly along the X-axis of the image.

As the cursor is moved through the 2D plot, the x period, y period and r period values are
displayed in a box to the right of the plot. Moving the cursor through the data cluster reveals that
shorter wavelengths lie around the periphery of the plot, while longer wavelengths lie near the
plot’s center. Notice that the plot is bandwidth limited at its exact center; that is, nothing larger than
the scan size of the image may be plotted here.

Note: The term “wavelength” as used throughout applies to actual surface features,
NOT the color of light used to represent those features.

The trick to using 2D spectral filtering lies in first identifying wavelength components of interest to
you. This requires some interpretive ability on your part and is perfected with practice. When the
sought-after component is identified, all that remains is to remove everything else.

One use of 2D spectral modification is in removing high frequency components, commonly

referred to as “noise.” (Whether the component is referred to as “noise,” or simply as “high
frequency features” of an image is analogous to whether or not to call unwanted plants “weeds.”)
High frequency components are rendered on images as finely spaced, jagged lines, spikes and fuzz.

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Assuming you want to remove high frequency noise, you would seek to eliminate outer portions of
the plot. This is easily done with the Spectrum 2D function by enclosing the central cluster of the
plot within a passband drawn on the transformed image.

The objective here is to pass (allow) the central, longer wavelength portions of the plot, while
stopping (disallowing) the shorter wavelength components located around the periphery of the plot.
The x period and y period of the enclosed area are displayed to the right as the boxes are drawn.

3. Click on Cursor / Box, then draw a passband box around the central portion of the 2D
spectral plot. Click INVERSE FFT to reconstruct the image with the high frequency
components removed. To obtain the best view of the image, click on the Offline / 3D
Surface Plot function (or 3D Surface Plot icon button). Changes to the image are most
obvious when viewing from an elevated angle.

When the image is reconstructed with its high frequency components removed, the most obvious
change is smoother, more contiguous image features. Jagged lines and spikes are reduced,
accentuating the longer wavelength features.

Note: Filtering may also be accomplished by utilizing the Offline / (Modify) >
Lowpass filter, although without selective wavelength controls.

7.10.4 Example 2—Highlighting Features Using 2D Spectrum Modification

Another use of the Spectrum 2D function is in highlighting certain surface features by filtering out
unwanted wavelengths. Continuing with the example of the lathed plastic, it is possible to isolate
and accentuate lathe lines. (This might prove useful to an analyst intending to examine how cutting
tool geometry imparts features to the surface of the plastic.) Conversely, it may also be used to
isolate and accentuate smaller surface features inherent within lathe lines, while reducing the
separation between lines.

1. Reload the image file used in Section 7.10.3; but do not save the previously filtered version
of the image. When the image is reloaded, select the Offline > Spectrum 2D function, then
click on the FFT button. As before, the 2D spectrum of the image is plotted. To isolate the

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lathe lines, draw a thin, horizontal passband box across the center of the plot (see Figure
7.10d).

Figure 7.10d Horizontal Passband Box Illustration

The intent is to pass most wavelengths inherent in the horizontally distributed lathe lines, while
stopping those wavelengths inherent in the vertically distributed features of each line (i.e., the
jagged contour running along each individual line). After the passband box is drawn, click on the
Inverse FFT button to reconstruct the image. Use the Offline> 3D Surface Plot function to look
closer at the reconstituted image. The change in the image quickly becomes evident; lathe lines
stand out more dramatically and have been smoothed along their length. By analyzing a section
across the lathe lines (Offline / Analyze > Section), a cleaner profile of lathe lines in the plastic is
obtained.

The vertically distributed features of the lathe lines may be similarly examined by filtering out the
horizontal components. By drawing a passband box vertically, it is possible to isolate and
accentuate the features running along each individual lathe line (see Figure 7.10e)

Note: This type of analysis might prove helpful in a study of how tool chatter affects
the surface, without regard to tool geometry.

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Figure 7.10e Vertical Passband Box Illustration

7.10.5 Example 3—Removing External Noise

In Example 1 above (see Section 7.10.3), high frequency surface noise was removed by drawing a
passband around the center spectral plot of the image. This type of noise tends to be evenly
distributed across the surface and is inherent to the surface itself. Another type of noise is externally
introduced, either due to electrical noise (especially during extremely high resolution, atomic
scans), or due to acoustic noise introduced from air blowers, loud sounds, etc. Distinguishing one
type of noise from another requires some experience. Here are a few guidelines.

• Steady acoustic noise (such as from a constant pitch sound or moving air) and steady
electronic noise, introduce diagonal bands to the image. These bands run parallel and
are produced when the noise is introduced in sync with the scan. If the bands change
their angle of orientation when the Scan size or Scan rate is altered, they are probably
from this source. This type of noise can be easily removed from the image by using the
Spectrum 2D function.

• Sporadic noise (such as from sudden, loud noises and/or powerful EMF spikes)
introduce isolated “noise lines” which run partially or completely across the image.
These may arise sporadically and without pattern. This type of noise cannot be removed
from the image using the Spectrum 2D function; however, another function (Offline/
Modify > Erase) easily removes this type of noise.

• To remove the diagonal bands characteristic of steady acoustic and electronic noise
using the Spectrum 2D function, do the following:

1. Load the image, then click on the Offline/Modify > Spectrum 2D function. Click the FFT
button to obtain the image’s 2D spectral plot. If the image is of a more or less isotropic
surface, search the spectral plot for bright “hot spots”—small islands of high spectral
concentration—near its center.

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Figure 7.10f Spectrum 2D Hot Spots

Spectral “Hot Spots”

Note: Click on the Zoom / 4:1 function to obtain a closer view of the “hot spots.”

Depending upon the distribution and orientation of the noise bands, the hot spots should be
distributed at the same angle in the spectral plot as they are on the image. There may also exist
other spectral hot spots which are actually part of the surface features; however, these are usually
distributed at some other orientation. If the surface is anisotropic and includes some type of
banding features naturally, isolating the noise bands proves more difficult, especially if they run
parallel to the noise bands.

When the hot spots are located, draw a stopband box around them, then click on the INVERSE FFT
button to reconstruct the image. The image should now appear without the noise bands. If noise
bands are still present, click on the RELOAD option and try again by stopbanding different hot
spots.

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Subtract Image

7.11 Subtract Image

The Subtract Image command enables data from one image to be subtracted from another. This
proves most useful when comparing two or more images from a surface to determine changes over
time, or to compare completely different images. The Subtract Image command cannot be directly
applied to images having different pixel sizes (Number of samples value). For example, a 256 x
256 pixel image cannot be directly subtracted from a 512 x 512 image.

Figure 7.11a diagrams an image subtraction and its effects. Surface 2, when subtracted from surface
3, yields surface 1 (“3” - “2” = “1”). Conversely, surface 1 plus surface 2 yields surface 3 (“1” + “2”
= “3”).

Figure 7.11a Effects of Image Subtraction

1

2771-110

2
3

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Subtract Image

1. Select an image file from the file browsing window at the right of the main window. Double-
click the thumbnail image to select and open the image.

2. Open the Subtract Image view using one of the following methods to open a separate
window which also displays the image (see Figure 7.11b):

• From the menu bar, click Offline > Subtract Image.

Or

• Right-click on the Image file name in the Workspace and select Add View > Subtract
Image from the menu.

Or

• Select the Subtract Image icon.

Figure 7.11b Subtract Image View

3. Select a file to subtract from the Inputs > Image to Subtract menu or click the LOAD
IMAGE button to browse for a file.

4. If necessary, right click in either panel to change the channel.

5. Click Subtract Image to subtract the image in the right panel from the image in the left
pane. The result, which overrides the data in the active channel, is shown (see Figure 7.11c)
in the left panel of the Subtract Image view.

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Subtract Image

Note: When Data types are not the same, the calculation is performed as follows:

• First Image Relative Z scale * first (left) image - Second image Relative Z scale
* second (right) image = new image. The Relative Z scale must be greater than
- 32767 and less than 32767.

6. Click Undo to restore the originally loaded file.

Figure 7.11c Subtract Image after channel 2 (right) was subtracted from channel 1.

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Chapter 8 AutoProgram

An AutoProgram is a sequence of operations that may be applied automatically to at least one

previously captured image. Typically, an AutoProgram is created to rapidly analyze a large
number of images taken under similar conditions. Any Offline command except for XY Drift and
Subtract Image may be included in an AutoProgram.

Refer to the following functions available in AutoProgram menu of the NanoScope software:

• Creating an AutoProgram: Section 8.1

• Example command: Flatten: Section 8.2

• Example command: Depth: Section 8.3

• Example command: Roughness: Section 8.4

• Running AutoProgram: Section 8.5

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Creating an AutoProgram

8.1 Creating an AutoProgram

Do the following to create an AutoProgram:

1. Select a directory, then an image file within it, from the file browsing window at the right of
the NanoScope main window. Double-click its thumbnail to select and open the image. The
image file name and the Offline icon, as well as a sunburst image icon and the word
“Image” are added to the Workspace, and the image opens in the viewing window (see
Figure 8.1a).

Figure 8.1a Open Image

2. In the Workspace, right-click on the image file name or its Offline icon and select Create
AutoProgram (see Figure 8.1b). You may also right-click on the Image icon or Image and
select Create AutoProgram.

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Creating an AutoProgram

Figure 8.1b Create AutoProgram

3. You are asked if you want to include the selected image to define the AutoProgram among
the images processed by the AutoProgram (see Figure 8.1c). (Typically: “YES.”) The Add
Linked box should also be checked. When linking, any changes made to the currently active
view will then alter any linked views.

Figure 8.1c Include Selected Image Box

4. In the AutoProgram Results View (see Figure 8.1d):

a. Right-click on Autoprogram, under the file name or icon appearing on the line under
Run Group.

b. Click Add View to add a view to the Autoprogram. This view will then be added to all
files in the Autoprogram if they are linked.

c. Click the view of an Offline command to be performed first by the AutoProgram.

d. Repeat for additional views.

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Creating an AutoProgram

Note: Example specifications of the Flatten, Depth and Roughness commands for
inclusion in an AutoProgram are described next. Similar actions apply to
include other Offline commands in an AutoProgram.

Figure 8.1d Add Views to be Included in an AutoProgram

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Example command: Flatten

8.2 Example command: Flatten

To open the Flatten View:

1. Click the command name or icon that has been added to the Run Group Autoprogram.

2. Click in the image and drag open a box over features in the image that are to be excluded
from the polynomial fit calculations (see Figure 8.2a). Typically, only featureless areas are
used for flattening an image.

3. On the right of the Flatten View, set parameter values to apply for all images operated on by
the AutoProgram.

4. Close the Flatten View.

Note: Check the box DO NOT USE DEFAULT CONFIGURATION SETTINGS (Default
Configuration Settings on page 85). This setting can affect drawn Stopband
boxes and cursors which can be subsequently changed and used for later
Autoprograms.

Figure 8.2a Specify a Flatten Operation

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Example command: Depth

8.3 Example command: Depth

To open the Depth View:

1. Click the command name or icon that has been added to the Run Group Autoprogram.

2. Click in the image and drag open a box over an area that contains a height step (see Figure
8.3a).

3. On the right of the Depth View, set parameter values that will apply for all images operated
on by the AutoProgram.

4. Close the Depth View.

Figure 8.3a Specify a Depth Measurement

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Example command: Roughness

8.4 Example command: Roughness

To open the Roughness View:

1. Click the command name or icon that has been added to the Run Group Autoprogram.

2. Click in the image and drag open a box over an area where you would like the sample surface
condition analyzed (see Figure 8.4a).

3. In the Inputs window, set parameter values that will apply for all images operated on by the
AutoProgram.

4. Close the Roughness View.

Figure 8.4a Specify a Roughness Measurement for Inclusion in an AutoProgram

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Running AutoProgram

8.5 Running AutoProgram

Once all commands are included in the AutoProgram list and their action specified, you are ready
to run AutoProgram.

1. Click the Add Files... button in the AutoProgram Results View (see Figure 8.5a). The Add
Files dialog box appears.

2. In the Add Files dialog box, select the Link Files box to have the same AutoProgram
instructions apply to each file. Select files of interest and click Add to have the selected files
included when the AutoProgram is run. Hold down the Shift key to select a consecutive
group of files or the Control key to select more than one individual file.

3. In the AutoProgram Results View, check the Hide Views box if you don’t want the images
displayed, as they are automatically analyzed by the AutoProgram. If you want to see the
images processed during AutoProgram execution, leave Hide Views unchecked. Increasing
the value in Computation Time allows more time to view operations during Autoprogram
execution.

Figure 8.5a Add Files Dialog Box

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Running AutoProgram

4. Click the Run button in the AutoProgram Results View to start the AutoProgram.

Note: The RUN button toggles to display Stop while the AutoProgram is running.
Click it if you need to stop the process before it is completed. Clicking the Run
button again restarts the AutoProgram at the first image.

5. Upon completion, the data appears in the Log File View property sheet (see Figure 8.5b).

Figure 8.5b Log File View Property Sheet

Export Report Clear Log

Print Report Save Log

6. Results for individual analysis steps can be found in the Analysis Results drop-down menu,
also shown in Figure 8.5b.

7. If you close the Autoprogram Results View without saving the Autoprogram, you will be
prompted to save the Autoprogram as an .apg file.

8. To save the log file, select the SAVE LOG button in the Log File View.

9. To clear the log file, select the CLEAR LOG button in the Log File View.

10. Autoprogram results, with statistical analysis (termed reports), can be printed or exported as
tab delimited text using the PRINT REPORT or EXPORT REPORT buttons.

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Chapter 9 Recipes

The optional Recipe system allows you to automate most microscope functions using an easy to
use graphical user interface (GUI).

Refer to the following analysis commands available in Recipe menu of the NanoScope software:

• Starting the Recipe Menu: Section 9.1

• Creating a Recipe: Section 9.2

• Running a Recipe: Section 9.3

• Meta tags: Section 9.4

• Recipe Functions: Section 9.5

• Example 1: Teach and Run a Basic Recipe: Section 9.6

Additional information about the Recipes function, including several example recipes, can be found
in The Recipes Cookbook, Veeco part number 004-1021-000.

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Starting the Recipe Menu

9.1 Starting the Recipe Menu

Start the Recipe view using one of the following methods:

• Click RECIPES in the Workspace window. See Figure 9.1a.

Figure 9.1a Recipe

• Right-click on REAL TIME1 in the Workspace and select Add View > Recipes from
the popup menu.

Or

• Select Acquire > Recipes from the menu bar.

A Recipes window will open.

9.1.1 Menu Bar Items

The menu bar includes:

• File—Accesses menu selections for opening and saving and recipe (.rcx) files.

• Edit—Allows the user to add or delete steps in the recipe.

• Launch—Allows the user to run a recipe.

• About—Provides access to online help “about” information.

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Creating a Recipe

Table 9.1a Recipe Menu Bar Items

New Recipe Clears the existing recipe and starts a new recipe.

Open Recipe Opens a window to allow you to select an existing recipe.

File
Save Recipe Saves the current recipe to disk.

Save Recipe As Saves the current recipe to disk under a new file name.

New Inserts a step below the current step.

Delete Deletes the selected step.

Cut Deletes the selected step and copies it to the clipboard.

Copy Copies the selected step to the clipboard.

Edit
Paste Pastes the contents of the clipboard below the selected step.

Professor Walks you through configuring the selected step.

Move To Moves the stage to the designated position.

Re-Teach Alignments Allows user to redefine alignments.
Open & Run Opens a window, allowing you to select a recipe and then runs it.
Launch
Run Current Runs the current recipe.

Help Opens this document.

About
About Recipe Plug-In Opens the About Recipe window.

9.2 Creating a Recipe

A new, blank recipe, “My Recipe,” is created when the Recipe window is opened. The FILE > NEW
RECIPE clears the current recipe and allows you to create a new recipe. FILE > OPEN RECIPE
clears the existing recipe (if saved) and opens a previously saved recipe.

The Edit > New function allows you to add recipe steps below a selected step. Right-clicking on a
step also provides access to the Edit functions. Only functions that are allowed can be added. Other
functions are grayed out. Recipe step order can be changed by dragging steps. Step order is
enforced, i.e. moving a step to a logically impossible location is not allowed. Table 9.2a shows a list
of allowable parent functions and Table 9.2b shows a list of allowed child functions.

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Table 9.2a Allowed Parent Functions

Function Allowed Parent Functions

Alignment Load Sample, Real-time
Auto Tune Alignment, Auto Tune, Image Analysis, Image Set, Load Sample, Real Time, Report, Site, Site Order
Capture Image Measurement
Image Analysis Alignment, Site, Site Order, Nanoscript, Real-time, Root
Image Export Image Analysis, Image Capture, Image Set
Image Set Alignment, Auto Tune, Load Sample, Measurement, Real-time, Root, Site, Site Order
Load Sample Real-time
Measurement Site
Move To Alignment
Nanoscript Alignment, Site, Site Order, Image Analysis, Root, Real Time
Real-time Root
Report Alignment, Site, Nanoscript, Image Analysis, Real-time, Root
Site Alignment
Site Order Alignment

Note: Root is displayed as My Recipe.

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Table 9.2b Allowed Child Functions

Function Allowed Child Functions

Alignment/Origin Auto Tune, Image Set, Move To, Report, Site, Site Order
Auto Tune Auto Tune, Image Set, Report
Image Analysis Any Offline function, Image Export, Report
Image Capture Auto Tune, Any Offline function, Image Export
Image Export Image Export, Report
Image Set (offline) Image Analysis, Report
Load Sample Alignment/Origin, Auto Tune, Image Export, Image Set, Report
Measurement Auto Tune, Capture Image, Image, Image Analysis, Image Set, Report
Nanoscript Auto Tune, Image Set, Nanoscript, Report
Real-time Alignment/Origin, Auto Tune, Image Analysis, Image Export, Image Set, Load
Sample, Report
Root (My Recipe) Image Analysis, Image Export, Image Set, Real-time, Report
Report No children allowed
Site Auto Tune, Image Analysis, Image Set, Measurement, Nanoscript, Report
Site Order Auto Tune, Image Analysis, Image Set, Report, Site

Note: Root may have only one Real Time child. Site may have only one Measurement
child.

You can browse for files by clicking the file browse button, shown in Figure 9.2a, that appears on
the right when you select a file name.

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Figure 9.2a File Browse Button

All recipe steps are given a NAME which you can override by typing in the NAME field.

All recipe steps have a NOTES field which allows you to insert comments.

Many recipe steps have a PROFESSOR associated with them. Click PROFESSOR to launch an
assistance wizard that guides you through programming this recipe step. The PROFESSOR generally
provides full access to the NanoScope software and interface for a given step.

You may delete a step by highlighting that step and selecting EDIT > DELETE or right-clicking and
selecting DELETE.

You may save you recipe with the FILE > SAVE RECIPE or FILE > SAVE RECIPE AS commands.

9.3 Running a Recipe

Click Launch > Open & Run or Run Current to run the current open recipe. This opens the

Recipe Runner window, shown in Figure 9.3a. Click the RUN icon in the Recipe Runner
window to start running the recipe.

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Figure 9.3a Recipe Runner Window

Stop
Pause
Run

Slider control

Highlighted step

You start the recipe from any position by:

• Moving the SLIDER CONTROL to the desired position.

• Highlighting (by clicking) the desired step.

Click the PAUSE icon in the Recipe Runner window to pause the running of the recipe.

Click the STOP icon in the Recipe Runner window to stop running the recipe.

The Log window displays the recipe status.

9.3.1 Report files

A Report step may be inserted anywhere in a recipe and reports the activity of all parent nodes.
Information in the report files includes all input and output parameters as well as run status
(Incomplete, Pass or Fail). If programmed, a Report xml file will be generated. The xml file can be
used as a data feed to generate multiple report formats. Use XSL Transformations (XSLT) — http:/
/www.w3.org/TR/xslt to create a formatted output file from this xml file. Several default XSLT

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Meta tags

files (html and text) are provided (in ..\plugins\recipes\stylesheets\). You can also make your own
xls translation file if you’re an advanced user to go from XML to any other text format. You can use
the report file (or translated version) to integrate recipe output information with custom post
processing software.

9.4 Meta tags

Meta tags can be used in all parameter fields that specify an output file name to be written and can
also be used in the notes parameter field for all recipe functions. Export text tag parameters also
support meta tags. For example, a time stamp meta tag can be entered into the name of a file to be
captured. "MyFileName<TimeStampMonth><TimeStampDay>.000" would drop the month and
day into a captured filename. Other recipe or microscope configuration data can also be used. For
example, you could use the <LocX> and/or <LocY> tags to include the sample site location in your
filename.

The most local version of the parameter is always used. This means that if the specified meta tag
does not exist within the current recipe function, the meta tag parser will traverse from parent to
grandparent function until the parameter is found. In this way, a notes parameter for a captured
image can contain information about the microscope configuration.

9.4.1 Special Meta Tags

Time Stamp Meta Tags

Time Stamp Meta Tags

<TimeStampMonth>

<TimeStampMonthName>

<TimeStampDay>

<TimeStampYear>

<TimeStampHour>

<TimeStampMinute>

<TimeStampSecond>

Parent Function Reference Meta Tags

Time Stamp Meta Tags

<ParentFileName>

<ParentName>

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Analysis nodes that produce a modified image can use <ParentFileName> in conjunction with the
file overwrite option to overwrite the input file. <ParentName> is used to reference the <Name>
parameter of the local function’s parent function.

9.5 Recipe Functions

All Recipe Nodes contain NAME and NOTES fields which are for personal notation only and are not
used for logical execution of the recipe.

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9.5.1 Alignment/Origin

Defines an origin and a sample deskew angle from which the coordinates of all subsequent child
site nodes are based.

Alignment Mode Origin Only, Origin using X deskew, Origin using Y deskew.

Origin X X-axis origin location in absolute stage units.

Origin Y Y-axis origin location in absolute stage units.

Origin Z Z-axis origin location in absolute stage units.

Speed Speed at which the stage should move in percent of maximum speed.

Deskew Angle Used to deskew the coordinate system defined by the above origin. In other words, all
subsequent child sites will be shifted by the origin values, and rotated by the deskew
angle.

Deskew Pt 1 - X X location of the first point used to calculate the deskew angle.

Deskew Pt 1 - Y Y location of the first point used to calculate the deskew angle.

Deskew Pt 2 - X X location of the second point used to calculate the deskew angle.

Deskew Pt 2 - Y Y location of the second point used to calculate the deskew angle.

Move To Moves the stage to the designated position.

Professor Yes

Meta Tags

Name <Name>

Notes <Notes>

Alignment Mode <Mode>

Origin X <OriginX>

Origin Y <OriginY>

Origin Z <Origin Z>

Speed <Speed>

Deskew Angle <DeskewAngle>

Deskew Pt 1 - X <DeskewPt1X>

Deskew Pt 1 - Y <DeskewPt1Y>

Deskew Pt 2 - X <DeskewPt2X>

Deskew Pt 2 - X <DeskewPt2Y>

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9.5.2 Auto Tune

Tells the systems to measure and calculate the cantilever drive amplitude and frequency.

Start Frequency Starting point of the Auto Tune frequency sweep.

End Frequency Ending point of the Auto Tune frequency sweep.

Target Amplitude Targeted output signal amplitude at the photodiode detector. This value should not be
confused with Drive amplitude, which is the amplitude applied directly to the cantilever
itself (see Drive amplitude).
Range and Settings: 0.00 to 8.00 V
Note: Dimension Series SPMs, nominal = 500mV
Small Sample MultiMode SPMs, nominal = 500mV

Peak Offset Percentage of cantilever’s free-air resonant frequency to be automatically offset. Peak off-
set is used to compensate for changes in resonance before engagement due to the tip’s
interaction with the surface after engagement.
Range and Settings: 0 to 50%; typical value = 0 to 10%

Minimum Q Q is the value defined by the amount of oscillation it takes for a wave to drop to 1/e (e =
2.718) of its amplitude value (i.e. a wave with an amplitude of ten would have a Q of 10/
e, or 3.6788). Minimum Q establishes a minimum “width of peak” value allowed by the
AutoTune function.

Professor No

Meta Tags

Name <Name>

Notes <Notes>

Start Frequency <StartFreq>

End Frequency <EndFreq>

Target Amplitude <TargetAmplitude>

Peak Offset <PeakOffset>

Minimum Q <MinimumQ>

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9.5.3 Capture Image

Captures and saves an image to disk in nanoscope format. This image can be exported as a BMP,
JPEG, or TIFF file. Captured images may be parent objects of analysis nodes so that the analysis
takes place immediately after the data has been captured.

Capture File Name Name of file to be captured. A full path may be specified, but if a complete path is not
specified the "default capture path" (displayed in the Properties window of the My Recipe
node) is used.

Overwrite Existing File Specifies if the resulting image should overwrite an existing image file of the same name.
If NO, a new, sequential file will be created.

Auto File Export DISABLED or the type of file to which the captured nanoscope image is exported.

Export Channel The EXPORT CHANNEL field specifies which channel should be exported.

Note: BMP, JPEG, and TIFF formats can not contain information about more than 1
channel.

Export Text Tags This field is used to put notes in the "notes" tag for TIFF files.

Professor No

Meta Tags

Name <Name>

Notes <Notes>

Capture File Name <FileName>

Overwrite Existing File <FileOverwrite>

Auto File Export <FileExportType>

Export Channel <FileExportChannel>

Export Text Tags <FileExportTextTags>

9.5.4 Image Analysis

Analysis nodes are children of CAPTURE IMAGE or IMAGE SET. In combination with image parent
nodes and report nodes as children, they are capable of producing numeric analysis results and/or
resulting images. Analysis nodes can also be child nodes of other analysis nodes when analysis of a

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filtered image (by another analysis node) is desired. E.g. if you want to perform a roughness
analysis of images that have been flattened, you would configure your image tree as follows:

#ORRECT )NCORRECT
)MAGE 3ET OFFLINE )MAGE 3ET OFFLINE

&LATTEN &LATTEN

2OUGHNESS 2OUGHNESS

Data Channel Selects which channel from the parent Image object to use for analysis.

Output Image Name Name of output image. A full path may be specified, but if a complete path is not speci-
fied the "default capture path" (displayed in the Properties window of the My Recipe
node) is used.

Overwrite Existing File Specifies if the resulting image should overwrite an existing image file of the same name.
If NO, a new, sequential file will be created.

File Export Channel The EXPORT CHANNEL field specifies which channel should be exported.
Note: BMP, JPEG, and TIFF formats can not contain information about more than 1
channel.

Export Text Tags This field is used to put notes in the "notes" tag for TIFF files.

Additional Fields… Additional fields are stored containing information about the analysis configuration.
These fields will vary depending on the type of analysis you are doing. These fields are
editable only through the Professor and the standard image analysis views.

Professor Yes

Meta Tags

Name <Name>

Notes <Notes>

Data Channel <Channel>

Output Image Name <Output File Name>

Overwrite Existing File <FileOverwrite>

Auto File Export <FileExportType>

File Export Channel <FileExportChannel>

Export Text Tags <FileExportTextTags>

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9.5.5 Image Export

Exports an image.

File Name Name of output file.

Overwrite Existing File Specifies if the resulting image should overwrite an existing image file of the same name.
If NO, a new, sequential file will be created.

Export Type The file type that will be exported: BMP, JPEG, TIFF.

Export Channel The EXPORT CHANNEL field specifies which channel should be exported.
Note: BMP, JPEG, and TIFF formats can not contain information about more than 1
channel.

Export Text Tags This field is used to put notes in the "notes" tag for TIFF files.

Professor No

Meta Tags

Name <Name>

Notes <Notes>

File Name <FileName>

Auto File Export <FileExportType>

File Export Channel <FileExportChannel>

Export Text Tags <FileExportTextTags>

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9.5.6 Image Set (offline)

Specifies a set of previously captured files. May also be exported as a BMP, JPEG, or TIFF file
using the Image EXPORT function.

Image List Names of previously captured NanoScope image files. A full path may be specified, but if
a complete path is not specified the "default capture path" (displayed in the Properties
window of the My Recipe node) is used.

Professor No

Meta Tags

Name <Name>

Notes <Notes>

Image List <ImageList>

Auto File Export <FileExportType>

File Export Channel <FileExportChannel>

Export Text Tags <FileExportTextTags>

9.5.7 Load Sample

Stops the recipe and moves the stage to a specified location so that a new sample can be loaded. An
option is provided to re-teach all alignment/origin objects so that associated sites will adjust
appropriately without being re-taught.

X X-axis stage location for re-load in absolute coordinates.

Y Y-axis stage location for re-load in absolute coordinates.

Z Z-axis stage location for re-load in absolute coordinates.

Speed Speed at which the stage should move in percent of maximum speed.

Re-Teach Alignments/Origin Turns on/off re-teaching of all alignment/origin objects in the recipe before continuing.

Professor No

Meta Tags

Name <Name>

Notes <Notes>

X <LocX>

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Y <LocY>

Z <LocZ>

Speed <Speed>

Re-Teach Alignments/Origin <TeachOrigin>

9.5.8 Measurement

Stores Real Time parameters used to configure the microscope. At run-time, it will use these
parameters to engage the probe and scan the sample. Site may have only one measurement step.

Nanoscope Parameters Lists Lists all parameters used to configure the microscope.

Professor Yes

Meta Tags

Name <Name>

Notes <Notes>

9.5.9 My Recipe

Root node of recipe containing default capture and report folders.

Capture Directory Default path to the directory that is used for storing and reading captured image files
when a full path is not defined by the CAPTURE FILE NAME.

Report Directory Default path to the directory used to store reports when a full path is not defined by the
REPORT OUTPUT XML FILE.

Version Contains Recipe plug-in version information (read only)

Professor No

Meta Tags

Name <Name>

Notes <Notes>

Capture Directory <CaptureDirectory>

Report Directory <ReportDirectory>

Version <Version>

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9.5.10 Real-time Configuration

Realtime stores reference information about the microscope hardware that the recipe was written
for. There may be only one Real Time step in a recipe.

Controller Specifies the controller.

Microscope Specifies the microscope.

Scanner Specifies the scanner

Vision Specifies the vision system.

Zoom Specifies the optical system.

Professor No

Meta Tags

Controller <Controller>

Microscope <Microscope>

Scanner <Scanner>

Vision <Vision>

Zoom <Zoom>

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9.5.11 Report

Report generates an XML formatted summary of recipe node results. Reports may be placed
anywhere in the recipe and are used for local or global reporting. The report looks to its parent node
and reports on all children of its parent, including itself.

All nodes in the recipe contain a "run status" output field that has the values PASS, FAIL, or
INCOMPLETE. All input fields are copied to the output parameters to be reported with results.

Nanoscope Parameters Lists Lists all parameters used to configure the microscope.

Report Output XML File Input file to the stylesheet transformation program.

Stylesheet File Specifies a xls xml transition file.

Formatted Output File Final formatted output file. Does nothing if left blank.

Professor No

Meta Tags

Name <Name>

Notes <Notes>

9.5.12 Site

Site moves the stage to a specified X, Y, Z position relative to its parent alignment/origin.

X X-axis stage location in relative coordinates.

Y Y-axis stage location in relative coordinates.

Z Z-axis stage location in relative coordinates.

Speed Speed at which the stage should move in percent of maximum speed.

Professor Yes

Meta Tags

X <LocX>

Y <LocY>

Z <LocZ>

Speed <Speed>

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9.5.13 Site Order

Site Order uses a comma separated values (CSV) file to re-order the sites at run-time. Sites to be re-
ordered need to be child nodes of this node.

CSV File Name Path and name of the CSV file.

Number of Columns Specifies the number of columns in the CSV files. The CSV file may contain more col-
umns than are used by the re-order operation. The unused columns will be ignored.

Site Reference Column Specifies which column (1...N) in the CSV file will be used to reference the subsequent
child site nodes. The data in the column may be a site number (By Index) or contain a case
sensitive name field value (of the referred site) (By Name). See Site Reference Type,
below.

Sort Weight Column Specifies which column (1...N) in the CSV file will be used to weight the resulting sort
order of the sites. This field may contain the resulting site index itself, a calculated float-
ing point value or a percentage.

Image Name Column Specifies which column (1...N) in the CSV file will be used to re-name sub-sequent Image
capture file names for each site. If data in the specified column is null, an empty string or
does not exist, this image re-name feature will be ignored. All child capture images will
be renamed.

Site Reference Type Specifies whether sites in the SITE REFERENCE COLUMN will be referenced by their
index or by their name field value.

Sort Direction Used to change the direction of the resulting site sort order.

Professor No

Meta Tags

CSV File Name <FileName>

Number of Columns <NumColumns>

Site Reference Column <SiteReferenceColumn>

Sort Weight Column <SortWeightColumn>

Image Name Column <ImageColumn>

Site Reference Type <SiteReferenceOption>

Sort Direction <SortOption>

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9.6 Example 1: Teach and Run a Basic Recipe

9.6.1 Teach a Real-time Recipe

1. Create a basic outline of the recipe.

a. Start the Recipe view using one of the following methods:

• Click RECIPES in the Workspace window. See Figure 9.1a.

Or

• Right-click on REAL TIME1 in the Workspace and select Add View > Recipes
from the popup menu.

Or

• Select Acquire > Recipes from the menu bar.

b. Add a Real-time step using one of the following methods:

• Right-click on MY RECIPE in the Untitled1.rcx window and click NEW > REAL-
TIME.

Or

• Click EDIT > NEW > REAL-TIME.

c. Add an Alignment/Origin step using one of the following methods:

• Right-click on REAL-TIME in the Untitled1.rcx window and click NEW >

ALIGNMENT/ORIGIN.

Or

• Click EDIT > NEW > ALIGNMENT/ORIGIN.

d. Add an Autotune step using one of the following methods:

• Right-click on ALIGNMENT/ORIGIN in the Untitled1.rcx window and click NEW >

AUTOTUNE.

Or

• Click on ALIGNMENT/ORIGIN and then click EDIT > NEW > AUTOTUNE.

e. Add a Site step using one of the following methods:

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• Right-click on ALIGNMENT/ORIGIN in the Untitled1.rcx window and click NEW >

SITE.

Or

• Click on ALIGNMENT/ORIGIN and then click EDIT > NEW > SITE.

f. Add a Measurement step using one of the following methods:

• Right-click on SITE in the Untitled1.rcx window and click NEW >

MEASUREMENT.

Or

• Click on SITE and then click EDIT > NEW > MEASUREMENT.

g. Add a Capture Image step using one of the following methods:

• Right-click on MEASUREMENT in the Untitled1.rcx window and click NEW >

CAPTURE IMAGE.

Or

• Click on MEASUREMENT and then click EDIT > NEW > CAPTURE IMAGE.

h. Select FILE > SAVE Recipe AS D:\RECIPES\EXAMPLE1.RCX. See in Figure 9.6a.

Figure 9.6a Example 1, Basic Outline

2. Teach Alignment

a. Open the Alignment PROFESSOR using one of the following methods:

• Right-click on ALIGNMENT/ORIGIN in the Example1.rcx window and click

PROFESSOR.

Or

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• Click on ALIGNMENT/ORIGIN and then click the QUICK LINKS: PROFESSOR

button.

b. Enter the relative stage speed and click NEXT.

c. Select the LEAVE STAGE IN CURRENT LOCATION radio button. Click NEXT.

d. Select the ORIGIN ONLY radio button. Click NEXT.

e. Using the NAVIGATE window, shown in Figure 9.6b, focus the optics on the tip and
click NEXT when you are done.

f. Using the NAVIGATE buttons, shown in Figure 9.6b, move the stage to the desired
origin. Click NEXT.

Figure 9.6b Navigate Window

g. Click FINISH.

3. Set Auto Tune parameters.

a. Click the Auto Tune step.

b. Set the following properties (TESP probe, for example):

• START FREQUENCY: 0 KHZ.

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• END FREQUENCY: 400 KHZ.

• TARGET AMPLITUDE: 500 MV.

• PEAK OFFSET: 5.00%.

• MINIMUM Q: 0.

c. SAVE the RECIPE.

4. Teach Site 1.

a. Open the Site 1 PROFESSOR using one of the following methods:

• Right-click on SITE 1 in the Example1.rcx window and click PROFESSOR.

Or

• Click on SITE 1 and then click the QUICK LINKS: PROFESSOR button.

b. Enter the relative stage speed and click NEXT.

c. Select the LEAVE STAGE IN CURRENT LOCATION radio button. Click NEXT.

d. Using the NAVIGATE buttons, shown in Figure 9.6b, move the stage to the desired
position. Click NEXT.

e. Click FINISH.

5. Set the Measurement parameters.

a. Open the Measurement PROFESSOR using one of the following methods:

• Right-click on MEASUREMENT in the Example1.rcx window and click

PROFESSOR.

Or

• Click on MEASUREMENT and then click the QUICK LINKS: PROFESSOR button.

b. Select the LEAVE SYSTEM IN CURRENT STATE radio button. Click NEXT.

c. Configure the scan parameters in the Scan Parameters window.

d. Click FINISH.

e. Verify the parameters in the Properties list in the Professor.

6. Set the Capture Image parameters.

a. Click the Capture Image step.

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b. Set the following properties:

• Give a Capture File Name including an appropriate three digit extension. E.g.
SITE1IMAGE.000.

• Select YES for OVERWRITE EXISTING FILE.

• AUTO FILE EXPORT: DISABLED.

c. SAVE the RECIPE.

7. Set the default folders:

a. Click the My Recipe step.

b. Set the following properties:

• Capture Directory D:\RECIPES\EXAMPLE1.

• Report Directory D:\RECIPES\EXAMPLE1.

c. Select FILE > SAVE RECIPE.

9.6.2 Run the Real-time Recipe

1. Click LAUNCH > RUN CURRENT to open the Recipe Runner window, shown in Figure 9.6c.

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Figure 9.6c Recipe Runner Window

Stop
Pause
Run

Slider control

Highlighted area

2. Click the RUN icon in the Recipe Runner window to start running the recipe.

3. You may start at any step in the recipe by highlighting (clicking on) that step and clicking
RUN.

9.6.3 Add an Additional Site

1. Add an additional Site step by cloning Site 1:

• Right-click on the SITE 1 step and click COPY.

Or

• Click on the SITE 1 step and then clicking the EDIT > COPY.

Then

• Right-click on the ALIGNMENT/ORIGIN step and click PASTE.

Or

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• Click on the ALIGNMENT/ORIGIN step and then clicking the EDIT > PASTE.

2. Change the settings for the cloned site:

a. Enter SITE 2 for NAME.

b. Open the PROFESSOR.

c. Navigate to the desired Site 2 location.

d. FINISH.

3. Repeat Step 5 and Step 6 in Teach a Real-time Recipe: Section 9.6.1, if necessary.

4. Select FILE > SAVE RECIPE.

9.6.4 Teach an Offline Recipe

1. Create a basic outline of the offline recipe.

a. Add an Image Set step using one of the following methods:

• Right-click on MY RECIPE in the Example1.rcx window and click NEW > IMAGE
SET (OFFLINE).

Or

• Click on MY RECIPE and then click EDIT > NEW > IMAGE SET (OFFLINE).

b. Add a Flatten step using one of the following methods:

• Right-click on IMAGE SET 1 in the Example1.rcx window and click NEW > IMAGE
ANALYSIS > FLATTEN.

Or

• Click on IMAGE SET 1 then click EDIT > NEW > IMAGE ANALYSIS > FLATTEN.

c. Add a Roughness step as a child of the Flatten step using one of the following
methods:

• Right-click on FLATTEN in the Example1.rcx window and click NEW > IMAGE
ANALYSIS > ROUGHNESS.

Or

• Click on FLATTEN then click EDIT > NEW > IMAGE ANALYSIS > ROUGHNESS.

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d. Add a Report step as a child of the MY RECIPE step using one of the following
methods:

• Right-click on MY RECIPE in the Example1.rcx window and click NEW >

REPORT.

Or

• Click on MY RECIPE and then click EDIT > NEW > REPORT.

2. Create the Image List.

a. Select Site1Image.000 in the D:\Recipes directory to add it to the Image List. See Figure
9.6d.

b. Place the cursor at the end of this and add “, D:\Recipes\Example1\Site2Image.000”

manually into the Image List textbox because this image does not yet exist and cannot
be selected from D:\Recipes. The Image List will now read
“D:\Recipes\Example1\Site1Image.000, D:Recipes\Example1\Site2Image.000.”

Figure 9.6d Add Files to the Image List

3. Configure the FLATTEN step.

a. Open the Flatten PROFESSOR using one of the following methods:

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• Right-click on FLATTEN in the Example1.rcx window and click PROFESSOR.

Or

• Click on FLATTEN and then click the QUICK LINKS: PROFESSOR button.

b. Make appropriate changes to the input parameters in the Flatten analysis window.

c. Click NEXT.

d. Click FINISH.

4. Configure the ROUGHNESS step.

a. Open the Roughness PROFESSOR using one of the following methods:

• Right-click on ROUGHNESS in the Example1.rcx window and click PROFESSOR.

Or

• Click on ROUGHNESS and then click the QUICK LINKS: PROFESSOR button.

b. Make appropriate changes to the input parameters in the Roughness analysis window.
See Roughness: Section 6.3 for details.

c. Click NEXT.

d. Click FINISH.

5. Configure the REPORT step.

a. Set the following properties:

• Name: REPORT1.

• Report Output XML File: D:\RECIPES\REPORT1.

6. Select FILE > SAVE RECIPE.

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Chapter 10 Tools

The Tools commands are in the right portion of the menu bar.

Refer to the following analysis commands available on the NanoScope software:

• Options: Section 10.1

• Programmed Move (Dimension Series Only): Section 10.2

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10.1 Options

10.1.1 Remove File on Close

Select Tools > Options > Remove File on Close menu item (see Figure 10.1a). You can also right-
click the workspace and select Remove File on Close. When selected, this option removes the
workspace item of the offline file when all views on that file are closed.

Figure 10.1a Remove File on Close Menu Item

Note: The entire Tools > Options menu, with the exception of Set Help File..., is
available when you right click in the workspace (not on a node).

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Programmed Move (Dimension Series Only)

10.2 Programmed Move (Dimension Series Only)

The Stage > Programmed Move function allows the stage to be automatically positioned at a
series of memorized positions. These positions are programmed into the controller’s computer, then
called out automatically in sequence. The operator may run either the entire memorized sequence,
or skip positions, as desired. This function is particularly useful for statistical quality assurance runs
on large numbers of identical samples, and as a basic inspection aid.

Refer to the following sections:

• Programmed Move Panels Section 10.2.1

• Procedure for Teaching a Programmed Move Section 10.2.2

• Procedure to Remove a Programmed Option Section 10.2.3

• Procedure to Insert a Step into an Existing Program Sequence Section 10.2.4

• Procedure To Run a Series of Programmed Moves Section 10.2.5

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10.2.1 Programmed Move Panels

To access this option, select on Stage > Programmed Move, shown in Figure 10.2a.

Figure 10.2a Selecting Programmed Move

You will be prompted for a new file name or an existing file:

Figure 10.2b Programmed Move File Name Selection

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After clicking OK, the main Programmed Move panel, shown in Figure 10.2c, will appear:

Figure 10.2c Programmed Move Window

Definitions

• Program Name Field—Provides the name of the move program currently loaded (in
this example, the program is called “move”). Moves are first programmed using the
ADD and REMOVE STEP functions. Later they may be executed using the Run option.

• QUIT (button)—Exits the Programmed Move panel.

• RUN (button)—Executes the specified program name.

Once a program sequence has been taught to the computer, the program can be run from
the Programmed Move panel. The stage will move to each position in the same order it
was taught, relative to the current origin point. At each program position, the sample
will be scanned for 1.5 frames, captured, then indexed to the next position. Captured
data from each position is stored on the hard disk; there should be sufficient memory to
record 100 frames at 256 samples each.

• Origin Points—Current origin at the time of programming.

Programmed Move positions are memorized relative to the current origin at the time of
programming. If the origin has been shifted from its original position since the time of
programming, it will be necessary to reestablish the original origin point to locate the
same positions on the sample. When generating maps of programmed moves, the origin
point should always be indicated.

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10.2.2 Procedure for Teaching a Programmed Move

To program (teach) a series of moves, do the following:

1. Select a file name for a new or existing Programmed Move file. See Figure 10.2b.

2. Click OK to proceed with programming moves. A new panel, shown in Figure 10.2c, will be
displayed.

3. Make a stage move using either the trackball or the Move To X,Y panel (i.e. enter X and Y
POSITION or POSition CHANGE and click MOVE).

4. Click ADD STEP.

5. This procedure may be repeated until all the desired positions have been programmed up to a
maximum of 100 steps. Each position will be automatically assigned a program step number.

It may prove helpful to draw a simple map of the sample, along with each programmed position,
before programmed moves are entered. If reducing cycle time is important, position order should
be optimized to reduce stage travel. Also, note the origin point at the time of programming.

6. When all stage positions have been entered into the program, click SAVE PROGRAM, then
QUIT.

7. Additional programs are entered in the same manner, using a separate program name for
each.

10.2.3 Procedure to Remove a Programmed Option

To remove a step from the programmed sequence:

1. Select a file name for an existing Programmed Move file. See Figure 10.2b.

2. Click OK to proceed with programming moves. A new panel, shown in Figure 10.2c, will be
displayed.

3. Click in the Step # field in the Select Step sub-panel.

4. Enter the step number to be removed into the keyboard, or drag the mouse to index to the
step number. The stage will simultaneously move to the new step position.

5. Click the REMOVE STEP button. When individual program steps are removed, all subsequent
steps are “moved up” by one count. (For example, after removing step #2 from a program,
step #3 would become the new step #2, step #4 would become the new step #3, etc.)

6. Click the SAVE PROGRAM button to save the edited version of program.

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Programmed Move (Dimension Series Only)

10.2.4 Procedure to Insert a Step into an Existing Program Sequence

1. Select a file name for an existing Programmed Move file. See Figure 10.2b.

2. Click OK to proceed with programming moves. A new panel, shown in Figure 10.2c, will be
displayed.

3. Click in the STEP # field in the Select Step sub-panel.

4. Enter one less than the step number to be added to the sequence, or drag the mouse to index
to the desired step number. (For example, if the operator wishes to add a new program step
#7, while leaving all preexisting steps intact, they would enter “6” in the STEP # field. The
stage will simultaneously move to the preexisting step position #6.)

5. Make a stage move using either the trackball or the Move To X,Y panel (i.e. enter X and Y
POSITION or POSITION CHANGE and click MOVE).

6. When new program steps are added, all preexisting steps beyond the new entry are “moved
up” by one count.

7. Click SAVE PROGRAM to save the edited version of program.

10.2.5 Procedure To Run a Series of Programmed Moves

1. Select a file name for an existing Programmed Move file. See Figure 10.2b.

2. Click on OK to proceed with programming moves. A new panel, shown in Figure 10.2c, will
be displayed.

3. Click the RUN button. If the program is being loaded and run from the beginning, the screen
will prompt the operator whether to refocus the screen:

Figure 10.2d Stage Panel

4. Clicking on Yes will transfer the user to the Focus Surface panel; the user may then make
focusing adjustments to better view the surface. Clicking on No will initiate the programmed
move from step #1.

If the program was previously run without finishing (aborted), the screen will request whether to
begin the program sequence at the aborted step; for example, if the operator left off at step #2:

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Figure 10.2e Stage Panel

5. The operator may wish to run the entire program from its beginning (step #1); if this is the
case, click No. Otherwise, click Yes. The screen will display the current program step in
progress:

Figure 10.2f Programmed Move Panel

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Appendix A File Formats

This appendix details file format information for NanoScope software Version 7.20. Customers often
upgrade to newer software, therefore, this appendix also includes compatibility and conversion information
for earlier software versions.

Note: For details on earlier file format information, refer to Support Note 330 File Formats.

This appendix includes the following information:

• Overview: Section A.1

• File Compatibility: Section A.2

• Data File Organization: Section A.3

• Converting Data: Section A.4

• Converting Raw Data: Section A.5

• Electrochemistry: Section A.6

• General Format for CIAO Parameter Objects: Section A.7

CAUTION: Before attempting data extraction on files, always make backup

copies of the originals. If files become damaged due to loss of data,
they may be irrecoverable.

ATTENTION: Toujours effectuer une copie des fichiers originaux avant d’en
extraire des données. Si la perte de données endommageait des
fichiers, ceux-ci pourraient être irrécupérables.

VORSICHT: Machen Sie bitte immer Backup-Files Ihrer Originaldaten, ehe Sie
versuchen, Datenfiles selbst zu bearbeiten. Wenn Files durch
Datenverlust beschädigt werden, könnten die Daten
unwiederbringlich verloren sein.

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Overview

A.1 Overview
File formats in the NanoScope software are of concern to users for at least two reasons:

• Compatibility—Processing older files using newer NanoScope software.

• Converting file data—Exporting data into third-party applications such as spreadsheets

and statistical packages to evaluate data in unique ways.

The ability to extract data from files is for the purpose of applying third-party software packages and
analyzing data in other formats. This may include displaying data in spreadsheets (e.g., Excel), statistical
packages and expert systems. Typically, you extract data from the image files, then filter the data according
to the requirements of their software. This section discusses how data files are organized to assist in
extracting the file data.

A.2 File Compatibility

Veeco updates file formatting to ensure cross-compatibility of files between different versions of the
NanoScope software. There are some exceptions.

Most NanoScope software can open files created by earlier versions of NanoScope software. Conversely,
image files captured and saved by an earlier version of NanoScope software should open on any later
version of NanoScope software. However, once the files are open and re-saved by a newer version, they are
no longer usable in older versions of NanoScope software.

IMPORTANT!: To analyze old files using newer software versions and then to
return the files to the older software version, make backup copies
of the files with the old software BEFORE loading them into the
newer software.

IMPORTANT!: Les Utilisateurs désirant analyser d’anciens fichiers en utilisant

une nouvelle version de logiciel, et désirant également les retraiter
par la suite dans l’ancienne version, doivent effectuer des copies
(backup) de leurs fichiers AVANT de les charger dans la nouvelle
version.

WICHTIG!: Anwender, die alte Datenfiles mit neuerer Software analysieren

und später die Files wieder mit der alten Software einlesen wollen,
sollten Backup-Kopien ihrer Files mit der alten Softwareversion
machen, EHE sie diese mit der neuen Software laden.

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Data File Organization

A.3 Data File Organization

Images which are captured by the user are immediately stored in the NanoScope’s capture directory as binary
files. Depending upon the Number of samples taken, files will vary in size from about 41KB to 52MB per
channel per image. Regardless of size, all files include: 1) a “header,” containing various parameter settings
used during the capture of the original image, a Ctrl-Z character to signal the end of the header, and
“padding,” comprised of random data; and, 2) data, stored two bytes (216) per pixel (2’s complement).

File organization includes the following:

• Header Files: Section A.3.1

• Parameters: Section A.3.2

• Control-Z (Ctrl-Z) Character: Section A.3.3

• Padding: Section A.3.4

• Raw Data: Section A.3.5

A.3.1 Header Files

The first portion of every image file contains a header file. The header file tells the software about the data
which follows. The header file size depends upon the number of parameters used at the time that data is
captured. Depending upon the type of file saved and the version of NanoScope software used when saving the
file, the header may contain more than 2,000 parameters.

Each header is divided into separate lists (beginning with the characters \*). Users typically, manipulate only
a few of the parameters for each application. See the Parameters section for a few of the most important
parameters and characters.

The header is also crucial to interpreting the data. The header information provides crucial parameter and
setting information for converting ASCII file data. The end of the header file reveals where the actual data
begins. Figure A.3a shows the size and relationship of the data file formats.

Figure A.3a Single and Two-Image Data File Structure

Parameters Padding data Image data

“Ctrl-Z”
Header (variable length)
SINGLE IMAGE DATA FILE
Parameters (Image #1) Padding data Image data (#2)

Parameters (Image #2) “Ctrl-Z” Image data (#1)

Header (variable length)
TWO-IMAGE DATA FILE

Two-Image Files

Files with two or more images contain separate parameter lists and image data. Figure A.3b illustrates data
organization of a two-image files.

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Figure A.3b Example of a Two-image Header File

Section
\*File list
\Version: 0x7100000
\Date: 10:43:31 PM Tue Feb 14 2006
\Start Context OL2BIG
\Data length: 40960

1
Image file
parameters
\*Equipment list (common to
both images)

\*Scanner list

\*Ciao scan list

\*Fast scan list

\*HSDC scan list

\*Ciao image list

\Data offset: 40960
\Data length: 52428800 2 Image #1
parameters

\*Ciao image list

\Data offset: 52469760
\Data length: 52428800 3 Image #2
parameters

^Z 4 Control-Z

D3F87F311F35E22CE9F55A8D9AE4B74

5
E9F55A8D6B4B7D111F35E22C297BA3F8 Padding data
9AE4B74D3F87F31297BA3F81F35E22C (random)

1F35E22C297BA3F89AE4B74D3F87F31
E9F55A8D6B4B7D111F35E22C297BA3F8
D3F87F311F35E22CE9F55A8D9AE4B74 6 Image #1 data

9AE4B74D3F87F31297BA3F81F35E22C

7
1F35E22C297BA3F89AE4B74D3F87F31
Image #2 data
E9F55A8D6B4B7D111F35E22C297BA3F8

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Analysis of the Two-Image Header File

• Section 1 includes parameters common to both images (only a few are shown here). The
parameters are included within various lists beginning with \*. The type of image and the
NanoScope software version also affect the lists and parameters. For example, the \Data
length parameter in the \*File list of this section is generally 40K and includes the entire
header.

• Section 2 contains parameters which are specific to image #1. In this example, only two are
shown; however, there may be dozens. The \Data offset parameter is very important because
it indicates the Nth byte where data for image #1 begins (here, it is 40960). The \Data length
parameter indicates the length of data for image #1 in bytes (here, it is 52428800). By adding
the \Data offset and \Data length together, the data offset for image #2 is found.

• Section 3 contains parameters which are specific to image #2. The \Data offset parameter
here indicates that data for image #2 begins at byte 52469760 and is 52428800 bytes in
length.

• Section 4 is a Ctrl-Z character which denotes the end of parameter lists.

• Section 5 contains random padding data. This is added to the header to make it a
predetermined length (specified in the first \Data length parameter at the start of the header)
and is used to read the file into NanoScope software. Image files containing multiple images
will have less padding than files containing only one image.

• Section 6 contains image data specific to image #1. In this example, it begins at byte 40960
and is 52428800 bytes in length. Depending upon whether the image was captured at 128,
256, 512... samples per scan line, the length of data will vary.

• Section 7 contains image data specific to image #2. In this example, it begins at byte
52469760 and is 52428800 bytes in length. The last data value in this section of the file
denotes the end of the file.

A.3.2 Parameters

\* File List—Denotes the beginning of several parameter lists. For example, \*Ciao Image list,
\*Equipment list, etc. Each image in the file has its own image list (e.g., \*Ciao image list).

\Version—Describes the version of software used.

\Data length—Length of header, Ctrl-Z character and padding in bytes.

\Samples/line—Number of pixels per scan line. This is the same as the Number of samples value on the
Real-time / Scan Controls panel.

\Scan size—Height and width of the square scan area in nanometers.

\Z atten—Z-axis attenuation value. The total Z-axis range of data may be calculated from this number as
follows:

Z atten value
Total Z-axis range = ------------------------------- ⋅ 440
65,536

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The Z attenuation value is divided by 65,536 (steps of resolution for Z scanner piezo), then multiplied times
the Z-axis scanner voltage range (± 220 Volts) to yield the total Z-axis range of data.

\Data offset—Nth byte in the image file where raw data commences.

\Data length—Length of raw data stream in bytes. Divide this value by 2 to obtain the total number of
pixels in the image.

\Z scale—Factor used to convert data to indicated units. E.g., for \Z scale: 20000 nm,
pixel value
data (nm) = -------------------------- ⋅ 20000
65,536

\Z sensitivity—Z-axis scanner sensitivity in nanometers per volt. To obtain the maximum Z-axis scanner
travel, multiply this value by 440.

\Z scale magnify—Multiplier applied to Z-axis height data to render a NanoScope image on the display
screen. For example, a value of 1.0 would render data on the display screen at the same scale as actual
features. This value is generally of no use outside the NanoScope software environment.

A.3.3 Control-Z (Ctrl-Z) Character

A Ctrl-Z (ASCII value 26) character is used to show the end of the parameter lists and the beginning of
padding. Users wishing to organize their data for spreadsheets may search for this character to locate the end
of the parameter lists.

A.3.4 Padding

After the Ctrl-Z character, a quantity of random data—”padding”—is inserted into the file to make the
header a fixed length specified in the first \Data length parameter at the start of the header. Padding
contains no information, and exists only to accommodate various lengths of parameter lists for different
image files.

A.3.5 Raw Data

Comprising the bulk of every image file is the raw data of the image itself. At the time of Capture, image
data is stored 16-bits per pixel in the capture directory on the computer’s hard drive. (Data is stored in 2’s
complement, LSB). The 16 bits accorded each pixel allows a 32K Z-axis resolution.

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A.4 Converting Data

Refer to the following sections for preparing file data:

• Preparing Data for Spreadsheets (Summary): Section A.4.1 on Page 345

• Preparing Data for Image Processing (Summary): Section A.4.2 on Page 345

• Converting Data Files into ASCII: Section A.4.3 on Page 345

A.4.1 Preparing Data for Spreadsheets (Summary)

You may load data files into third-party, spreadsheet software (e.g., Excel, Igor Pro, Mathematica, etc.). To
convert data in to a spreadsheet program, complete the following:

1. Convert the data into ASCII format—for example, by using the File > Export > ASCII command.
(NOTE: This may increase the size of the file substantially.)

2. Select desired settings (see Converting Data Files into ASCII: Section A.4.3 on Page 345), then
SAVE.

3. Load the file into a suitable editor where it may be prepared for third-party applications.

4. Load the raw data into the third-party software program and, if needed, condition the data
according to important header parameters and requirements of third-party software application(s).

5. Analyze or modify the conditioned data as required.

A.4.2 Preparing Data for Image Processing (Summary)

You may convert data files into third-party, image processing software (e.g., Photoshop, CorelDraw). To
convert the data into image processing software, complete the following:

1. Convert the data into TIFF format—for example, by right-clicking on the image thumbnail in the
Browse window and selecting EXPORT > TIFF > 8-BIT COLOR, 8-BIT GRAY SCALE or 16-BIT
GRAY SCALE.

2. Load the TIFF file directly into the third-party, image processing software.

3. Process the image file. This may include cropping the image, filtering the image, adjusting
contrast, brightness, color, etc.

A.4.3 Converting Data Files into ASCII

When NanoScope image files are captured and stored, they are in 2-byte, binary (LSB—least significant bit)
form. Although some programs import raw, binary files, most users find they must convert the files into
ASCII form first to use them. The converted file allows users to read the header information directly and
works with many third-party programs requiring ASCII formatting. (Some users prefer to download the
original, raw binary files into their third-party program, while using their ASCII version of the file as a guide
map.)

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Note: Depending upon the software version used during capture of the image data, the actual file
format and file size varies. Headers may include more than 2000 parameters, followed by Ctrl-
Z, data padding, and raw data.

Convert captured data in to ASCII format by using the File > Export menu command. To convert files,
complete the following:

1. Make a backup copy of the file to be converted and save it to a safeguarded archive.

2. Select a directory, then an image file within it, from the file browsing window at the right of the
NanoScope main window. Right-click in the thumbnail image to open the menu shown in Figure
A.4a.

Figure A.4a The ASCII Export Command

3. Click Export > ASCII to open the Export dialog box (see Figure A.4b).

4. Select the data CHANNELs to be exported.

5. Choose the COLUMN format.

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Figure A.4b The File Export Dialog Box

6. Select the units (nm, V, Deg...) in which to record the data in the new file by checking the
appropriate boxes. Export the image header, ramp, or time information by selecting those check
boxes.

Note: In order to convert the ASCII data from binary (LSB) data to useful values (Phase, Frequency,
Current, etc.), you must save the information in the header.

7. Click Save As..., designate a directory path and filename, and click Save.

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A.5 Converting Raw Data

Before bringing raw data into a third-party application, the user can first convert the data.

Usually, this means simply multiplying all values by a constant to convert them into common measuring
units. Once converted, the data becomes more meaningful to analyze.

By using parameters in the header, it is possible to convert and analyze data for various purposes. Users
need only understand how parameters are related to extract the maximum amount of information from their
files. In the raw data information, each numeric value is relative horizontally and vertically.

A.5.1 Data Organization

Data is row-ordered starting at the lower left corner. See Figure A.5a.

Figure A.5a Exported image data organization

ROW 

ROW 

A.5.2 Calculating Scaling Values

In order to calculate height data from LSB form (no longer necessary if you export the data in DISPLAY
Units — see ASCII Export: Section 2.4.7 on Page 32), convert it by using the Z scale value. Recall that
raw data recorded from each scan is scaled to the maximum resolution of the Z-axis scanner (± 32,768).
Whether features are related in terms of “height” or “depth” is irrelevant. What matters most is that features
be accurately represented in meaningful units.

To convert raw data into metric units, use the following relation:
( data point value ) ( Z scale ) ( Sens. Z scan )
Z height = ----------------------------------------------------------------------------------------------------
-
2 16

Note: The Z scale value in a parameter list includes the value and the units (for example, \Z scale:
1.57541 μm). In this example, the units of measure are in microns (μm).

Calculating X and Y Pixel Width from Raw Data

To obtain the X axis pixel width, use the following relation:

Scan size
X = --------------------------------------------
( Samples/line ) – 1

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To obtain the Y axis pixel width, use the following relation:

Scan size
Y = ------------------------------------------------------
( Number of Lines ) – 1

A.5.3 Calculating Raw Data Values

This section details equations to calculate values for analysis (e.g., amplitude, phase, etc.).

Note: Only one set of values may be found for each Z scale. That is, the Zscale units are different for
each type of image (Hz for Frequency, or nA for Current), and the Zscale for a Height image (for
example) may not be used to find values for Phase.

The equations for converting the LSB data points into various values are as follows:

Height
data point
Height = ------------------------ × Z scale height value
65536

Phase:

Data point 180°

Phase = ⎛ ---------------------------⎞ ¥ Z scale phase ¥ ⎛ ----------------⎞
⎝ 65536 ⎠ ⎝ 65536⎠

Frequency
Data point ⎛ 25e 6⎞
Frequency = ⎛ -------------------------⎞ × Z scale freq × ⎜ ----------
-⎟
⎝ 65536 ⎠ ⎝ 2 32 ⎠

Potential
Data point 2 ⋅ In 2 max
Potential = ⎛ -------------------------⎞ × Z scale pot × ⎛ ----------------------------⎞
⎝ 65536 ⎠ ⎝ 65536 ⎠

Current (nA)
Data point 2 ⋅ In 1 max
Current = ⎛ -------------------------⎞ × Z scale amplitude × ⎛ ----------------------------⎞ × In sensitivity
⎝ 65536 ⎠ ⎝ 65536 ⎠

Amplitude (nm)
Data point 2 ⋅ In 1 max In sensitivity
Amplitude = ⎛⎝ -------------------------⎞⎠ × Z scale amplitude × ⎛⎝ ----------------------------⎞⎠ × ⎛⎝ ------------------------------⎞⎠
65536 65536 Detect sens

For LFM Aux data, the torsional deflection of the cantilever in volts (or whatever else, depending, on the
definition of the input sensitivity) can be calculated by applying the following formula to each point in the
data file:
Data point 2 ⋅ In 2 max
Deflection = ⎛⎝ -------------------------⎞⎠ × Z scale Aux A × ⎛⎝ ----------------------------⎞⎠ × In sensitivity Aux A
65536 65536

In this formula, the parameter Aux A and In sensitivity aux A can be substituted with the corresponding
parameters for Aux B, Aux C, and Aux D. In order to get the In sensitivity aux (A,B,C,D) parameters to

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appear in the header, you must select Tools > Calibrate > Detector, highlight the parameter, and then press
enter.

A.5.4 Force Curve File Format Information

When exporting the force curve in ASCII format, it is recommended that the file be exported twice, once
with the header and once without. The one without the header should be exported in Spreadsheet format
(comma delineated).

When you import the file without the header into MS Excel each value should come up as a separate entry.
\Samps/line in the \*Ciao force list displays the number of samples in the retract curve
followed by the number of samples in the extend curve. \Data length is the number of samples/line *2
(2 bytes/point) *2 (extend + retract). The scan size in Z is calculated by looking at the \Z Scan size
value in the \*Ciao force list in the header and the Sens. ZSens in the \*Scanner list.
Then do the following calculation.

In the header, find the line “\*Ciao force list” and “\Scan Size”. The Scan Size is in 16-bit
values. Convert to nm by:
Z Scan size ⋅ Sens. Zsens
Size (nm) = ----------------------------------------------------------------------
( Number of Data points – 1 )

In some cases it may be necessary to calculate the force to determine the vertical (Deflection) axis of a
curve. The following calculation may be used, as long as the microscope is in ContactMode and Input
Atten is set to 1x.

Value (nm) = data point (LSB) ⋅ Sens. DeflSens ⋅ Z scale

Note that the above equation only works when calculating force vs. separation. When calculating force vs.
Z, Z magnify force must be removed from the calculation. When calculating deflection vs. Z, the spring
constant must also be removed from the calculation.

When interested only in the deflection of the curve, the calculation below will suffice. Divide by the number
of samples to get the Z step per data point. This value is also found in the “\*Ciao force image
list” near the header end.

Force Data Organization

In later versions, the data changes and is opposite from previous versions of software. For example, the first
n samples of data includes the Extend curve from the closest approach to the farthest distance. The next n
data points are the Retract curve data from the closest to farthest distance.

Converting the Force Data to Volts

The actual data is again in 16-bit values for the input signal. Convert to volts by:
Value (LSB)
Value (V) = ------------------------------ ⋅ (Full Volt Range)
65536

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The volt range is 20V for Contact Mode when In Atten is 8X. Its 2.5 for 1X In Atten. If you are in
TappingMode looking at deflection (normal mode using Nanoindentation), it's 5V (see the table below).

Microscope Mode InAtten / Deflection Volt Range

Contact mode 8X 10V
Contact mode 1X 1.25V
TappingMode (normal mode) 5V

V of detector
The Detector Sensitivity is under the “\Ciao scan list”, as “\DeflSens” in units of ------------------------------- .
nm of Z

Force Curve File Format

To find the Z scan size and steps, refer to the Sample Parameter List for an Image File, Figure A.7a and
complete the following:

1. Under \*Ciao Force List are the parameters that describe Z:

\@Z scan start: (last number is in volts)
\@Z scan size: (last number is also in volts)

You can convert using the \@Sens. Zscan: which shows the value and units (typically 12.5 nm/V) under
the \*Scanner list line.

2. Find the number of pixels/line of data is under the \*Ciao force image list (usually last) as:
\Samps/line: nnn [where nnn is the number of pixels in each direction]

Also in the \*Ciao section is the Data Type:

\@4: Image Data: S [data type] “data description”

Data type is usually Deflection or Amplitude and can be “Deflection”, “TM Deflect.” or
“Amplitude”.

A.5.5 Force Volume File Format Information

The curve data should be right after the image height data. The curve data is the data collected at each Z point
as in a normal single force curve file. If deflection, volts is given by:
Data point (LSB) 10(V)
Deflection (V) = ------------------------------------------ ⋅ ---------------------------------------------
65536(LSB) Input atten (1 or 8)

Using the value for deflection in volts (V), it is possible to calculate the deflection in nanometers (nm) using
the equation:
Deflection (V)
Defl (nm) = -------------------------------------------------------------------
Detector Sensitivity (V/nm)

The way force volume works, it gets tricky to figure which image pixel corresponds to which force curve
data. The data and force curve are in the same order: bottom to top, left to right. There are three pixel numbers
that are needed:

• Under “\*[NC]AFM” image list, “\Samps/line” gives the number of image pixels/
line, 128, 256, 512...

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Electrochemistry

• Under “\*Force” image list, “\Samps/line: n m”, where n is the number of

samples per Force line.

• Under “\*Force cal.” list is the “\force/line: n m” parameter, where n is the

number of force curves / image line.

Consider a square block of pixels that represents one force curve. Including the data in the bottom left
corner, a simple analysis allows the identification of which pixel corresponds to which curve. If the number
of samples/force line is 128 and the number of force curves/image data is 32 and there are 256 pixels/image
data, then there is a curve every 256/32 or 8 pixels. The next image data line with force curves is the 8th one
from that line. Since there are 128 samples/force curve, they are 256 pixels or 512 bytes each. Thus, the first
image pixel matches the first force curve, the 8th pixel matches the second force curve 512 bytes later, etc.

Even though there are 3 data displays during Force Volume (Image, Force plot and FV Image), the FV
image is NOT SAVED. It is calculated during both the Real-time and Off-line display from the force curve
data as described above.

A.6 Electrochemistry

A.6.1 EC File Format

The EC file format is:

1. Header: ASCII plus padding to make it 40960 bytes long. Data offset and length of each segment
are specified. Image parameters are also recorded.

2. Image data body, 2 bytes/datapoint.

3. EC data: Potential vs. Time, 2 bytes/datapoint.

4. EC data: Current vs. Time, 2 bytes/datapoint.

A.6.2 Data Conversion

Potential
data point
Potential = ------------------------ × 20 × Potential Sensivity value
65536

Current
data point
Current = ------------------------ × 20 × Current Sensivity value
65536

Potential Sensitivity and Current Sensitivity can be found in the header file as EPotSens and ICellSens
respectively. For example:

\@Sens. EPotSens: V 1.000000 V/V

\@Sens. ICellSens: V 100.0000 ~A/V

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General Format for CIAO Parameter Objects

A.7 General Format for CIAO Parameter Objects

In the file header some parameters start with '\@' instead of simply '\'. This is an indication to the software
that the data that follows is intended for a CIAO parameter object. After the '@', you might see a number
followed by a colon before the label. This number is what we call a “group number” and can generally be
ignored.

Further, after the label and its colon, you will see a single definition character of 'V', 'C', or 'S'.

• V means Value – a parameter that contains a double and a unit of measure, and some scaling
definitions.

• C means Scale – a parameter that is simply a scaled version of another.

• S means Select – a parameter that describes some selection that has been made.

A.7.1 Value Parameters

The Value (identified by the letter “V”) parameters have the following format:
[soft-scale] (hard-scale) hard-value.

Example 1: Value parameter format

CIAO Parameter Indicator

“Group” Number Soft-Scale Hard-Value

(usually ignored)

\@1:Z limit: V [Sens. Zsens] (0.006714 V/LSB) 440.0 V

Parameter Hard-Scale
Parameter Type

LSB

Since the NanoScope is a digital device, all data is numeric. We call this number in its rawest form a LSB
(i.e., scaling values on ADCs and DACs as Volts per Least-Significant-Bit). The LSB is the digital
representation of volts or frequency and is a 16 bit integer.

Hard value

The hard value is the analog representation of a measurement. It is simply the value read on the parameter
panel when you set the Units: to Volts. The hard-value is the value you would read with a voltmeter inside of
the NanoScope electronics or inside the head. This value is always in volts with the exception of the Drive
Frequency (which is in Hertz) and some STM parameters (which are in Amps).

A value parameter might be missing a soft-scale or a hard-scale, but must always have a hard-value.

Hard Scale

The hard scale is the conversion factor we use to convert LSBs into hard values. We use the prefix “hard-” in
hard-scale and hard-value because these numbers are typically defined by the hardware itself and are not
changeable by the user.

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General Format for CIAO Parameter Objects

Soft Value

A soft-value is what the user sees on the screen when the Units: are set to Metric.

Soft Scale

The soft-scale is what we use to convert a hard-value into a soft-value. Soft-scales are user defined, or are
calibration numbers that the user divines. Soft-scales in the parameters are typically not written out —
rather, another tag appears between the brackets, like [Sens. Zsens]. In that case, you look elsewhere in the
parameter list for tag and use that parameter's hard-value for the soft-scale.

Note: The name of a soft scale can change from one microscope, controller or software version to the
next. A common problem occurs when users create programs that look for the soft scale
directly instead of parsing the value parameter to find the name of the soft scale that must be
used.

A.7.2 Scale Parameters

The Scale parameters (identified by the letter “C”) have the following format:
[soft-scale] hard-value.

Example 2: Scale parameter format

CIAO Parameter Indicator

Soft-Scale

\@Z magnify: C [2:Z scale] 0.599

Parameter Hard-Value
Parameter Type

• The hard-value is almost always a scalar value.

• The soft-scale always points to another parameter – this parameter is the target of the scaling
action.

• Most often used for the Z magnify parm to allow user to change scaling of Z scale in Off-
line without actually affecting the real data in the file.

A.7.3 Select Parameters

The Select parameters (identified by the letter “S”) have the following format:
[Internal-designation for selection] “external-designation for selection”

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 File Formats
General Format for CIAO Parameter Objects

Example 3: Select parameter format

CIAO Parameter Indicator

Internal-Designation
“Group” Number for Selection
(usually ignored)

\@2:Image Data: S [Height] "Height"

Parameter Parameter Type External-Designation

for Selection

A.7.4 Procedures to Interpret Data in a Height Image

To find the Z scale conversion factors, refer to Figure A.7a to complete the following calculation:

1. Find the Z scale line. Note that the parameter “Sens. Zsens” appears in brackets and specifies
the soft scale to the user.

2. Locate the [Sens. Zsens] in the Scanner List.

Figure A.7a Sample Parameter List for an Image File

\*File list
\Version: 0x07200000
\Date: 06:47:11 PM Fri Apr 20 2007
\Start context: OL2BIG
\Data length: 40960
\@Sens. Zsens: V 12.50000 nm/V
.
\*Ciao scan list
\Scan Size: 2000 nm //Scan Size
\X Offset: 0 nm
\Y Offset: 0 nm
\Rotate Ang.: 1.5708
\Samps/line: 512 // # Pixels in each image line
\Lines: 512 // # of lines
\Y disable: Enabled
\Aspect Ratio: 1:1
\Bidirectional Scan: Disabled
\Scan line shift: 0
\Scan Rate : 0.498246
.
.
\*Ciao image list
\Data offset: 40960 // Offset from file start to binary data for this channel
\Data length: 524288 // Length of data in this image channel
\Bytes/pixel: 2
.
.
\@Z magnify: C [2:Z scale] 0.5987848
.\@2:Z scale: V [Sens. Zsens] (0.006713765 V/LSB) 5.344157 V
\@2:Z offset: V [Sens. Zsens] (0.006713765 V/LSB) -21.60000 V

The hard scale (e.g., 0.006713765 V/LSB) is the scale at which the file was originally captured. However, to
help minimize round off errors in the off-line processing, the software automatically scales the image data to

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File Formats
General Format for CIAO Parameter Objects

the full range of the data word. While the hard value of the Z scale is updated, the hard scale is not.
Therefore, this hard scale should be ignored and we will calculate a corrected hard scale:
hard value
corrected hard scale = -------------------------
65536

Once we know the corrected hard scale, we can convert the LSBs that represent the data points in the image
to hard or soft values.
hard value = LSB × corrected hard scale

soft-value = soft-scale × hard value

Using these formulas, it is possible to deduce all one might want to know about the data.

Converting Raw Data into Height

The raw data in the file is a series of signed 16 bit (2 byte) integers. The numbers in the data file are called
LSBs (and, for our purposes, assigned a unit of ‘LSB’). In order to convert the raw data in the file, use the
number from the file and multiply it by both the hard-scale and the soft-scale.

For example, using the above parameter list in Figure A.7a, the corrected hard scale would be:
5.344157V-
-------------------------- 5.344157V V
(8 ⋅ 2)
= --------------------------- = 0.00008154536 -----------
2 65536 LSB

Now, if we had a value of 54 in the data file, the result would be:
V nm
( 54LSB ) ⋅ ⎛⎝ 0.00008154536 -----------⎞⎠ ⋅ ⎛⎝ 12.50 --------⎞⎠ = 0.005504nm
LSB V

Note: The same procedure may be used to calculate frequency, current, potential, amplitude data, etc.,
by using the appropriate Z scale. However, each data set requires a specific Z scale. For
example, the Z scale for potential may not be used to calculate frequency.

What is the range of the data in the file?

The range of data in the file may be found by multiplying the hard-value by the soft-scale. Using the hard-
value and soft-scale values from the example above:
nm
5.344157V ⋅ 12.50 -------- = 66.80nm
V

How can I calculate the displayed Z scale for use in my own analysis programs?

Data is expanded in the NanoScope file after capture to prevent round-off in the Off-line calculations. The
expansion procedure changes the Z scale to correspond with the new scale of the expanded data. Yet, in Off-
line, the software displays the data with the original Z scale used to capture it.

You can use Z magnify to discover the displayed Z scale. The modified Z scale is 67 nm. Z magnify (from
the Sample Parameter List for an Image File, Figure A.7a) tells us there is a scale of 0.5987848 missing. So
the data on the screen in the NanoScope off-line is displayed at 40 nm. This trick also works if the user
changed the displayed Z scale in Offline.

356 Nanoscope Software 7.30 User Guide Rev. G

 Index

Offline planefit 68
parameters 66
Numerics
Realtime Planefit 68
3D Surface Plot 191
Scan line 67
A
Clean Image 246
Abort Capture button 60 Clean Image Analysis
AC Bias Parameter 145 Execute button 249
Alt button 17 Reload button 249
Analysis Commands
Color Bar 56
3D Surface Plot 191 Commands
XY Drift 240 Off-line Modify
Zoom 194, 250 Spectrum 2D 280
Area, Width 238 Offline View
Aspect ratio, Scan Controls panel 62 Surface Plot 191
Auto Tune 51 Contact AFM
and Interleave mode 51 Setpoint 71
Overview 49 Crop and Split 250
parameters 52 Ctrl-E 91
Auto Tune Controls panel D
Auto Tune 51 Data Type
Auto Tune, Auto Tune Controls panel 51 Phase 66
AutoTune 50 Potential 66
Av max depth (Rvm), Roughness 219 Depth Analysis 198, 233
Av max ht (Rpm), Roughness 219 interface 201, 237
B procedures 200
Bidirectional scan 77 theory 198, 233
box cursors 18 Depth at Histogram Max 202
Box x dimension, Roughness 219 Depth at max 202
Dialog Boxes
Box y dimension, Roughness 219
Spectrum 2D, Box 1 281
Box, 282
Surface Plot 191, 208
Browse window 172
Drive amplitude, Feedback Controls tab 71
C Dual-Scan Image 187
Capture button 29, 60
E
Channel
selection of 56 Electric Tune 53
Channels tab 65 Engage button 60
Line direction 67 Engage delta setpoint, Delta Setpoint 92
Engage final delta setpoint, Final setpoint 92

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Index

Engage min setpoint 93 Histogram, Depth 198, 234

Engage test threshold slope, Test threshold slope I
92 Image Mean, Roughness 219
F Image Parameters 56
Feedback Control tab
Image Projected surface area, Roughness 219
Drive amplitude 71
Image Ra, Roughness 219
Feedback Controls Tab
interface 68 Image Raw mean, Roughness 219
parameters 69 Image Rmax, Roughness 219
SPM feedback 70 Image Rq, Roughness 219
Feedback Controls tab Image Surface area difference, Roughness 219
Integral gain 70 Image Surface area, Roughness 219
Proportional gain 71 Image Window 55
Flatten 257 Image Z range, Roughness 219
Flatten Analysis Images View 182
Execute button 262 Integral gain, Feedback Controls tab 70
inputs parameters 262 Interface
interface 261 depth 201, 237
polynomials 258 Interleave Controls tab
procedures 259 Lift scan height 73
theory 258 Lift start height 74
Undo button 262 Proportional gain 72
Interleave mode
Flatten Order 262
Auto Tune 51
Flatten Threshold for 262
disabled 73
Flatten Z Thresholding % 262
K
Flatten Z Thresholding Direction 262
Kurtosis, Roughness 219, 220
Fluid TappingMode 69
Force Cal Control Panel L
Number of samples 106 Level, Stepheight 231
Force Curves 100 Lift scan height, Interleave Controls tab 73
Frame Down button 60 LiftMode 72
Frame Up button 60 line cursors 18
G Line direction, Channels tab 67
Gaussian Analysis Lines, Scan Controls panel 64
Execute button 265 M
Reload button 265 Main Tab
Gaussian Filter 263 interface 60
Generic Lock-In 159 setting the parameters 61
grid markers 18 Max height (Rmax), Roughness 220
H Maximum depth (Rv), Roughness 220
Height 73 MCA 189
and Data Scale 67 Mean Roughness (Ra), Roughness 220
and Data Type 66 Mean, Roughness 220
and Interleave mode 72 Measure, Stepheight 231
Color Bar 56 Microscope Mode Parameter 143
Z Motion 44 Microscope mode, Other Controls panel 75
Modify
High Speed Data Capture 164, 194
Flatten Manual 257
Histogram filter cutoff, Depth 202, 237

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 Index

Spectrum 2D 280 Point and shoot 47, 167

Subtract Image 289 Polynomials
Modify Commands Flatten 258
Crop and Split 250 Plane Fit 275
Multiple Channel Analysis 189 Potential
triple-scan 188 Data Type 66
N Power Spectral Density 204
Number of Peaks Found 202 Power Spectral Density 204–213
Number of samples, Z Scan Controls panel 106 PR ampl limit Parameter 146
O PR Drive Amplitude Parameter 145
PR Drive Frequency Parameter 145
Offline planefit, Channels tab 68
PR Drive Phase Parameter 146
Offline, Subtract Image 289
Origin points PR lockin BW Parameter 145
Programmed Move 335 PR phase limit Parameter 146
Other Controls Panel Pre engage setpoint 95
Piezoresponse Mode 143 Projected Surface Area 220
Other Controls panel Proportional gain, Feedback Controls tab 71
Microscope mode 75 Proportional gain, Interleave Controls tab 72
Units 76 Q
P quick key 17
Parameter
R
AC Bias 145
Ra (Mean Roughness), Section 226
MIcroscope Mode 143
Ra, Roughness 214
PR ampl limit 146
Raw mean, Roughness 220
PR Drive Amplitude 145
Realtime Planefit, Channels tab 68
PR Drive Frequency 145
Recipe 303
PR Drive Phase 146
Restore, Stepheight 231
PR lockin BW 145
Rmax (Maximum Height), Section 226
PR phase limit 146
RMS (Rq), Roughness 220
Passband,Spectrum 2D 282
Roughness Analysis 213
Peak Count 220
interface 216
Peak Parameters, Roughness 217
procedures 215
Peak to peak, Depth 202
Phase theory 214
Data Type 66 Roughness measurements 219, 226
Piezoresponse Force Microscopy 143 Roughness, effects of plane fitting on 214
Piezoresponse Mode 143 Rz 220
Plane Fit Analysis 274 Rz (Ten+Point Mean Roughness), Section 226
Buttons 279 Rz Count 220
inputs parameters 279 Rz, Roughness 220
interface 278 S
polynomials 275 Samples/line, Scan Controls panel 64
procedures 276 Scan angle, Scan Controls panel 63
plane fit order 279 Scan Controls panel 62–64
Plane Fit, effects on roughness measurements Aspect ratio 62
214 Lines 64
Plot type 192 Samples/line 64

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Index

Scan angle 63 Stopband,Spectrum 2D 282

Scan rate 63 Subtract Image 289
Scan size 62, 63 Surface area diff, Roughness 221
Slow scan axis 64 Surface area, Roughness 221
Tip velocity 64 Surface Plot Dialog Box
X offset 63 Light horizontal angle 193
Y offset 63 Pitch 192, 193
Scan line shift 77 Rotation 192
Scan line, Channels tab 67 T
Scan rate, Scan Controls panel 63 Tapping Engage 91
Scan size 96 TappingMode
Amplitude feedback 70
hints to optimize 96
Deflection feedback 70
Scan size, Scan Controls panel 62, 63
Scan Tab Setpoint 71
interface 62 Test threshold dZ 93
parameters 62 Three Dimensional Surface Plot 191
Scan View Tip velocity, Scan Controls panel 64
Channels Tab 65 tip-sample force 111
Feedback Controls Tab 68 TM Deflection 66
Main Tab 60 TM engage gain 93
Scanning Tunneling Microscopy (STM) Total peaks, Depth 202
Linear feedback 70 Trigger safety 95
Log feedback 70 Triple-Scan Image 188
Scan-Single
2D, Power Spectral Density 208
overview of interface 55
Scope U
color 58 Units, Other Controls panel 76
filter 58 Units, Z Scan Controls panel 107
Section Analysis 221 V
interface 225 Valley Count 221
procedures 224 Vision Window 56
roughness measurements 226 W
Setpoint Width 233
Contact AFM 71 Width Analysis
STM 71 procedures 235
TappingMode 71 Withdraw button 60
Sew tip 94 Workspace 11
Sewing trigger 94 X
Signal Access Software 98 X mean, Width 238
Skewness, Roughness 221 X offset, Scan Controls panel 63
Slow scan axis, Scan Controls panel 64 X sigma, Width 238
SPM feedback, Feedback Controls tab 70 XY Drift Analysis 240
Stage Y
Programmed Move 333
Y mean, Width 238
Step 230
Y offset, Scan Controls panel 63
STM
Y sigma, Width 238
Setpoint 71
Stopband, 282
Z
Z range, Roughness 221

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 Index

Z Scan Controls panel

Number of samples 106
Units 107
Z Thresholding parameters
Flatten 262
Plane Fit Analysis 279
Zoom Analysis 194, 250
interface 252
procedure 250

Rev. G Nanoscope Software 7.30 User Guide 361