Apreo 2

User Operation
Manual

Revision C
Sep-2021
 Trademark Acknowledgments

Microsoft® and Windows are registered trademarks of Microsoft Corporation.

This manual was produced using FrameMaker™ document publishing software.
FrameMaker™ and Adobe are registered trademarks of Adobe Systems Incorporated.
Other product and company names mentioned herein may be trademarks of their respective owners.

Copyright © 2021 by Thermo Fisher Scientific Company

The information and materials contained herein are proprietary to Thermo Fisher Scientific Company.
They are provided for your organization's internal use on a need-to-know basis.
They cannot be duplicated or disseminated for any third party without the express consent of
Thermo Fisher Scientific Company.

Limited Rights

Contractor Name:
Thermo Fisher Scientific
Contractor Address:
5350 NE Dawson Creek Drive, Hillsboro, Oregon 97124, USA
The Government's rights to use, modify, reproduce, release, perform, show, or disclose these technical data
are restricted to those rights specified in:
DFARS 252.227-7015(b)(2), FAR 52.227-14(g)(2) (Alternate II) and FAR 12.211.
Any reproduction of technical data or portions thereof marked with this legend
must also reproduce the markings.
Any person, other than the Government, who has been provided access to such data,
must promptly notify the above named Contractor.

Manufacturer & Technical support

To provide feedback on this document, please submit via

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Table of contents

Chapter 1 System overview

User manuals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. . . . . . . . . . . . . . . 1-1
Apreo 2 User safety manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
User operation manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1
System capabilities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-2
System performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

Chapter 2 System control

System layout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Other software and hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Interface elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-2
System states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4
Overnight state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Standby state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Complete shutdown. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-6
Vacuum system . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-7
Vacuum status . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8
Vacuum modes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9
Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Detector types and application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Stages and accessories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12

Chapter 3 Software control

Software interface elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Icons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Tooltips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Pull-down menus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Command buttons . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Property editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Edit boxes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Radio buttons / Check boxes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2
Adjusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-3
2D controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Modules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Dialogs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Tabs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
Progress bars. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4
xT microscope Server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-5
Microscope Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Entering Commands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Workspace customization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-6
Menu bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-8
Toolbar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-23
Imaging area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-27
Status bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-29
Control pages and modules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-30
Preferences dialog . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-39
Account Manager application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-54
Password policy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-54
Accounts control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-54
User Logins and Account Settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-56

Revision C Sep 2021 User Manual C-i

 Table of contents

Chapter 4 Alignments
Common Rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Buttons and Control Elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1
Alignments module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

Chapter 5 Operating Procedures

Specimen Preparation and Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Needed Items. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Natural Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Coated Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Mounting Specimen on Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2
Specimen Baking Unit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-3
Microscope Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Operation Pre-Check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6
Inserting / Exchanging Specimen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Selecting Vacuum Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-7
Imaging Onscreen . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Optimizing Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Principles of SEM Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8
Magnification. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Scan Speed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Contrast & Brightness . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9
Focusing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Correcting Astigmatism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-10
Auto Flash Predefined / Customized . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11
Direct Adjustments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-12
Digital Imaging Enhancement / Imaging Mixing / Coloring . . . . . . . . . . . . . . . . . . . . . . 5-13
Accelerating Voltage and Beam Currents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-15
Column Use cases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-16
Standard Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Retractable detectors control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Infrared CCD Camera . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-17
Everhart Thornley Detector (ETD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Low Vacuum Detector (LVD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-18
Trinity Detectors T1 / T2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
T1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
T2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
T3 (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-19
Beam Deceleration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Detection Principles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-20
Beam Deceleration module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-21
Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-22
Electron Channeling Pattern . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Sample preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-23
Stage Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
Eucentric Position . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25
Software control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-27
Stage Related Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-31
Capturing and Handling Single Image. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
Image Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-38
Saving / Opening / Printing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-39
Recording Movies (Saving Multiple Images) . . . . . . . . . . . . . . . . . . . . . . . . . 5-40
Movie Settings Dialog. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-40
Movie Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-42
Movie Creator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-43
Patterns / Measurements / Annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-46

C-ii User Manual Sep 2021 Revision C

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Chapter 6 Maintenance
Cleaning procedures overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
List of applied cleaners . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1
Cleaning column parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Materials and technique . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2
Cleaning stage mechanics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Cleaning stage parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-3
Refilling water bottle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4
Water chiller . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-5

Chapter 7 System Options

Manual User Interface . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Joystick . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-2
Uninterruptible Power Supply (UPS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-3
Optional Detectors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Optional detectors connection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
Trinity Detector T3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-4
RGB Cathodeluminescence detector (CLD) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5
Directional Gaseous Analytical Detector (GAD). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-6
Directional Backscattered Detector (DBS) –
Angular Backscattered Detector (ABS) / Concentric Backscattered Detector (CBS) . . . . . . . 7-8
Retractable Annular Scanning Transmission Electron Microscopy Detector
(STEM 3 / STEM 3+) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-9
Nav-Cam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
Capturing Navigation Image Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-12
External Current Measurement (Keithley Picoamper Meter) . . . . . . . . . . . . . . . . . . . 7-13
Energy Dispersive Spectroscopy (EDS) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-13
EDS analysis and microscope configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-14
ColorSEM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-15
Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-16
Analytical layout. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-17
Analytical page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-20
EDS Pulse Processor Alignment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-21
Patterning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-22
Patterning Control module. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-23
Patterns Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-26
Gas Injection module (option) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-28
Application Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-29
CleanConnect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Mechanical Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-30
Procedures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-35
Manual Loader Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-38
MAPS Mineralogy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-39
μHeater . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-40
μHeater installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-41
Software control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-44
High vacuum heating stage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-47
High vacuum HS installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-50
Software control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-52
Remote Imaging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-56
Connection to Microscope PC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-56
Quick Loader . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-58
Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-58
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-61
Operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-62

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 Table of contents

UMB Stub Holder Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-63

CryoCleanerEC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-64
Parts and Accessories. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-64
CryoCleaner Operation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-65
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-66
Spare Vessel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-66
Plasma Cleaner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-67
Sample Cleaning Procedure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-68
Chamber Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-68

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1
System overview

User manuals

Apreo 2 User safety manual

The safety manual provides information for personal safety and maintenance procedures while
operating this system.
This manual is required reading for the end user.

User operation manual

The User Manual is delivered as an electronic PDF file only. However, it is possible to print parts of the manual if
this is desired.
We recommend reading the appropriate User Manual section before operating any microscope function. Most
importantly, you should locate the topics necessary to operate the microscope in the proper way to safely achieve
the best results.
The manual is divided into the following chapters:
1. System overview (this chapter)
gives an overview of the user manual and system capabilities.
2. System control
describes the system hardware (interface elements, vacuum system, system states, equipment).
3. Software control
describes the interface that sets and controls system operation; gives the function of each tool, menu item and
control page.
4. Alignments
explains how to align the equipment to achieve the optimal performance.
5. Operating procedures
gives procedures for how to use the system’s features.
6. Maintenance
gives allowed step by step cleaning and maintenance procedures.
7. System options
explains relevant options that can be integrated into or added as accessories to the system.
One can take advantage of the search and navigation possibilities within the PDF file. In addition, the following
conventions are applied:
• A reference to the specific software element is highlighted in italics. For instance:
“Clear the Stage menu / Beam Shift Reset item.”
• Some software functions use shortcuts, which are given beside the heading in brackets.
For instance: Save (Ctrl + S). They are also given in the Help menu / Keyboard Shortcuts.

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 System overview: System capabilities

System capabilities

The Apreo 2 is a Scanning Electron Microscope (SEM) that produces enlarged images of a variety of specimens,
achieving magnification over 100 000× and provides high resolution imaging in a digital format. The instrument
provides optimum throughput, resolution and automation.
This important and widely used analytical tool provides exceptional field of view, requires minimal specimen
preparation, and has the ability to combine the technique with X-ray microanalysis.
The instrument provide an expanded range of capabilities:
• High-resolution electron beam images
• High resolution elemental microanalysis of defect cross sections
• Imaging of sample surfaces with the electron beam during navigation without erosion

System performance
The main instrument components used for imaging of the samples are:
• Electron source
The beam of electrons (particles) is emitted within a small spatial volume with a small angular spread and
selectable energy.
• Lens system
The beam enters the lens system consisting of several electromagnetic or electrostatic lenses and exits to hit
the specimen surface.
• Scan unit
The scan generator signal, fed to the deflection systems, moves the beam in a raster pattern over the specimen
area. This signal, modulated by the detection system signal, produces the onscreen image of the specimen’s
surface.
• Detection unit
Particles (electrons) striking the specimen react with atoms of the sample’s surface in various manners to
produce electrons and photons (X-rays).
The detector system picks up the particles or photons and converts them into a digital signal that is then sent to
the control PC and shown on the monitor.

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 System overview: System capabilities

FIGURE 1-1: Column schematic overview

Electron
Source

CONDENSER LENS SYSTEM

LENS(ES)
SCAN UNIT

DEFLECTION SCAN GENERATOR M

SYSTEM

FINAL LENS

R
TO
T EC DETECTION UNIT
DE

SPECIMEN

Computer control
The xT microscope Server and Microscope Control (User Interface) software integrate SEM functionality within a
Windows 7 operating environment.
This software consists of programs defining specific instrument settings for particular applications, ensuring
reproducibility of complex procedures (for instance imaging, management of image capture, storage, and data
output devices etc.). They also control instrument hardware (the column, detector(s), stage, EDX, vacuum
functions etc.).

Vacuum system
The entire particle path from a source to a specimen must be under vacuum so that the particles do not collide with
air molecules.
Various levels of vacuum are necessary, so a Turbo Molecular Pump (TMP) backed by a scroll pre-vacuum pump
(PVP) obtains the necessary specimen chamber pressure.
High Vacuum (HiVac) mode
This is the conventional operating mode associated with all scanning electron microscopes.
Low Vacuum (LoVac) mode
In the gaseous mode the electron column is under lower pressure than the specimen chamber. This mode can use
water vapors from a built-in water reservoir, or an auxiliary gas that is supplied by a user and connected to the gas
inlet provided for this purpose. Observation of outgassing or highly charging materials can be made using this
mode without the need to metal coat the sample, which would be necessary for the conventional HiVac mode.

Stage
The Apreo 2 has a computer-controlled high-accuracy five-axis stage for small samples. It offers precision
specimen computer controlled manipulation and automation of all axes for overall spatial orientation on highly
repetitive or extremely irregular samples.
Specimen exchanges take place through a chamber door that exposes the specimen stage when opened or through
the Quick Loader (option). An exchange time takes a few minutes; with the Quick Loader, an exchange is much
faster. Software and interlocks protect the system against damage and users against an injury.

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 System overview: System capabilities

Image viewing and capture

Because the amplified detector signal is shown synchronously with the beam scanning, there is a relationship
between brightness of an image point on the monitor screen and the signal detected at the corresponding point on
the specimen.
Magnification is the ratio of the size of the viewing monitor screen to the size of the area scanned on the specimen.
Higher magnification is achieved by reducing the size of the area scanned on the specimen.

Gas injection system (GIS)

Multiple GIS (option) can be installed for material deposition in conjunction with electron beam pattern definition.
Electron beam-induced deposition offers the advantage of not sputtering of the deposited material.
Several GIS chemistries can be installed on the instrument, depending on system configuration. This self-contained
apparatus allows the material to be contained entirely within the vacuum system for simple, flexible, and safe
operation.

Analysis capability
Convergence of the SEM and X-ray detection system (e.g.
EDX – Energy Dispersive X-ray – option) at a short
working distance allows precision chemical analysis at
high resolution of surface and subsurface features.
Various vendor options are compatible with the
instrument (see Chapter 7).

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2
System control

This chapter describes the layout of the system, interface elements and equipment.

System layout

The basic system layout is based around the dedicated Microscope computer with the LCD monitor and
Microscope console. Optionally it is possible to have a second LCD monitor with the Microscope computer or the
Support computer, using the LCD monitor and the switch box with keyboard and mouse to switch between the two
computers.

FIGURE 2-1: Apreo 2 standard layout scheme

Caution!
– If the equipment is used in a manner not specified by the manufacturer, the protection provided by the equipment may
be impaired.
– Mains power must be connected to a grounded socket that is visible and easily accessible!
– A user must not disconnect any parts of the equipment or connect any equipment not approved in this manual or in the
Apreo 2 User safety manual!
– All power and external equipment connectors should be covered by stoppers (part of delivery) when not used!

Other software and hardware

Call customer service for advice before installing software or hardware that is not required for system operation.
Other software, such as screen savers or hardware network cards, may corrupt the xT microscope Server /
Microscope Control software under some circumstances and may invalidate the warranty.
For more detailed information about Windows 7™, refer to the Microsoft® Windows™ User’s Guide shipped with
your system.

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 System control: Interface elements

Interface elements

Software
The software control contains graphics applications within the Windows 7™ operating environment:
• xT microscope Server: starts and stops basic microscope functions
• Microscope Control (UI – User Interface): controls all system functions including imaging, image
and movie gathering / manipulation / output, detection and analysis, scanning, magnification,
stage navigation, chamber and column pressure, etc.
• User Management: ensures users admission to both the operating system, Windows 7, and the
Microscope Control software
For information on all the features of these applications see Chapter 3.

Hardware
The system is computer-controlled. As such, it has a Microscope Computer that must be turned on (use the power
button on the PC) to operate the microscope by means of the software. The support computer (option) can hold some
other software utilities. The switch box switches the keyboard and the mouse to either of the two computers. The
control software facilities and data are shown graphically on the LCD monitor and are superimposed around and on
the image. The other LCD monitor is used either as an extended desktop of the Microscope computer or as the
Support computer monitor. To control software utilities, one can use a keyboard, a mouse, the joystick (option) or the
Manual User Interface (option).

Power button
The console / system power is activated by pressing the power button located on the microscope console front
panel. This switches the sub-systems on and allows the interface and communication with the Microscope
computer, from which most of the functions are activated via the software control.
The power button indicates several system states:
• green lit – the Full Operation state
• amber lit – the Standby system state
• not lit – the Complete shutdown system state

FIGURE 2-2: Control panel Power button

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 System control: Interface elements

External connectors panel

It is located on the back of the microscope console.
It is used to connect 3rd party equipment to the
following connectors:
CONTROL SIGNALS / E-BEAM SCAN INPUT /
VIDEO OUT
These connectors are used for the connection of EDX,
WDX and lithography systems, provided by 3rd party
suppliers. Do not connect anything else to these
connectors!
SPECIMEN CURRENT
This connector is used together with the Keithley
picoamper meter (option) equipment.
Ground point
The point is intended for a defined ground connection
between a microscope and a 3rd party module. This
connection is not a safe ground!
ELPHY SCAN & BLANKING IN
Not used.

Mains switchboard
The Mains switchboard is located on the back of the microscope console.
WA R N I N G !
Power sockets labeled X1–X4 are used for equipment delivered and installed by Thermo Scientific. It is forbidden to use
these sockets by a user for any purpose!
Breaker switches
• Mains switch S1 – entire system mains power switch
• PVP Breaker F1/5A – pre-vacuum pumps power
switches
• Mains Breaker F2/10A – system pumps power
switches
Power sockets are used for other microscope equipment
and options.
• Main input 230 VAC – input mains power cord
• PVP X5 – output power supply for pre-vacuum pumps
• X1 – not used
• X2 – optional equipment output power supply
• X3 – optional equipment output power supply
• X4 – output power supply for Microscope PC, LCD 1,
optionally for Support PC,LCD 2, LCD 3

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Power off
The system has protection against power failures in the sense that the different components of the system are not
likely to be damaged. However, a power failure is never good for the system. It might affect the ultrahigh vacuum
levels of the columns and the overall stability of the system.
Take sufficient measures to avoid power failures. If a power failure occurs while the instrument is completely
operational, the microscope enters a safe state and the following happens:
• Electron accelerating voltage is switched off.
• Electron emission is switched off.
• The specimen chamber automatically vents gently.
The vacuum in the instrument is no longer supported by running pumps. The column isolating valves close to
save the vacuum in the source area.
• The Microscope computer and the Support computer are switched off. The momentary adjustments of all
system parameters (accelerating voltage, magnification, stage positions, etc.) are lost if they were not saved.
Note
If mains failures occur occasionally, using the Uninterruptible power supply (UPS – option) is recommended.

Emergency off
To switch off the electrical power completely in case of emergency, push any of the red EMERGENCY OFF buttons
(located in the vicinity of the system (see the Apreo 2 User safety manual). This turns off all hazardous system
voltages, the impact is the same as Power off (see above).

FIGURE 2-3: EMO button

Caution!
Always keep all control elements accessible! This is especially important in case of emergency.
WA R N I N G !
The microscope console water chiller (option – separate device in the microscope vicinity) is powered separately via its
individual power cord. Hazardous voltages may be present in this equipment even when the microscope power plug is
disconnected!
Because the electron column IGP’s are supported by internal batteries, some parts of the microscope are still under power.

System states

There are several system states:

• Full operation – all microscope equipment and accessories are in use or ready to use
The system is intended for continuous operation.
• Overnight – not using the system overnight
• Standby – not using the system for a longer period
• Complete shutdown – service and emergency reasons
See detailed description of all following processes and elements further in this manual.
The Complete shutdown system state and the System startup are restricted to the Thermo Scientific Service
Engineer or an authorized user.

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 System control: System states

Overnight state
In the Full operation state all microscope equipment and accessories are in use or are ready to use. When leaving
the system, we advise bringing it to the Overnight state by following this procedure:
1. Select (a) the File menu / Log Off “present user”; the Log On
dialog appears for entering another one.
2. Switch off the monitor.
Several days
1. Click on the Column module / Beam On button to switch off
the beam.
If you need to remove a sample:
2. Click the Stage menu / Tilt 0° (Ctrl + E). Click on the Vacuum
module / Vent button. Wait for the Vented status, then
remove your sample.
3. Click on the Vacuum module / Pump button to pump to the
High Vacuum. (b)
4. Click (d) the xT Microscope server / Stop UI button. This
action also logs off the current user.
5. Switch off the monitor.
Returning to operation
1. Switch on the monitor.
2. Click (a) on the xT Microscope server / Start UI button to start
the Microscope Control software. This step can take place
automatically, if the Advanced / Autorun UI check box has
been ticked. The main window appears behind the UI Log On
dialog.
3. Enter your Username and a Password (c).
4. Click on the Column module / Beam On button to start the
beam. The source awaking progress bar indicates the actual
status and the button turns orange when finished.

Standby state
In the Standby state, electron emission remains on, and the
chamber vacuum is maintained by running vacuum pumps.
1. Follow the first 3 steps to bring the system to the Overnight
(Several days) state.
2. Click on the xT microscope Server window / Standby button.
Confirm the dialogs and wait until the UI state and Server state
are STOPPED.
This stops the UI, the xT microscope Server application
services and switches off the console (the green power button
on the microscope front control panel changes to the amber
button). (d)
It is possible now to shut down the operating system and
support computers if needed.
Returning to operation
It is assumed here that all external supplies are present. The
startup procedure is fully automatic.
Caution!
When the Standby state was just entered, wait a minimum of
10 seconds before starting the microscope operation again (by
pressing the power button on the microscope front control panel)!

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 System control: System states

1. Push the amber Power button on the Microscope console panel

– it changes to green. (e)
2. Turn on the computers and start the operating system.
3. Double-click on the xT microscope Server icon to start the
software (all visible LED’s should be green – Initialized).
4. Follow the steps from No. 2 to No. 4 above (Overnight state /
Returning to operation).
Note
a)
Waiting for a new user leaves the status of the Microscope Control
software non-operational and only the xT microscope Server software is running. Therefore changing users does not
require Logging off / Logging on at the Windows 7™ level.
b)
We strongly recommend always leaving the chamber evacuated when it is not being used. When the sample chamber is
left in the LoVac mode, water vapor is likely to accumulate in it, PVP lifetime decreases, and the water reservoir or gas
cylinder empties prematurely.
c)
Take note of the Password policy and the Account Manager application (see Chapter 3). The system starts with the
setting last in use when the Microscope Control software was closed. This allows quick resumption of daily operation.
d) The system can be left in this state if electrical power is supplied to the instrument because the pumps are running and
pumping the column.
e)
When switching the console on (starting from the Standby state), the SEM aperture becomes heated. It may take several
(5–10) minutes before it is at the proper temperature. Do not make any adjustments during this interval! The microscope
could become misaligned when the aperture reaches the operational temperature.

Complete shutdown
In case of emergency, bring the system to the Complete shutdown state by following this procedure:
1. Switch off the Emitter with the use of the E-column: Emitter Startup alignment. (f)
2. Set the system to the Standby state (see above).
3. Shut down the Microscope and Support computers and switch off the monitors.
4. Set the eConnection kit (placed visibly on the wall around the microscope system) > MAIN SYSTEM DISCONNECT
switch to OFF. (g)

FIGURE 2-4: eConnection box

5. If necessary, stop gasses and cooling water flow in the Connection box (see the Apreo 2 User safety manual).
Note
f)
Switching off the console when the Emitter is on is not optimal for the emitter – it may deteriorate its filament lifetime.
g)
The Complete shutdown procedure brings the system to the non-powered state, in which the vacuum in the column area is
no longer supported by running pumps. Normally this is used for system transportation or for service actions, such as repair to
essential systems (electrical and air supplies).

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 System control: Vacuum system

Vacuum system

Model difference
There are the High Vacuum and Low Vacuum variations of the
Apreo 2 system. This manual describes the Low Vacuum model.
For the High Vacuum model, some controls are missing and
functionality is modified accordingly.
The system has the these vacuum sections:
• Electron source
• Electron column
• Specimen chamber
When in operation, the electron source and column section are
always under high vacuum. The specimen chamber is at the
pressure required for the given state (Pump / Vent) or mode
(HiVac / LoVac).
Note
When the LoVac mode is chosen, the ChIV is closed. All valve and
pump operations are fully automatic.

FIGURE 2-5: Apreo 2 high vacuum / Apreo 2 low vacuum Vacuum system

AGV . . . . . . Auxiliary Gass Valve IGP . . . . . . . .Ion Getter Pump

BPV . . . . . . . By Pass Valve NAV . . . . . . .Nitrogen Admittance Valve
BG . . . . . . . . Buffer Gauge NVC . . . . . . .Needle Valve Control
BV . . . . . . . . Buffer Valve PVP . . . . . . .Pre Vacuum Pump
CIV . . . . . . . Column Isolation Valve SIV . . . . . . . .Servo Isolation Valve
ChEV . . . . . . Chamber Evacuation Valve TMP . . . . . . .Turbo Molecular Pump
ChIV . . . . . . Chamber Isolation Valve TVV . . . . . . .Turbo Venting Valve
EG . . . . . . . . Environment Gauge VV . . . . . . . .Venting Valve
HVG . . . . . . High Vacuum Gauge WBV . . . . . .Water Bottle Valve

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 System control: Vacuum system

Vacuum status
The vacuum status controls are in the Vacuum module. The Pump
button starts pumping the chamber for the operating pressure
and the Vent button starts venting the chamber for a sample
exchange.
At the bottom right side of the status bar the actual vacuum
status is represented by the colored icon, which may have three
possible colors with the following meanings:
• Green: PUMPED to a desired vacuum mode
• Orange: TRANSITION between vacuum modes
(pumping / venting / purging)
• Gray: VENTED to atmospheric pressure

Pump button
When the Pump button is clicked and the status is Vented or when changing the vacuum mode, the system starts to
pump. The target pressure depends on the selected vacuum mode. The Pump button is highlighted and is not
accessible.
For High Vacuum, the system achieves the lowest pressure possible. For Low Vacuum, it achieves the pressure
specified in the Vacuum module / Chamber Pressure adjuster. The purge function can be defined in the Preferences…
dialogue / Low Vacuum tab (see Chapter 3).
When the Pump button is clicked and the status is Transition (venting), the venting procedure stops and the system
immediately starts to pump to the actually selected vacuum mode.

Vent button
When the Vent button is clicked and the status is Pumped, the
confirmation dialog appears. After confirmation, the system
switches off the detector voltages, high voltage supplies, vacuum
pumps and uses the appropriate valves to vent the system with
the use of the dry nitrogen brought to the Nitrogen Inlet. Nitrogen
is recommended to obtain a better vacuum for high resolution
imaging in HiVac mode.
The Sample Exchange window and progress bar are shown; the
Vent button is highlighted but not accessible. After a specified venting time, the venting valve closes and the
vacuum status should indicate Vented (see Preferences… dialogue / General tab / Venting valve opening time item).
The chamber door can be opened and the button is again enabled.
When the Vent button is clicked and the status is Transition (pumping), this dialog appears. After confirmation, the
pumping procedure stops and the venting procedure starts.
When the Vent button is clicked and the status is Vented, this dialog appears. After confirmation, the venting valves
re-open for the specified venting time and then the valves close.
Note
If you vent the system in order to change a detector, wait until the icon with a gray specimen chamber appears in the Status
module. Otherwise there is a risk of a detector assessment malfunction, and as a result, the PLA will not be known by the
system.

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 System control: Vacuum system

Vacuum modes
The Vacuum module / High Vacuum or Low Vacuum radio buttons
are used to select the instrument target operating mode when a
Pump sequence is initiated.
When changing the vacuum mode from one mode to another, a
confirmation dialog appears.

High Vacuum (HiVac) mode

For High Vacuum, the system achieves the lowest pressure
possible throughout the column and specimen chamber. The
typical pressure value is within the order of 10-2 to 10-4 Pa.

Low Vacuum (LoVac) mode

In this mode, the column section is under lower pressure than the
specimen chamber, where the pressure ranges from 10 to 500 Pa
(0.08 to 4.0 Torr) depending on the Use case and PLA used:
• Standard Use case without PLA: 10 – 50 Pa
• OptiPlan Use case with PLA: 10 – 150 Pa
• Standard Use case with PLA: 10 – 500 Pa
This mode uses water vapor from a built-in water reservoir, or a gas from an auxiliary gas inlet (the drop-down list).
When entering the LoVac mode from the vented state or when changing the gas type, chamber pressure goes to
the HiVac value and subsequently to the desired LoVac value, so the old gas mixture in the chamber is first
exhausted and then replaced by gaseous atmosphere. Entering the HiVac mode can by unwanted for highly
outgassing samples (see the Preferences… dialogue / Low Vacuum section / Fast Low Vacuum Pumping Through High
Vacuum check box functionality).
The system automatically detects any Low Vacuum detector installed (LVD and GAD) and offers to switch to the
LoVac vacuum mode. If a relevant detector is not in place, a warning appears informing the user that the detector
should be installed for the mode selected. However, the system will not abort the pump sequence.

Pressure
The Chamber Pressure adjuster is used to set and show the target chamber pressure. Pascal, Torr or Millibar units
are available and can be selected in the Preferences… dialogue / Units tab.
When the system is in LoVac mode and the Chamber Pressure value is changed, the pressure automatically changes
to the new value. When the system is in any other status and the chamber pressure value is changed, the new
value is used as the target pressure when the system starts pumping to a Low Vacuum mode again.
The actual specimen chamber pressure is shown in the Status bar /
Chamber Pressure field.
PLA (Pressure limiting aperture) Accessories
When the LoVac mode is entered from the HiVac mode or from the Vented
status, the PLA Accessories dialogue prompts to inform the system about
the accessory installed by selecting the actual accessory.
Note
The number and types of accessories within the PLA Accessories dialog vary
according to the actual system configuration.
The maximum allowed specimen chamber pressure in LoVac mode is
determined by the PLA size and the gas type. This information sets
pressure limits and rates for pressure changes.
Clicking the Cancel button leaves the system in its actual status mode
(Pumped or Vented).
X-Ray Cone (500 µm)
This automatic aperture is used for EDX analysis (option) and for the
LoVac and low voltage imaging (i.e. below 5 kV) to reduce beam loss in the
gas. For EDX, samples are scanned at a 10 mm working distance, which is
the stage eucentric position and the collection point of the EDX detector.
The cone height is 5.5 mm and restricts the field of view. The longer profile of
this cone minimizes low voltage beam dispersion and skirting of the primary beam in the gaseous environment of the
chamber, allowing more electrons to interact with the specimen when focused and increasing the signal to noise ratio.

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 System control: Vacuum system

See the Chapter 5 / Selecting vacuum mode.

Note
The PLA also acts as a final or objective aperture, so the pressure over it is considered very low. Any pollution that
accumulates on the aperture edge greatly affects imaging. If it is not possible to correct astigmatism, it is usually a sign
that this aperture needs to be cleaned or replaced (see Chapter 6).
Warning!
Applying a cone or a detector with an integrated cone scales down the space between the top sample surface and the
cone (at the particular working distance) by the value equivalent to the cone height.
Using gas
The Low Vacuum mode allows a user to image samples in a gaseous atmosphere, which
can be selected in the drop down list box:
• Auxiliary (option) gaseous environment, which is supplied via the inlet placed on the
back of the console.
• Water vapor is supplied from a built-in water reservoir located on the left side of the
microscope console.
Note
On occasion the water reservoir needs to be filled (see Chapter 6).
Caution!
Maximum overpressure for the Auxiliary gas and Nitrogen inlets is 10 kPa (0.1 bar). The Nitrogen inlet is used only for
venting the chamber with air, or preferably with nitrogen.
When using a particular pressure limiting aperture, there are pressure limits for different gasses.

Table 2-1 Maximal chamber pressure under different gaseous environment

Maximum chamber pressure [Pa] (Torr)

Working gas Standard without PLA OptiPlan + PLA Standard + PLA
Water - H2O
Nitrogen - N2
Air
50 (0,4) 150 (1,2) 500 (4)
Carbon Dioxide - CO2
Nitrous Oxide - N2O *)
CxHy **)

Caution!
The system doesn’t watch the limits, and higher overpressure (especially for gasses not listed) set by a user could switch
off the emitter! In some cases, the system would need to be restarted by a service engineer.
Note
*) N2O is an oxidizer, use pumps designed for such an environment!
**) Combustible gases (acetylene for instance) must always be used with respect to safety issues.

Purging
During this procedure the specimen chamber is automatically pumped down to a lower pressure to remove the old
gas and is then is flooded with the new gas (selected in the Vacuum module) to a higher pressure. This takes place
several times, until the old gas is removed and the chamber is mostly filled with the new gas. This is applied when
the system is in the LoVac mode and the Purge button is pressed (see the Preferences… dialogue / Low Vacuum
section). The procedure is also started automatically with factory presets in these situations:
• when the LoVac mode has not been used for 1 week or more;
• after water bottle venting when refilling the water level (see Chapter 6).
Note
The automatic procedure can take a while (up to 10 minutes). Wait until the Vacuum status indicates Pumped, because the
detectors do not start operation until desired pressure is reached.

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Equipment

Detector types and application

There are several either standard or optional system detectors. The Detectors menu
shows all installed detectors. The accessibility / inaccessibility of detectors (black /
gray label) depends on actual system conditions.
Note
For settings and handling of particular standard / optional detectors, see Chapters 5 and 7.

Table 2-2 Apreo 2 detectors list

Detector name Tag Vacuum mode Detected signal Note

Everhart-Thornley ETD HiVac SE (tunable energy) / BSE S
T1 T1 HiVac / LoVac SE (for OptiPlan and Immersion S
Use cases)
T2 T2 HiVac / LoVac SE (for OptiPlan and Immersion S
Use cases)
Low Vacuum LVD LoVac SE S
CCD camera CCD light, infra-red light S
External EXT detector-dependent
T3 T3 HiVac SE (for OptiPlan and Immersion O
Use cases)
RGB Cathodeluminescence CLD HiVac / LoVac Light O
Directional Gaseous GAD–ABS / LoVac BSE O, LM
Analytical GAD–CBS
Directional Backscattered ABS / CBS HiVac / LoVac BSE O, LM
(DBS)
Retractable Directional ABS / CBS HiVac BSE O
Backscattered (DBS)
Retractable Annular STEM STEM 3 HiVac TE O
STEM 3+

SE = secondary electrons, BSE = back scattered electrons, TE = transmitted electrons,

S = standard, O = optional, LM = lens mounted version
Note
In case the vacuum safety interlock is activated, it is necessary to confirm switching the detector voltage on after pumping
the system.

FIGURE 2-6: Safety interlock message

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Stages and accessories

The chamber is equipped with an 110 × 110 mm stage, that can be oriented with reference to five axes: X, Y, Z,
Rotation and Tilt. All movements are motorized and software controlled (an integrated part of the Microscope
Control software). Stage positions are shown on the screen.

Holders
The Sample Exchange dialog / Holder list shows all possible holders
and its accessories to be selected when pumping the system from
the vented state.

Single stub holder

The holder (option) has 1 position for 12.5 mm stub. It enables the
biggest stage movement and tilt scale. To mount the holder on the
stage plate, screw it to the stage plate central hole thread by hand.
To fix the stub tighten the side grab screw by 1.5 mm hex wrench.

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CleanConnect Pre-tilted holder

This holder is used with the CleanConnect option (see Chapter 7).

Multi-purpose specimen holder

The holder contains 18 horizontal and three pre-tilted positions for
12.5 mm stubs. Horizontal and pre-tilted positions for the STEM
row holder are also included, together with a sample clamp and a
Faraday cup. All positions are marked for easier navigation. Stubs
can be mounted to most of the positions without any tools.

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Stage movement limits

The motorized movements of the stage can be operated under software control for more advanced location
mapping. This includes Shift, Get, Track and Stage module functionality. A live image can be repositioned either by
the stage movement or by the Beam Shift.
Note
When moving the stage or tilting the specimen, the magnification may need to be reduced so as to not lose the feature of
interest from the screen.

FIGURE 2-7: Stage movement schema

Table 2-3 Stage features and limits

Item 110 × 110 mm Note

X -55 to +55 mm
Y -55 to +55 mm
Z 66 mm
R 360° continuous
T -15° to +90° maximally
Eucentric distance 10 mm
Maximum sample weight No restriction: 500 g including stub holder
No Tilt: 2 000 g
X and Y movements only: 5 000 g

Caution!
The positive Z value direction depends on the Link Z to FWD status (see Chapter 5).
If the maximum sample size is near the limit, stage tilt can be limited. Beware of hitting the objective pole piece!

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3
Software control

This chapter describes the functionality of each part of the user software interface within the Windows 7™
operating system:
• xT microscope Server
• Microscope Control (UI – User Interface)
• User Management

Software interface elements

Icons
Icons are small symbols indicating a specific software application. Double-
click on an icon located on the desktop or within a folder to activate its
program.
There are also function icons in the toolbar for selecting some software
functions quickly. Clicking on a function icon causes it to be highlighted and
activated. Clicking on it again or clicking on another one (depending on the
particular case) causes it to become normal and deactivated.
Some function icons have an additional down arrow. Clicking on that arrow
reveals a pull-down menu with choices, while clicking on the icon performs a
particular function (cyclic changeover of choices, setting the default
parameters, etc.).
There are also some informational icons in the status bar, such as those that
indicate a particular system status.

Tooltips
The Tooltips functionality activates when the cursor is left over an item on the user interface for
more than two seconds. A short explanation of the item appears until the cursor is moved away
from it.

Pull-down menus
The microscope uses menu-oriented software; you perform
functions by choosing items from the Menu bar. The Menu bar
contains pull-down menus that show grouped listings of available
commands or settings. Some menu items are shown in gray and
are not accessible because of the system’ immediate condition.
Pull-down menu items followed by an ellipsis (…) indicate that
this is a command and a dialog box will show. A right arrow on
the right side indicates that an additional submenu of choices will
show. If an item is a parameter value, the new value is updated
immediately and a check mark appears in the pull-down menu.
Context menus
Right-click on some items to call out a context menu with other
corresponding choices.

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Using the mouse

Click on / right-click on / wheel-click on represents clicking with the left / right / wheel mouse button on an item
throughout this manual. The click on & drag / right-click on & drag / wheel-click on & drag means holding the
mouse button during a dragging action.
Click on & drag the cursor down the menu to a desired item and then release the mouse button.

Using the keyboard

Press Alt + the underlined letter (for example, Alt + F for the File menu), and then select from the choices by
clicking on one of them or by hitting the Enter button after selecting one with the up / down (left / right for
submenus) arrow keys.
Some often-used commands can be quickly activated with the use of shortcut keys (a combination of
simultaneously pressed keys) at any time. This possibility is given by a particular button combination on the right
side of the pull-down menu adjacent to the appropriate command (see Help menu / Keyboard Shortcuts).

Command buttons
Command buttons carry out or cancel functions. They activate
when clicked and some are highlighted (orange background) to
show corresponding function activity.
Command buttons have labels that describe the actions performed
by clicking on them. The most common ones, which are typically
used in dialogs, are:
• OK button – applies all changes made in the dialog and closes it.
• Finish button – saves new settings, ends the procedure and closes the dialog.
• Save button – saves new settings at that point without closing the dialog.
• Apply button – saves and applies new settings at that point without closing the dialog.
• Cancel button – discards all changes (made from the last save) and closes the dialog. It has the same effect as closing
the dialog by clicking the red cross (Alt + F4).
• Next button – moves a user to the next dialog after necessary settings have been performed.
• Previous button – moves a user to the previous dialog when settings need to be changed.

Property editor
The Property editor is the list of related parameters and their
values. A user should click on in the Value side of the relevant
property Name and then select its value from the drop down list
or enter it using a keyboard.

Edit boxes
One can input text information (such as passwords, labels or
precise numbers) using the keyboard within a corresponding edit
box. Some edit boxes, that are not part of a dialog require
confirming the input by pressing the Enter key. If you press the Esc
key before leaving the edit box, its previous value will be restored.

Radio buttons / Check boxes

Within a group of related round Radio buttons, only one selection
can be active at any time by clicking on the individual box.
One square Check box or a group of boxes can be ticked / cleared
by clicking on the individual square box.

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Adjusters
Adjusters allow the user to change parameters (such as contrast,
brightness, etc.) in a continuous way.
Right-clicking on the adjuster shows a context menu with
choices. Checking / not-checking the Slider Mode option switches
between two possible ways of controlling the slider. Checking the
Mode Switch option adds the mode switch button to the right side
of the slider, which enables quickly switching between these
modes.

Slider mode
In this mode, the adjusters always have a label and a readout at
the upper right corner. Double-clicking on it enables entering a
precise value and a unit in particular cases using the keyboard.
Clicking on & dragging the middle adjuster button or clicking on
the bar is used for coarse adjustments, while clicking on the end
right arrows is for fine adjustments (single step increments).
• Slider Mode (Non-linear Slider clear) – the adjuster button
position always corresponds to the actual parameter value
within an available range.
• Slider Mode (Non-linear Slider checked) – the slider has an
exponential response – the farther from the center the adjuster
button is pulled, the larger the relative change. The adjuster
button always snaps back to the center of the slider, but the
small bar under the slider corresponds to the actual parameter
value.
It is possible to increase / decrease the Slider Mouse Speed (sensitivity) by dragging the context menu slider to the
right / left.

Not Slider mode – drop down list boxes

This mode is used for values that have both a continuous range
and a list of presets. It also offers direct value editing to achieve
total control.
Clicking on the - / + sign selects the previous / next value from
the predefined list (see appropriate Preferences), but only shows
one value in the text area. Clicking on the down arrow on the right
side of the adjuster or the value itself expands a drop down list of
available values – if it extends further than is visible, a scroll bar
appears. Clicking on a value from the list enters it as the actual
one. The drop down list automatically closes, and the setting
changes immediately.
Double-clicking on a value in the text area enables editing it. It is also possible to click on & drag the small bar
under the numerical value to continuously change the setting (where applicable).

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2D controls
This control method is represented by an X-Y box. The position of the crosshair
corresponds to the actual parameter value; its full range is represented by the
perimeter of the box.
Clicking on & dragging anywhere inside the box changes the active cursor to the
4-ended arrow and positions it at the screen point corresponding to the actual
control value (minimum in the middle of the screen and maximum at the edges). It
can be dragged in four directions. Clicking on & dragging directly on the X / Y axis
changes the active display cursor to the 2-ended arrow, which can be dragged only
in the corresponding direction. To apply the value(s), release the mouse button.
Right-clicking on the 2D box opens a context menu with choices:
• Coarse / Normal / Fine item – sets the mouse sensitivity necessary for the full
range from a long to a short mouse path.
• Adaptive Sensitivity item – adjusts the mouse control response to be the
same at any magnification.
• Zero item –brings the control value to zero and the cursor to the center of the
box.
• Clear Memory item – clears condition values, that have been remembered
automatically during the relevant 2D control use. These remembered values
are used to estimate new values, that have not yet been remembered.
The menu may contain fewer functions or some other functions that are available for that particular parameter.
Selecting the corresponding menu item activates the function.

Modules
Modules visually combine various software elements, that are
related into a labeled group. Complex software elements such as
Control pages or dialogs are typically composed of modules.

Dialogs
A dialog appears when the system needs more information from
you before it can carry out a command, or when the system
wants to give you some important information. Some dialogs do
not let you access other functions until you close them. Others let
you perform other tasks while they remain on-screen and running
(for example, the Preferences dialog can remain opened while
performing other tasks).

Tabs
In modules or dialogs containing more interface elements than
would fit into the limited area, Tabs are used. These related
elements are split into groups (sections), and each one is
represented by a labeled Tab. Clicking on the Tab brings it to the
foreground showing the corresponding group of interface
elements. Tabs where some parameters were changed are highlighted (orange background).

Progress bars
The progress of long, ongoing procedures is indicated in dedicated dialogs or modules.

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xT microscope Server

The xT microscope Server application starts and stops the software

service controlling basic microscope functions as well as the user
interface (UI) Microscope Control software.
Start the xT microscope Server from the Windows Start menu or
by double-clicking its icon.

FIGURE 3-1: xT microscope Server window

Right-clicking on the title bar opens a context menu with options.

Double-clicking on the title bar switches between full and
miniature views. Some Microscope area buttons change their
labels and behaviors depending on their actual state.
• Server State / UI State area shows the STARTING / RUNNING /
STOPPING / STOPPED state of the xT microscope Server /
Microscope Control software service.
• Clicking on the Start / Stop button starts / stops xT microscope
Server services. If the UI is running, the Stop button first closes
it.
• Clicking on the Start UI / Stop UI button starts / stops the UI.
• Clicking on the Show UI / Hide UI button shows / hides the UI
main window.
• Clicking on the Standby button closes the UI, stops the xT
microscope Server services and brings the console to the
Standby state (see Chapter 2).
• Clicking on the Enter Service Mode button starts the special
mode intended for service actions.
• Clicking on the Up / Down arrow shows the Administration area
containing information helpful for a service intervention.
(specifying the software operation / hardware function state).
When the Autorun UI check box has been ticked (default), the
Start button automatically starts the UI after starting the xT
microscope Server.
When the Follow Active check box is ticked (default), devices
and drivers bullets roll down as the startup proceeds.

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Microscope Control

The Microscope Control application – simply the User Interface (UI) – is made up of several elements that
compose the main window, showing status and control features within the Windows 7 operating system.

FIGURE 3-2: Microscope Control window

2 1
3 6 5

4 - display 1 4 - display 2

7
4 - display 3 4 - display 4

1. xT microscope Server – minimized application window

2. Menu bar – contains all operation menus and submenus
3. Toolbar – functional icons for the most frequently used microscope controls
4. Imaging area – also shows the adjustable Databar
5. Control pages – set of modules
6. Modules – microscope and imaging control elements
7. Preferences dialog – presetting of operating conditions

Entering Commands
Enter commands by using shortcuts – combination of the mouse buttons and/or keyboard keys. To overview
factory preset shortcuts list, click the Help menu > Keyboard shortcuts item.

Workspace customization
It is possible to change the UI layout by right-clicking any free toolbar or
sidepane (pages) area and selecting the Customize… item.
A user can save / load layouts by selecting the Export / Import Workspace… item
to / from the Workspace configuration (*.workspace) file.
Clicking the Reset to Default Workspace item restores the factory UI layout, the
one described in this manual.

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Toolbar customization
Selecting the Toolbar tab adds a red triangle to each toolbar item, that allows
changing its size. By clicking & dragging any item, that item can be moved to a
new position within the toolbar area; dragging it out of the toolbar area to the
customization window eliminates it from the layout. Clicking & dragging a new
item from the Toolbar tab to the toolbar area adds it to the layout.

FIGURE 3-3: Toolbar customization

Sidepane (Pages) customization

Selecting the Sidepane tab adds a red border to the pages
area. By clicking & dragging any module, that module can be
moved to a new position within the pages area; dragging it
out from the pages area to the customization window
eliminates it from the layout. Clicking & dragging a new item
from the Sidepane tab to the page area adds it to the layout.
Clicking the + page button calls up a dialogue requiring a
New page name input; clicking the OK button creates a
custom page.

FIGURE 3-4: Pages customization

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Menu bar
The pull-down menus are shown across the screen.

FIGURE 3-5: The Menu Bar

Expand pull-down menus from the menu bar by:

• Clicking on the Menu title
• Entering Alt + underscored keyboard letters
• Entering Alt + keyboard arrows + the Enter button
Note
Some menu functions have their equivalents in the toolbar. When this is the case, the corresponding toolbar icon is shown
next to the function title in the following text.

thermoscientific menu
Standalone applications for particular use are listed here. It is also
possible to start them.
• Movie creator
• Working folder
• If there are more applications installed with the system, they
are listed here just as in the Windows start menu:
all programs / FEI company / Applications / for instance: VolumeScope, Auto Slice and View, iFast, AutoTEM, …

File menu
opens the File menu administrative functions:
Open (Ctrl + Shift + O)
shows a standard dialog for opening images previously stored to
media. Supported digital file formats are TIF8/16/24, JPG and
BMP (see Chapter 5). The dialog shows, by default, the location
(path) last used to open or save files from the UI.
Save (Ctrl + S)
saves the image using the format, location and base name set by
the last used Save As function in that display. An incremental
suffix with a selectable number of digits ensures that every image
is saved as a new file, e.g. Name_001.tif, Name_002.tif, etc.

Save As
opens a dialog for saving images, which provides an opportunity
to change an image’s file name and location. An image can be
saved in TIF8/16/24, JPG or BMP file format.
The dialog shows, by default, the location and the name last used
to save / open a file for the active display. A user can change a
location, name base or suffix, select a different image format
(Save as type), and also choose whether to Save the image with /
without Databar, with / without overlaid graphics and with /
without ColorSEM Legend by ticking / clearing the appropriate
check box. The settings are remembered and used for
subsequent Save actions.
Clicking the File Saving Settings button opens the same dialog as the Preferences dialog > File Saving settings.

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Save All (Ctrl + Shift + S)

opens a common dialog for saving images from each display,
providing an opportunity to change the file names and locations.

Record Movie (Ctrl + Shift + M)

allows a user to make digital video files (AVI) for dynamic
experiments. The corresponding icon next to this menu item – red
circle / square – indicates that movie recording is stopped / in
progress (see Chapter 5).
Print (Ctrl + P)
opens the print dialog enabling a choice of printer and settings
suitable for printing an image.

Import / Export
opens a sub-menu with choices for importable / exportable items. Selecting
an item opens a standard Open / Save As dialog for choosing the location and
file name. Following items can be imported (i.e. loaded and used) / exported:
• Stage Positions (.stg files) – stored stage positions
• Patterning Application Files (.xml files) – to export from the list that appears;
each application is exported as individual file.
• Patterns (.ptf files) – active display parameters of (all) pattern(s)
By importing these parameters, (all) exported pattern(s) is/are drawn back
into the active display.
• Endpoint Monitor Graphs (.epm files) – enables to save graphs in
EPM / Image / CSV file formats.
• Scanning Presets (.scp files) – preset scanning parameters
• Display Presets (.qps files) – active display parameters: Beam type /
Detector type / Detector Mode / Detector contrast & brightness / Digital
Contrast / Digital Brightness parameters
• System Parameters (.par files)
A wide range of selected actual microscope settings are
stored, including most of those mentioned above. When
importing them back, only the selected settings are loaded.
• System Presets (.syp files) – preset system parameters
• Intensity Profile Data (.csv files) – this can not be imported
• Measurements and Annotations (.shp files) – graphic objects
• Temperature Profile (.trp files) – available with a Temperature
stage.
Log Off #user name#
logs off the present User and provides the Log On dialog for the
next microscope user. When a user logs off, the system goes into
a safe state; the accelerating and detector voltages are
automatically switched off.
Caution!
Logging off the actual user does not close all microscope operations!
(see Chapter 2)
Enter Service Mode
starts the special mode intended for service actions.
Exit
closes the Microscope Control software (the actual user is
automatically first logged off) and leaves a user in the operating
system environment. The xT microscope Server is still running
and still controls the microscope in operation.
Lock
Locks the microscope to prevent undesirable operation of another user.

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Edit menu
opens some helpful functions:
Undo (Ctrl + Z) / Redo (Ctrl + Y)
reverts / restores some of the last used actions.
Copy (Ctrl + C) / Cut (Ctrl + X) / Paste (Ctrl + V)
These functions are commonly used operating system functions.
Select All (Ctrl + A)
selects All graphics in the active display.
Delete (Delete)
deletes all selected graphics in the active display.

Detectors menu
opens the choice of all installed Detectors (see Chapters 5 and 7).
Detector list
contains various detectors for the microscope’s operation. Detectors not mounted or
not serviceable under actual microscope conditions are disabled (grayed out). The
selected detector is remembered for the display. A tick shows next to its label, and its
mode acronym is shown beside it in brackets.
• The 3rd party detector / video signal is indicated as “External”.
Contact an Thermo Scientific service person about connection details.
• The CCD camera reflects the inner space of the specimen chamber.
• Mix sets the possibility of interfusing signals from 2 or 3 detectors.

Scan menu
opens the scanning control functions:

Pause (F6)
pauses imaging. This function is used automatically with Snapshot and
Photo functions.
Select the Scan menu / Pause, or press the F6 button, or click on /
double-click on the toolbar pause icon, to stop scanning at the end of
the actual frame / immediately.
When the imaging is going to be paused at the end of a frame, the
toolbar pause icon becomes highlighted (orange background) and there
is a frame around it. When the imaging is paused, the icon is highlighted
(orange background) and the green pause icon appears in the
corresponding display.
Select Scan menu / Pause item, or press F6 button, or click on the pause
icon on the toolbar or in the display to release the pause function (the
icon background becomes gray), returning the scanning to the previous
state.
Shift + clicking on the toolbar pause icon pauses / activates all displays
at once if the detectors in different displays are mutually compatible.
Snapshot (F4) / Photo (F2)
activates a preset scan (see the Preferences / Scanning section) to
acquire an image.
Active Preset Snapshot (Ctrl + F2)
This item starts acquiring a snapshot with parameters corresponding to
the active (highlighted by orange background) toolbar Scanning Preset
button (labeled s#) (see further).
Note
Shift + clicking on the Photo (Snapshot) icon / Scanning Preset button, or
pressing Shift + F2 (F4) / Ctrl + Shift + F2 key immediately takes a Photo
(Snapshot) / Scanning preset snapshot from all displays with the same
beam.

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Videoscope (F3)
This function shows the video signal intensity along the actually scanned horizontal line for correcting the contrast
and brightness.

Reduced Area (F7)

This mode is useful when focusing and correcting astigmatism, as the imaging update is faster in the smaller area.
When a Reduced area is chosen, the green frame appears at the last used place onscreen. It can be adjusted by
clicking on it & dragging. It is also possible to adjust the scan parameters independently in the full-frame setting.
• Moving: Place the mouse cursor over the selected area. The cursor changes to a 4-ended arrow. Click on & drag
the selected area to the desired position and release the mouse button.
• Changing the size: Place the mouse cursor over the edge of the selected area. The cursor changes to a 2-ended
arrow, either horizontal or vertical. A corner can also be used to move two sides. Click on & drag the side out or
in to obtain the desired size and release the mouse button.
When the Reduced area frame is being manipulated, it turns yellow until released. It then reverts back to green.
Full Frame (Ctrl + M)
This is the default scanning mode. It is typical for navigation and imaging.
Spot (Ctrl + K)
When starting this mode, the actual beam position is represented by a green cross in all imaging displays. You can
click on & drag it, or click anywhere around the screen, to change its position.
Line
In this mode, the green horizontal line is shown in all imaging displays. The beam scans along this line. You can
click on & drag it, or click anywhere around the screen to change its position.
External
switches to activate external control of the scanning system, such as an EDX system beam control.
The external scanning mode is indicated by the External label shown in the upper right corner of all
imaging displays.
Beam Blank (Ctrl + B)
If its functionality is active, this is indicated by the icon next the scan menu item. It deflects the beam off-axis, high
in the column, and protects the specimen from unnecessary exposure. Selecting the item again releases the
blanker and returns the beam to scanning the specimen.
Slow / Fast Scan (Ctrl + Shift + , / .)
brings the scanning condition to the preset Slow / Fast scan value (see the Preferences / Scanning section).

Slower / Faster Scan (Ctrl + , / .)

sets the scanning condition to the next preset Slower (-) / Faster (+) value (see the Preferences / Scanning section).
The adjuster shows the actual dwell time, but does not enable directly editing its value. The value can be selected
from the drop-down list (see the Preferences / Scanning section).
Mains Lock
When ticked, the scanning (line sawtooth signal) is synchronized with the mains AC oscillation. This greatly
diminishes blurring and jittering of the electron imaging, resulting in smooth image edges at higher magnifications
and slow scan conditions.
Line Integration
With this function, each line scan is repeated several times (from 2 to
255) before proceeding to the next line. Signal data collected from these
passes are integrated and shown as an actual image line.
This imaging method reduces sample charging (in comparison with a single
pass with a longer dwell time) and improves the overall image quality.
Scan Interlacing
This function splits an imaging area into a large number of blocks defined
by the number of lines (from 2 to 8). The first line of each block is scanned,
followed by the second one, etc. This imaging method significantly
reduces sample charging.

Note
These two functions cannot run simultaneously. When any of them is active, it is indicated in the toolbar dwell time adjuster
by the letters LI / SI. Its status is also depicted next to the Scan menu / Line Integration or Scan Interlacing item within the
brackets.

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Live
is the default mode, leaving the imaging unfiltered for collecting raw direct images. One frame follows another.

Average
Filter continuously averages a specified number (2 or more) of frames, resulting in a better signal-to-noise ratio.
This process continues until stopped by changing the scanning condition or by pausing the imaging.
This is used mostly for fast scanning to reduce imaging noise. During averaging, the image is updated continuously,
and actions such as focusing, moving the stage, etc., can still be performed.
Note
The Average is also set independently for the optical window, but using averaging with more than 4 frames is not
recommended, especially when moving the stage.

Integrate
Filter allows cumulative noise reduction by true integration over a specified number (2 or more) of frames. This
process continues until the selected number of frames is reached. It then automatically pauses the imaging.
This can be used as an alternative to slow scanning to obtain high quality images of slightly charging specimens.
Note
Clicking on the down arrow below the toolbar icon shows menu items Live /
Average (# frames) / Integrate (# frames) / Number of frames, enabling the
user to select the number of averaged or integrated images (depending on the
actually active filter indicated by the icon for the active display). Clicking on
the toolbar icon itself changes the Live / Average / Integrate filter in cycle.
The Number of frames is set and remembered independently for the
Average and Integrate filters. Both the filter and Number of frames are
set and remembered per display, so live and filtered imaging can run at
the same time. Settings are particular for the Reduced Area, Full Frame
and for the Line scan. The Photo / Snapshot function uses the Integrate
and Number of frames pre-set (see the Preferences / Scanning section).
As scanning can take a significantly long period of time, one can restart
scanning from its beginning by pressing the Ctrl + R keys.
Scan Rotation (Shift + F12)
This on-screen tool is activated to rotate the scan field. It has no effect on the stage movements, and is solely a
scan coil/electrode function used to orient the imaging relative to a specimen feature and/or detector direction.
A non-zero scan rotation is indicated by an icon in the Status bar.
Preferences (Ctrl + Alt + S)
Clicking this item opens the Preferences dialog / Scanning item (see further).

Beam menu
opens the Beam menu functions:
Home SEM Apertures
This function sends the SEM final lens aperture (Automatic Aperture
System – see Chapter 2) to its home position in case of trouble.
Degauss (F8)
This feature triggers the procedure that puts all actually used electron
lenses to a normalized state by removing their hysteresis effects. For a few seconds, while the procedure is running,
all live imaging disappears or turn fuzzy. It then returns.
Use this function with (almost) focused imaging to obtain the most accurate Magnification, Horizontal Field Width
(HFW) and Working Distance (WD) readouts.

Lens Alignment (Shift + F4)

This feature activates / deactivates the final lens alignment mode for the fine alignment of the electron beam only.
The scanning conditions change to the last selected value, the lens modulator turns on, and the alignment cross
appears in its respective position in all imaging displays.
Clicking on & dragging within a display activates a 4-ended arrow cursor and starts the final lens alignment.

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Magnification Correction
Applies the Magnification Correction alignment influences on imaging. The
letter “c” is added to the appropriate image databar fields (Mag, HFW),
and the text Magnification Correction is added to the imaging display.
Note
Switch on the functionality on only for calibrated conditions. Otherwise it can worsen magnification accuracy.

Patterning menu
opens the Patterning menu functions (see Chapter 7):

Start / Pause / Resume Patterning

in Display # (Pause button)
starts / pauses patterning of the enabled pattern(s) in the active
display. The menu item and the corresponding toolbar icon
change according to the actual condition.

Reset Patterning in Display # (Ctrl + Pause button)

cancels the patterning procedure.
Next Pattern (Shift + P)
In the serial patterning mode the actual patterning is stopped and the procedure continues with the next pattern (if
present).
Autostart Real Time Monitor
When selected, it releases the pause function for the display with patterns, enabling an automatic start of the real
time monitoring (RTM) of the milling process.
Live RTM after Snapshot
After acquiring a snapshot, the RTM feature continues automatically.
Blackout Pattern Area for RTM
In case the Real Time Monitor is running, the area not milled is darkened to enhance the visibility of the RTM
information. The visibility of the individual patterning pixels is greatly enhanced (this is especially important for
patterns with extremely large pitch or very thin lines).

FIGURE 3-6: Imaging with / without Blackout Pattern Area

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Stage menu
opens the stage and sample navigation functions
(see Chapter 5):
Align Feature
opens the procedure that helps set a stage position for any
elongated feature (extending off the screen at the desired
magnification). The procedure uses the stage rotation.
Compucentric Rotation (F12)
places a green circle in the active display. By rotating the circle, a
different viewing orientation of the sample area can be achieved
by a physical stage rotation and adjustment of the X and Y axes.
Stage rotation keeps the observed feature in the center of the
field of view. If this does not occur, an alignment should be
performed to locate the stage center and calibrate the stage (see
Chapter 4).
Z Tracking (Ctrl + F12)
Sets the Z-axis movement control overlay in the selected display
on / off.

Click and drag up / down inside of the Jog Z arrow area on the right side of the display to move the stage in Z-axis
direction precisely.
Define User Units
Activates a procedure guiding a user to determine User Units for X and Y stage axes. These are used for relative
stage movements associated with the regular features mapping (in particular integrated circuit applications).
User Units
Organizes the stage software to recognise the defined user units rather than the default metric measurements. The
X and Y coordinates now operate in User Units which are indicated in the Stage module by the UU symbol.
Beam Shift Reset
zeroes the beam shift. A feature observed with a non-zero Beam Shift is automatically moved back to the imaging
center using the stage.
Auto Beam Shift Zero
automatically resets the beam shift each time it reaches the maximal value during the Get function (the point-to-
point stage movement) and corrects the imaging position with a stage movement.
Home Stage (Shift + F3)
starts the procedure that moves all motorized axes to their
hardware limits and ensures that the physical stage position
agrees with the coordinates readout. During the home stage
procedure the Stage Homing dialog shows its progress. The stage
axes are moved to their end-switches in the following order:
1. Z (lowest position); 2. T (tilt); 3. X, Y and R (rotation) at the
same time.
When the stage is homed correctly it ends up in the following
position:
The X / Y position is set to the factory pre-set stage rotation
center; R = 0° / T = 0° / Z = preset long working distance.

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Home Stage Without Rotation

executes the Home Stage function without rotation. When the stage is homed without rotation, the stage Rotation
reference is grayed out. This is useful when a large specimen is inserted and stage rotation can cause a collision
with equipment inside the chamber.
Center Position (Ctrl + 0 - digit)
moves the stage to coordinates X = 0, Y = 0.
Recovery to Safe Position
Returns the stage position to standard boundary limits. The dialog warns and refers to run this functionality.
External Current Measurement
Click on this item when you need to use an external measuring device (option). The Status bar / Specimen Current
value shows N/A from that point on.
Unlink Z to FWD
This feature functions in the opposite way as the Link Z to FWD
(see below). The Z coordinate value then represents the distance
from the Z-axis home position (stage base). The dialog warns of
the stage Z-axis positive move direction.

Link Z to FWD
This functionality provides the system with definite stage
positioning to perform accurate and secure movement between
the sample top surface and the end of the objective lens. The
Z coordinate value then represents the actual Free Working
Distance (FWD) value. The related toolbar icon changes
according to the Z-coordinate status:
• Grayed icon: the function is disabled – the tooltip gives the
reason (for instance, high voltage is switched off, all displays
are paused, beam is not on,…).
• Red question mark: the function is enabled – Z is not linked to FWD. Use this function as soon as possible after a
proper focus.
• Red circle arrow: the function is enabled – Z is roughly linked to FWD, but it needs correction. It happens e.g. after:
pumping the chamber when specimens were exchanged, or focusing and linking Z to FWD at a long WD and then
moving the stage to a short WD. In this case, focus carefully at a WD of around 7 mm, and use this function again.
• Green 2-ended arrow: the function is enabled – Z is properly linked to FWD. Now it should be safe to change the
working distance by setting the Z coordinate in the Stage module.
Note
The Do not show this message again check box disables this notice permanently.
Enable Z-Tilt Map
Some movements of the tilted stage are not safe because of a possible collision with the final lens. The table (not
user editable), with pairs of values, indicates the maximum safe Tilt angle for a certain Z value when linked. It can
be used to guarantee safe usage of the stage (tilt restriction) for flat samples only and when a proper Link Z to
FWD has been established.
Enable Safe Stage Moves
When ticked, the software takes into account all accessories installed inside the chamber. It is why the stage
doesn’t move to the target position in a straight path. When the magnification is large and stage movements are
expected to be minute, it is not necessary to switch on this functionality.
Tilt 0° (Ctrl + E)
This menu item tilts the stage to 0°.
Sample Navigation (Ctrl + N)
toggles on / off the function that enables navigating electron imaging (scan field) towards desired points on a
specimen using either a paused or a loaded sample image (usually captured at much lower magnification).
The Sample Navigation can be selected independently for any display, regardless of its
actual content and status. A tick next to the menu item indicates that the function is active
for the active display. As soon as imaging is paused, the Sample Navigation indicator
appears in the upper right corner of the display. The indicator is green as long as the paused
imaging can be used to navigate the live one. Otherwise it turns red.

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Navigation Montage
This procedure enables capturing the sample Navigation image to be used in the Sample Navigation.
Navigation Alignment
This procedure aligns the Navigation image according to the live reference image.

Tools menu
opens the Tools menu functions:

Image Registration
This functionality is used to interconnect images of the same area of
interest acquired from different sources or at different conditions
(for instance images acquired from optical and SEM microscopes,
images acquired at various depth of focus etc.) (see Chapter 5).

Auto Contrast Brightness (F9)

activates the automatic contrast and brightness routine. The system
attempts to set the Contrast & Brightness of the selected detector in
the active display to suit the actual sample and conditions so that
the majority of gray levels are shown. This functionality is also
available for paused imaging.
Note
Pressing the Shift + F9 hot key starts the Auto Contrast Brightness
functionality in all live displays.
Default Auto FLASH / Customized Auto FLASH
(Alt + F11 / Shift + F11)
Activates the automatic factory preset / customized routine (see
Chapter 5).
User Auto Contrast Brightness
examines gray levels of the active display imaging and stores their
minimums and maximums. The next time the Auto Contrast
Brightness (ACB) function is used, it attempts to set the Contrast & Brightness so that the resulting imaging gray
levels lie between these minimums and maximums instead of full black and white.
A tick next to this menu item indicates that the user gray level limits are active. Clearing the tick reverts the ACB to
its default setting.

Auto Focus (F11)

activates the automatic focus routine for either beam. The system attempts to correct focus at any working
distance.

Auto Stigmator (Ctrl + F11)

activates the automatic procedure to correct any astigmatism.
Note
Auto-functions are only enabled during live imaging.

Auto Lens Alignment

activates the automatic Lens Alignment functionality (see above).
Alignment Scheduler
The Tip-drift Compensation alignment can be scheduled for a regular
automatic execution (see Chapter 4).

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Sample Cleaning
This feature starts the sample cleaning procedure according to the Plasma
Cleaning alignment (see Chapter 4 and the Chapter 7 – Plasma Cleaner).
The procedure removes thin contamination layers which could typically be
formed by hydrocarbons residues remaining on vacuum parts after
conventional cleaning or could be transferred into the microscope chamber
with a sample.

Set HFW (Ctrl + H)

enables setting the desired Horizontal Field Width, i.e. the width of
the scanned area. This is an alternative to setting the
magnification.
Display Saturation (Shift + F10)
shows signal clipping in the active display by means of replacing
the full black / white with dark blue / yellow color. The function
can be used for electron imaging, but cannot be applied to optical
imaging.
Showing saturation is selected independently for each display. A tick next to the menu item indicates whether the
function is active for the active display.
Movie Creator
Opens the standalone application (see Chapter 5).
Batch Databar Editor
This functionality enables to edit the image databar for image files selected in the Input area by clicking the Add
button. Use the Remove / Remove All button to remove selected / all files.

In the Output area set the output Folder and new files name rules (Name Prefix, Name Suffix), together with the
Image Format.
In the Databar area right-click above the databar and set items from the Available / Visible lists by dragging them.
By clicking the Start / Stop button the process starts / stops.

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Application Status
The dialog shows continuously updated system Messages. The System status tab offers information about the
system hardware. That information is used by service engineers.
• Show this window on (Info / Warning / Error / Never) specifies the kind of messages that are automatically
called up on-screen.
• Three icons enable separately switching on (orange background) / off (gray background) the showing of Error /
Warning / Information messages.
• Clear button clears all present messages from the window.
• Hide button hides the Application Status window.

FIGURE 3-7: Application status

Preferences (Ctrl + O – letter)

Clicking this item opens the Preferences dialog (see further).

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View menu
opens the Window menu functions:
Center Cross (Shift + F5)
places a cross in the center of all imaging displays. This function
is automatically used in Alignment procedures to aid the
centering of features and can be used to align a sample against a
stored image in another display.
Alignment Rectangle (Shift + F6)
places a dashed rectangle in the center of all electron imaging
displays. This function is automatically used for some Alignment
procedures.
CCD Axis Marker
places axes indicators in all optical imaging displays to help the
user with 3D orientation.
CCD 10 mm Marker
places a short horizontal line with a 10 mm label in all optical
imaging displays to help the user with positioning a sample to a
correct working distance and with the first focusing.
Crosshair Cursor
shows the cursor as a rectangular cross through the entire display.

Working Distance Indicator

Checking this item displays the working distance indicator within
the optical display.
The small green triangle on the left of the vertical line depicts the
actual working distance. The marked positions on the right are
dynamically changed according to imaging conditions. They correspond to different applications and are described
via the tooltip. If an imaging within specific working distance range is not optimal or possible, the green line turns
to gray.

Note
The BSE range is shown only when the feature is installed on the system (see the Compound Lens Filter module below).

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Measurements and Annotations

Checking this item enables to use the measurements and annotations functionality within all displays. Not
checking this item makes dedicated toolbar icons inactive and hides all measurements and annotations graphics,
which is convenient during working with patterns.
Undo / Redo digital zoom
When any Digital zoom is applied, this functionality switches between the applied zoom factor and no zoom (a
factor of 1).
Note
To revert the last step, use the Edit menu / Undo (Ctrl + Z) functionality, which is also available at the toolbar.
Large Image Window (Ctrl + F5)
This function activates / deactivates full screen imaging on the secondary monitor.

FIGURE 3-8: Large image window

Large Image Window Configuration

Here one can select, whether to show the Active display, or any selected display. Activating the Use Single Image Size
option sets the imaging window size corresponding to the Single Image mode size. These options are also available in
the bottom right corner of the large image window.
Remote Mode
When ticked, this feature enables correct UI imaging at a remote site. It is also used for remote servicing. Use of
this function slightly decelerates the UI performance.
Full Screen
Selecting this option sets the application to be shown in full screen. De-selecting it shows the application as a
window within the screen.
Single / Quad Image Mode (F5)
toggles the imaging area between two possibilities:
• Single image mode shows one display over the whole UI imaging area (useful for observing details).
• Quad image mode is useful for comparing imaging of the same sample area taken with different detectors or
under different scan conditions.
In the Single image mode, the active display fills up the screen.

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Help menu
opens the Help menu and system information functions:
Documentation (F1) / Apreo 2 User safety manual
The complete User operational manual / Apreo 2 User safety manual in PDF
format is opened using an embedded Acrobat Reader, with its useful
navigation, search, and selection facilities. The window remembers its
position and size for the next time it appears.
Note
It’s a must for any microscope operator to read the Apreo 2 User safety manual
before using a microscope for the first time.

FIGURE 3-9: Online documentation

Keyboard Shortcuts
Clicking on this item starts Adobe Reader to show the shortcuts list. We advise printing out this document and
place it near the microscope workplace in a location where it can be easily seen.

FIGURE 3-10: Keyboard shortcuts

ENTERING COMMANDS – USING KEYBOARD

Microscope Control (UI) Function & Specific Keys

Key(s) Function Key(s) Function

F1 shows documentation Ctrl + H sets Horizontal Field Width (HFW)
Shift + F1 shows Image properties Ctrl + K sets Spot mode conditions
starts / stops Photo with an active beam Ctrl + M sets Full Frame scanning conditions
(Shift +) F2
(in all displays with the same beam at once)
Ctrl + Shift + M starts movie recording
Ctrl + (Shift +) F2 starts / stops Active Preset Snapshot (from all displays at once)
Ctrl + N toggles Sample Navigation On / Off
(Ctrl+) F3 toggles Videoscope On / Off (in all displays)
Ctrl + O letter / +Alt + S opens Preferences dialogue / Preferences Scanning item
Shift + F3 starts Home Stage procedure
Ctrl + P opens Print dialogue
F4 starts / stops electron imaging Snapshot from active display
Shift + P proceeds with next pattern
Shift + F4 starts / stops Lens Alignment procedure
Ctrl + R restarts scan
F5 toggles Single / Quad Image mode Ctrl + (Shift +) S saves image(s) (from all displays)
Ctrl + F5 toggles Large Image Window mode On / Off Ctrl + Y redoes last operation
Shift + F5 toggles Center Cross On / Off Ctrl + Z undoes last operation
F6 pauses / releases scanning Ctrl + Shift + Z starts Take Nav-Cam Photo procedure
Shift + F6 toggles Alignment rectangle On / Off (Ctrl +) Pause
starts / stops (/ resets) patterning
F7 toggles Reduced Area On / Off keyboard key

Ctrl + F7 starts Image Post Processing Ctrl + (Shift +) , sets one step slower (preset slow) scanning

F8 starts Degauss procedure Ctrl + (Shift +) . sets one step faster (preset fast) scanning

starts Auto Contrast and Brightness procedure Ctrl + (Shift+) Tab activates displays stepwise (backward)
(Shift +) F9
(in all active displays) Ctrl + Page Up / Down switches within control pages stepwise
(Ctrl +) F11 starts Auto Focus (Auto Stigmator) procedure Ctrl + 1 / 2 / 3 … selects the particular page – the number corresponds to the
Shift + F11 toggles Display Saturation tool On / Off letter keyboard toolbar page icon sequence

(Shift +) F12 toggles Compucentric (Scan) Rotation tool On / Off (Ctrl +) + / - keypad increases / decreases the magnification 2× (Digital Zoom)

Ctrl + 0 number moves stage to X=0, Y=0 – Center Position procedure * keypad rounds off the magnification / HFW to a nearest round value

Ctrl + B toggles Beam Blank function On / Off Ctrl (+ Alt) + arrow moves the digital zoom area (the pattern)
keyboard by one screen pixel in the corresponding direction
Ctrl + E tilts stage to 0°
(Shift +) arrows moves the stage approximately by (40%) 80%
Ctrl + F sets Electron beam focus to eucentric WD (10 mm) keyboard of the field of view in corresponding direction

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User guidance
This pop-up window contains detailed instructions about some complex procedures and/or settings. Click also the
icon next to the pages on the right side of the screen.

FIGURE 3-11: User Guidance

About Microscope Control

The window containing information about the product version is shown. It automatically disappears after the first
click anywhere.

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Toolbar
The toolbar shown below the Menu bar is made up of functional graphical elements (icons, adjusters, etc.) linked
to the most frequently used system controls.

Note
The default workspace is described here, for custom settings see corresponding sections of this manual.
Rest the cursor over the icon for two seconds without clicking on it to see its
explanatory tooltip. Right-clicking on some toolbar icons calls up a context
menu with other functionality choices. For instance, a user can move directly
to the Preferences setting (by clicking on the Edit item) or to change a mode
of value depiction.
Whenever a function is selected, the corresponding icon is highlighted
(orange background) to indicate the function is active.
Note
If any icon represents a menu function, refer to the corresponding menu for its
description.

Undo / Redo
The undo / redo buttons assist undoing / re-running the last actions. Actions used in history are
accessible by clicking the down arrow. They can be re-used separately, or any continuous sequence of
actions can be selected and re-used as a group.
Note
Some particular actions (alignments etc.) cannot be undone, and sometimes the system clears the history of actions.

Sample exchange
The window contains controls for sample exchanges, working conditions and start-up actions settings and
information about the system vacuum status (see Chapter 5).

• Working Folder:
File Saving Settings for images storing (see the Preferences)
• Chamber:
Pump / Vent buttons, Sample Cleaning check box to start the procedure when pumping out,
High Vacuum / Low Vacuum radio buttons for selecting the Vacuum mode and associated parameters,
Take Nav-Cam Photo automatically, starting the chamber Purge process, Inserting / Retracting the X-Ray Cone
• Sample:
When processing a Magnetic Sample, ticking this check box prevents the Immersion lens and Compound Lens
Filter to be switched on.
• Holder: select the stage holder and accessories from the list according to actual situation (see Chapter 2).

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Electron beam / Camera / Nav-Cam

Selecting an item from the drop down list makes the display or single screen show the
Electron Beam / Camera / Nav-Cam imaging with respect to the source, column, scanning,
and detector settings. Only one is selected at any given time, but they can be operated
independently for each display.
Another way to change the beam for a particular imaging is clicking on the image databar
beam icon.

Column Use cases

The electron column can be operated in different column Use cases optimized for
specific applications. Selecting a desired Use case can be done with the toolbar / Use
case drop down list box and also within the Use Case module (see Chapter 5).

Magnification (HFW) / High voltage /

Spot size (Beam current) list boxes
Click on the list box to expand a list of pre-set and allowed values.
Choose one by clicking on it; it is applied immediately (see the
Preferences / Presets section).
• The Spot is defined as the actual electron beam diameter on the
specimen surface. It is expressed by a relative number. The optional
way (representable in the toolbar) to express the Spot is the
electron beam current value. (see the Preferences dialog / General
section / Beam current control item). Both physical quantities are
related. The electron beam current shown in the toolbar list box
(and optionally in the image databar) is approximate and is valid
only if the microscope is well-aligned.

Imaging pixel resolution list box

This list contains the available imaging pixel resolutions (also used for captured images). Selecting
a new resolution results in the immediate change of the scanning raster. Since the present dwell
time remains unchanged, the actual scanning frequency (both Line and Frame time) changes.

Patterns / Measurements / Annotations

There are 2 pointers (from top left): the normal cursor (white arrow) and the
selection cursor (gray rectangle – all objects included within its area are
selected). Other icons represent the four shapes that were most used
recently. check image
Clicking the down arrow reveals more shapes and enables quick access to the
Patterns / Measurements / Annotations tool. Clicking on the icon activates
(orange background) / deactivates (gray background) the appropriate
functionality.
To deactivate the drawing mode at any time press the Esc key (keyboard).
The numerical values of linear distances, diameters, angles, or areas of the
image are updated during drawing and are shown alongside of or within the
finished measured item. The Measurement tool dimensions scale with the
image; when changing magnification, the tools shown change their size
accordingly. In contrast, the Annotation shapes and texts have their sizes
fixed relatively to the display.

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The Measurements / Intensity profile delineates the imaging profile across a freely
drawn line.

ColorSEM / Analytical layout

Clicking the icon starts the analytical functionality (see Chapter 7).

Pattern presets
Note
These buttons are hidden under the triangle down arrow, or within the
Workspace customization (see above).
By default there are 6 empty toolbar Pattern presets (labeled p#). Any pattern preset can be assigned to an
individual .ptf file with all patterning parameters exported via the File menu / Export / Patterns item. Clicking on any
pattern preset loads its parameters from this file, and corresponding patterns are drawn in the active display. To
start patterning under loaded conditions, follow the patterning process.
Right-clicking on any Pattern preset button calls up the context menu:
• Clicking on the Apply item (the same as clicking the button directly) loads
parameters from this file and corresponding patterns are drawn in the active
display. To start patterning under loaded conditions follow the patterning
process.
• Clicking on the Update with Current Selection item assigns patterns directly
from the active display, saves the setting to the file and automatically
applies it to the selected preset button. Tooltip shows the location and a file
name.

• Any toolbar Pattern preset button can be assigned to an individual .ptf file (with all patterning parameters
exported via the File menu / Export / Patterns or System Parameters item) by selecting Import from File item.
• To rename the pattern preset button click the Rename item.
• Clicking on the Reset to Default item brings all settings to the factory presets.

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Scanning presets
By default, there are 6 factory toolbar Scanning presets (labeled s#).
Clicking on any one starts image acquiring with the corresponding
parameters.
Right-clicking on any Scanning preset button calls up the context menu:

• Clicking on the Activate item highlights the button (orange background) and starts image acquisition, or just
activates the preset according to the Scanning presets property editor / Shared Settings section / Start scan on left
click item setting (Yes / No). The Multiple Activate item has the same functionality in all compatible displays
(same beam).
Starting image acquisition is also possible using the Scan menu / Active Preset Snapshot (Ctrl + F2) item.
• Clicking on the Snapshot / Multiple Snapshot item starts snapshot acquisition from active / all compatible
displays.
• Clicking on the Update with Current Settings item updates the selected Scanning preset with the actual scanning
settings.
• Clicking on the Edit item opens the selected Scanning preset property editor. It is also possible to use the toolbar
down (expand) / up (hide) arrows with the same effect.
• It is possible to Import / Export Scanning Presets from / to a file (.scp).
• Clicking on the Reset to Default item brings all settings to their factory presets.
A tooltip is shown when the mouse cursor hovers over any preset button, giving the
parameters overview. The parameters colors indicate:
• Green: actual microscope setting matches the column preset
• Dark red: actual microscope setting differs from the column preset
• Gray: Value is not relevant when the respective component is switched off

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Imaging area
The Microscope Control software (UI) uses 4 independent displays for imaging samples. Each display can contain
images from any detector (including External and CCD), paused imaging or images loaded from a file. Additionally,
display 3 can show a mix of images from displays 1 and 2, and display 4 can show a mix of images from displays 1,
2 and 3.
The Quad image and Single image modes are available. The Quad Image mode shows 4 displays at the same time.
The Single Image mode shows one display over the UI imaging area.
Each display consists of its imaging area, an adjustable Databar containing the imaging parameters, a selectable
overlay (user-defined coloring, annotations, measurements) and some status icons (Pause, Sample Navigation,
etc.).
At any one time, just one display is active (has focus), and all functions related to it (Pause, Sample Navigation,
image processing) apply only to imaging on this display. The active display is marked by the highlighted (blue
background) Databar and optionally also by a blue frame (see Preferences / General).
Depending on the display content and the status, some mouse functions are available over its area:
• Electron imaging (incl. External and Mix): focus, astigmatism correction, Beam Shift, magnification change
(coarse, fine), zoom (in / out), Contrast & Brightness, lens alignment, Scan / Compucentric Rotation, XY-move
(get or track mode)
• Optical imaging: 10 mm Marker placement, Compucentric Rotation, Z-move (track), Tilt, Working distance
indicator
Optical imaging is automatically activated (if it is paused) when the venting procedure starts.
When it is paused and any stage movement takes place, the pause icon turns red, and a list of
changed axes is shown.
Note
Due to hardware limitations, some detectors cannot be used simultaneously. They can still be selected
for different displays at the same time, but if one of them is started, other imaging with the incompatible
detector is automatically paused.

Image databar
Optional instrument, imaging and labeling information are shown at the base of all displays. The configuration and
available items differ for the beam selected (Electron / Optical / Nav-Cam) for the active display.

FIGURE 3-12: Databar examples

Active electron display

Inactive electron display

Inactive optical display

Active Patterning display

Inactive Patterning display

Inactive Nav-Cam display (option)

Note
The Databar information always relates to the live imaging. If imaging is paused or an image is loaded from a file, the
information can differ from what is in the actual system conditions.

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Clicking on some of the image databar fields induces an active menu related to it with appropriate
choices.
Clicking on the label field brings up the label-editing menu.
Double-clicking on the micron bar induces the Image properties window showing multiple
parameters at which an image was captured. The same functionality is caused by pressing the
Shift + F1 keys.
To set which information is included in the databar right-click on any display databar and click on
& drag the desired Available Item to the Visible Items field. Items can be placed in any order (by
dragging items up / down within the list). They expand or contract automatically to fit the display
width as long as there is enough room. This influences all displays with the same beam.

FIGURE 3-13: Databar configuration / Image properties

To label a databar, double-click on the Label field and fill in the

dialog. It can be set independently for each display.
The Micronbar area scales to the magnification.
Clicking on the Choose Bitmap item opens a dialog to choose a
bitmap to be loaded into the databar (if the Bitmap item is ticked).

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Status bar
The Status bar can be found at the base of the UI screen. It contains several user selectable items along with
information about running system processes (for instance, patterning).

FIGURE 3-14: Status bar (divided into left / right part)

Right-click on the Status bar and check items to be shown:

• Chamber Pressure – the specimen chamber pressure
• Specimen Current – the electron current reaching the specimen
• Emission Current – the electron current leaving the source
• Electron Source Pressure – pressure in the corresponding vacuum system section
• EDS Count Rate – ColorSEM (see Chapter 7)
• EDS Dead Time – ColorSEM
• Clock – can be shown at the bottom right window corner
• Messages – Application Status incoming notices can be shown
The system conditions are shown by means of the icons:

Table 3-1 Status Icons

Icon Status
Source space vacuum / Chamber vented

Source space vacuum / Chamber pumping or venting

Source space vacuum / Chamber vacuum

(ready for the microscope operation)
Stage axes locked (any one)

Dynamic focus is ON

Tilt correction is ON

Scan rotation is not zero

External scanning mode is on

ColorSEM Analytical mode is on

When you hover the mouse over any icon, a corresponding tooltip appears with
either the actual status of the parameter(s) or just with information.

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Control pages and modules

The software controls on the right side of the screen are organized into Control pages, which are divided into modules /
tab modules holding specific functions. The required page can be selected either by clicking on the corresponding icon
or with the use of shortcuts (see further). The Control pages and modules available for the system are:

• Beam control page

1. Vacuum, 2. Column, 3. Magnification, 4. Compound Lens Filter, 5. Beam, 6. Beam Deceleration,
7. Scan Rotation, 8. Detectors

• Navigation page
9. Stage, 10. Stage Z, 11. Tilt Correction

• Detectors page
12. Detector Settings, 13. Detection Space, 8. Detectors

• Patterning page
14. Patterning Control, 15. Properties, GAS Injection (option – see Chapter 7)

• Processing page
15. Properties, 16. Digital Zoom, 17. Enhanced Image (LUT / Mix 3 / Mix 4 / Color / Process)

• Direct adjustments page

18. Direct Adjustments (Beam / Stigmator Centering / Focus), 8. Detectors

• Column presets page

19. Use Case, 20. Column Presets, 8. Detectors

• Analytical page
21. EDS Acquisition Progress, 22. Analysis History, 23. EDS Detector Status

• Electron Channeling Pattern page

24. Electron Channeling Pattern, 17. Enhanced Image tab modules, 8. Detectors

• Microscope alignments page

25. Alignments (Instructions / Individual steps)
Note
The number in front of the module name represents the order in which the modules are introduced in the following text.
Some of the module controls are beam-dependent. In this case, the actual beam type is indicated by the
corresponding icon at the right-hand side of the module.

1. Vacuum module
This module is used to control the pressure in the specimen
chamber. Clicking on the Pump button starts the pump-down
procedure for the specimen chamber and the column. The
system allows switching the accelerating voltage on only when
the chamber is sufficiently evacuated. Clicking on the Vent button
starts chamber venting for a sample or detector exchange after
user confirmation.
Ticking the Sample Cleaning check box pumps the system, starts
the Sample Cleaning procedure (duration can be set), and keeps
the column pumped.
The Mode radio buttons bring the system to:
• the High Vacuum mode, which is the conventional operating mode (associated with all scanning electron
microscopes). It is used for observing conductive specimens that can withstand low pressure conditions and do
not release gas.
In this mode, the system pumps continuously to achieve the lowest possible pressure.
• the Low Vacuum mode is for observing non-coated and non-conductive or partially conductive specimens.
In this mode, the chamber pressure is controlled using the Chamber Pressure adjuster, while the column is at a
much lower pressure. The gas environment can be selected from the list box.

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The system automatically switches to one of the modes when the chamber is Vented and a dedicated detector is
installed. If no dedicated detector is installed, the user is asked to determine a detector mounted by the PLA
accessories dialog (see chapter 2).
Clicking the X-Ray Cone / Insert button attaches the X-Ray cone on the Final lens pole.
2. Column module
contains the controls for setting the electron beam conditions:
Beam On button
switches the accelerating voltage on (orange background) / off
(gray button). If the source is not started (empty progress bar),
this button starts the electron source first (green progress bar).
Beam current / Spot size adjuster
enables adjusting the electron Beam current / Spot size with adjustable accuracy (see the Preferences / General
section). The actual value (from the factory preset list) is shown in the adjuster text area, toolbar and imaging
databar (if selected). Only values applicable for actual imaging conditions are shown.
Note
The Spot size influences both the focused electron beam area and the Beam Current: the smaller the Spot size, the lower
the Beam Current.
High voltage adjuster
enables adjusting the overall electron beam accelerating voltage (from 200 V to 30 kV) either continuously or
using the pre-set values (see the Preferences / Presets section). The actual High Voltage value is shown in the
adjuster text area, toolbar and imaging databar (if selected).

3. Magnification module
The adjuster offers a variety of ways to control imaging
magnification. The magnification range changes dynamically
according to the working distance and can also be controlled with
the use of other tools.
Magnification control
• Clicking on the end right / left arrow increases / decreases magnification by 5%.
• Clicking between the right / left end arrow and the button increases / decreases magnification by 20%.

4. Compound Lens Filter module

The compound lens filter uses the advantages of the compound
final lens, that combines the magnetic final lens inside the pole
piece, the immersion magnetic lens and the electrostatic lens
formed by the potential at the T1 detector. Main function of the
compound final lens is to focus the primary electron beam to the sample. However, independent control of these
three lenses together with continuous control of the immersion lens enables to filter back-scattered (BS) electrons
reaching the T1 detector. The compound lens filter behaves as a chromatic sensitive lens, which focuses the low
energy BS electrons into the aperture of the annular T1 detector. The high energy BS electrons are less sensitive to
the magnetic field and reach the T1 detector. Secondary electrons also pass through the aperture in the T1 and are
collected further in the column by the T2 and T3 detectors.
The compound lens filter is available in the OptiPlan and Immersion Use cases with or without the Beam
Deceleration. The main goal of the compound lens filter is the enhancement of the compositional contrast of the
sample. Besides that, it can be successfully used for imaging of insulating samples without charging - secondary
and low energy BS electrons which are most sensitive to charge are filtered out from the T1.
When clicking the On button the Threshold Energy slider becomes active to define threshold energy of BS electrons
– energies lower than threshold are filtered out and don't contribute to the T1 signal, energies higher than threshold
contribute to the T1 signal. The filter functionality is also visible within the image databar via the Treshold item and
via the Detector type item – T1.
The compound lens filter works ideally at low landing energies – 5 keV and less. Typical imaging conditions are:
WD = 4 mm / Landing Energy = 1 keV / Beam current = 100 pA / Threshold Energy = 500 eV
Start imaging with the T1 detector with the OptiPlan Use case, activate the filter and gradually increase the
Threshold Energy – T1 imaging gets dark as the lower energy backscattered electrons are filtered out of the detector
surface. The filter can be applied also with the Immersion Use case; in this case the starting Threshold Energy is
maximal.

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Caution!
Magnetic samples must not be used (see Sample exchange above), otherwise it can be torn away from the holder and
stuck to the final lens pole.

5. Beam module
Stigmator 2D control
enables correcting of image astigmatism. The crosshair indicator
indicates the actual setting.
Shift + Right-clicking on an imaging display triggers astigmatism
correction. Unlike the 2D box control, this is magnification-
sensitive and is therefore suited for fine corrections at high magnifications, or for employing the Adaptive
Sensitivity functionality.
Beam Shift 2D control
indicates and controls the beam shift with respect to the objective lens axis. It is useful for fine imaging shifts
without stage movement.
Shift + Clicking on an imaging display triggers the Beam Shift function. The standard mouse cursor changes to the
“hand” cursor, and the imaging can be dragged on the screen. Because of a limited Beam Shift range, this works
well only for high magnifications or when employing the Adaptive Sensitivity functionality.
Note
Right-clicking on the 2D box opens a context menu with the following choices (for more, see
Software Interface Elements / 2D Controls):
• The Reset sets the Beam Shift value to zero and moves the stage to compensate for
the resulting imaging shift (same as the Stage menu / Beam Shift Reset function).

6. Beam Deceleration module

In the Beam Deceleration mode (option), a negative potential
Stage Bias, is applied to the stage, which influences both primary
and detected electrons. This functionality is standard for biases
ranging from -50 V to +50 V. There is an option for biases ranging
from -4 000 V to +50 V.

7. Scan rotation module

controls and shows the Scan Rotation value.

8. Detectors module
contains adjusters to control the actual detector Contrast
(electronic gain) and Brightness (voltage offset). The values are
remembered for each detector. The adjusters are disabled if the
detector is not available or cannot be controlled (e.g. CCD camera
or an External detector).
Contrast / Brightness / Enhance adjusters
Regardless of the detector’s actual gain range, the Contrast & Brightness range is always 0 - 100 (%) and the small
/ large step size is 0.1 / 1 (the Brightness step size may differ for some detectors in order to achieve sufficient
sensitivity). A direct value can be entered by double-clicking on the Contrast / Brightness value.
Ctrl + clicking on while left-right / up-down dragging within an imaging display controls the Contrast / brightness.
The Low Vacuum detectors could have specific controls within
the Detectors module.

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9. Stage module
consists of elements enabling:
• showing the numerical values of a particular position;
• showing the stage positions locations in a visual map form and
as a list for selection;
• navigating across the sample surface.
Note
The stage movement can be aborted by pressing the keyboard Esc key.
Don't hesitate to do so if you are not sure that the initiated movement
is safe!

10. Stage Z module

This module enables slowly moving the stage in the Z-axis direction.
The more the slider is pushed to the each side, the faster the
stage motion will be. Clicking on the slider bar moves the stage
by small steps.

11. Tilt Correction module

This module enables correcting the imaging distortion when tilting
the stage.

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12. Detector Settings module

enables choosing the active display detector and adjusting its
parameters.
The Detector list box contains the list of detectors actually
available for the active display (the same as the enabled items in
the Detectors menu). The detector actually used in the active
display is always shown.
The rest of the module dynamically changes according to the
selected detector and its parameters, which may change from
display to display.

13. Detection Space module

This informational module gives overview of the ETD, T1, T2, T3
detectors imaging with respect to the working distance. The color
code (see the bottom) gives an estimate of predominant imaging
information.
When changing the High Voltage / Stage Bias values, the asterisk
sign appears next the legend and the Preview mode / Apply / Reset
buttons becomes available. check

14. Patterning Control module

A pattern type can be selected and handled by using the icon
buttons at the top of the module. It can be drawn in the active
display; it is then shown in the pattern list with a number. The
pattern properties can be changed via the Property module. The
Progress indicator shows the Overall / Current (pattern) Progress
(over time) of the actual patterning.

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15. Properties module

Some features (Measurements, Annotations, Patterns) require an
individual set of parameters which are editable within this module,
by clicking on the edit field or the down arrow to choose a value.

16. Digital Zoom module

This procedure takes place in computer memory only and helps
navigate across the enlarged view. Click on the + / - button to
enlarge / reduce the view in an active display or to select a zoom
factor from the drop-down list. Click on the Undo button at the
top right side of the module (visible only when applicable) to
switch between the digital magnification last used and the normal
view.
Click on & drag the green bordered area inside the Digital Zoom
image, or move it by Ctrl + keyboard arrows, to change the
observed area in the active display. Change the observed area by
dragging the green borders. Press the Ctrl + + / – keyboard button
to enlarge / reduce imaging in the active display. When digital
zoom is applied, the magnifying glass icon appears in the
appropriate display.

17. Enhanced image tab modules

consists of tabbed sections offering various digital image enhancements (in contrast to the Detector module /
Contrast & Brightness functionality). These enhancements are applied only to the active display, independently of
any other. In case a user changes the default settings of the LUT / Color / Process tab, its background changes to
orange. The digital processing can be applied to any live, paused or loaded image, including an optical one (see
Chapter 5).

FIGURE 3-15: Enhanced image module

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18. Direct Adjustments module

This control page serves for fine-tuning of beam geometry to achieve the best focus and brightness (see Chapter 5).

FIGURE 3-16: Direct Adjustments module

19. Use Case module

Use the drop down list box to select the desired Use Case for the
specific application (see Chapter 5).
Note
In addition to restoring the factory Column presets, this function also sets some other microscope parameters.

20. Column Presets module

Column Presets in combination with Use cases (see above) simplifies
microscope operation for users. The microscope software comes
with pre-defined sets of various column parameters for the actual
beam and Use cases represented by the Column presets buttons
labeled c#. A user can change these settings to easily choose the
operating conditions according to his needs.
The column preset is applied with a click. A progress dialog is
shown. The button becomes highlighted (orange background)
when all actual microscope settings match the preset parameters.
The bold labeled button indicates the last applied column preset.
Note behaviors that are not obvious:
• Beam is not switched on automatically when a column preset
is applied.
• It can happen that a column preset cannot be completely
applied because it is not possible to set some parameter (a
particular detector might not be available, or a stage bias value
might be out of range). In such cases an application status error
message is shown.
• Tooltip dialog / Detector settings contains information in the
format <detector>, <detector mode>. Particular settings for a
detector custom mode are not supported in column presets.
• Mix detector cannot be used for a column preset.
Right-clicking on any preset button calls up the context menu:

• Clicking on Edit opens the selected preset button properties for

editing with sections for Column / Beam Deceleration / Detector Settings / Beam Corrections. It is also possible to
use the down (expand) / up (hide) arrows next to the preset buttons with the same effect.

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• Clicking on the Update with Current Settings item updates the selected preset button with actual settings.
• Clicking on the Rename item allows renaming of the selected
preset button.
• It is possible to Import / Export Column Presets from / to a file
(.clp).
• Clicking on the Reset to Default restores the default settings for
all column presets (for both beams and for all use cases).

A tooltip is shown when leaving the mouse cursor over any preset
button. The tooltip gives a parameters overview divided into 3
areas (Preset name / Key parameters / Other parameters). The parameters are
colored. Color indications are:
• Green – actual microscope setting matches the column preset
• Brown – actual microscope setting differs from the column preset
• Gray – Value is not relevant when the respective component is switched off

21. / 22. / 23. Analytical page

Contains ColorSEM related controls (see the Chapter 7).

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24. Electron Channeling Pattern module

An image of the crystallographic reflections (Kikuchi lines) can
be observed with the help of this module (see Chapter 5).

25. Alignments module

contains alignments that enable optimizing system performance
(see Chapter 4).
The list box contains a list of Alignment procedures available for
the actual user level (User or Service).
Caution!
A user must understand the procedures at the appropriate level
before proceeding with any adjustment. Improper alignments can
make the system difficult to use.
Note
Some alignment modules may have some features distributed differently
than others, but their functionality is the same unless otherwise explicitly
stated.

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Preferences dialog

This dialog can be opened by selecting Preferences from the pull-down menus: Scan (Ctrl + Alt + S) and
Tools (Ctrl + O - letter). The Ctrl + O shortcut opens this dialog on the last used item.
The Preferences dialog consists of sections listed on the left side of the window. The menu chosen dictates which
section is opened on entry.
Once the Preferences dialog is opened, any section can be chosen. Clicking on a required section opens it and
allows changing and presetting conditions for a group of related functions. The items changed remain valid for a
specific user when logged on next time.
Some of the preference controls are beam dependent. In this case, the actual beam type is
indicated by its corresponding icon, and controls change accordingly.

Shortcuts
List system shortcuts for activating various system Commands (functionalities).

FIGURE 3-17 Shortcuts settings

To customize factory shortcuts click the shortcut in the Primary column and activate new keyboard keys
combination. Click the shortcut in the Secondary column and activate the MUI 5 button to assign it to this
functionality. If a new shortcut is already used, it is not possible to set.
To revert to the factory setting click the Default button.
Note the Help menu / Keyboard Shortcuts item shows default factory primary shortcuts list.

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Presets
Use this section to change the preset values within the High Voltage, Magnification, Stage and Pressure tabs.
• High Voltage – values must be entered in kilovolts (0.2 kV = 200 V) and span from 350 V to 30 kV.
• Magnification – can be changed to hold frequently used magnifications from 20× to 1 000 000×. Values that are
in the list but cannot be applied to the actual SEM conditions are not shown in the toolbar Magnification list box.
Note
Alternatively, magnification could be shown as the Horizontal Field Width (see the Preferences… dialog / General section /
Image dimensions control item).
• Stage – Tilt and Rotation presets can be set in Absolute or Relative values.
• Pressure – list can be changed to hold specific values frequently used in the Low Vacuum / ESEM mode within
the range of 10 to 4 000 Pa.

FIGURE 3-18 Presets settings

Click the Add button, add new value and confirm the entry; the new value is sorted into the list. Click the Delete
button to delete selected value. The Default button on each tab sets the factory presets values.

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Scanning
allows a user to change the toolbar dwell-times (scanning speeds) table and to set-up the Slow scan / Fast scan /
Snapshot / Photo function. The configuration and available items differ for the beam selected for the display.

FIGURE 3-19: Scanning settings

On the left side of the module, there is a dwell-time preset list with the fixed number of
entries. Selected Preset values can be changed in the Property editor on the right side of
the module. The following properties are editable (depending on the type of preset):
• Dwell Time – the period of time during which the beam remains at the scanned point
• Line Integration – number of line scanning repetitions
• Resolution – number of points, Width × Height (imaging resolution)
• Integrate – number of integrated frames in the range of 1 to 512
• Bit Depth – (8 bits / 16 bits) sets the captured image bit depth
• Drift Correction (Yes / No) – corrects imaging drifting when the integration filter is
active. When activated, the text below the blinking pause icon within the display
notifies a user.
• Continuous Scan (Yes / No) – when set to yes and the Snapshot / Photo function is
started during scanning, the scanning finishes and the resulting image is acquired
according to the preset.
This functionality requires the same scanning conditions for the scan in progress and
the Snapshot / Photo preset (Dwell time, Line integration, Resolution, Bit depth…). If
they are not the same, an Application status warning message is shown. The
functionality is convenient for charging samples.
• Action – activated at the end of Photo / Snapshot function:
Save – saves the image using an automatic file name and format
Save As – opens the Save As dialog to save the image
None – just pauses imaging
The following properties are informative and non-editable:
• Line Time – the line scan duration time
• Frame Time – the scan duration time
• Refresh Rate – imaging refresh frequency
Slow (large green sector) / Fast (small green sector) preset icons indicate the matching dwell-time values. To
change it, move an icon up or down just by clicking on & dragging it.

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Snapshot (camera with small green sector) / Photo (camera) preset icon indicates the matching dwell-time value.
Set all possible properties in the Property editor.
The Default button restores the default dwell-time list and preset settings.

Magnification
When storing / printing an image (while in Single image mode / Quad image mode / Large Image Window), the
databar magnification representation might not be correct. This functionality is activated by checking the Beam
menu / Magnification Correction item.

FIGURE 3-20: Magnification settings

The Screen preferences area sets the image databar magnification representation behavior while the File/Print
preferences area sets the storage / printing databar magnification representation behavior. Clicking the radio button
activates the correction technique:
• Real screen size: the imaging pixel width is handled.
– Active view: The databar magnification value depends on whether the Single or
Quad Image mode is selected. It is shown in the image databar and stored /
printed with an icon representing the Single / Quad Image mode.
– Single image / display mode: Single image mode magnification value is shown in
the databar and stored / printed with an image.
– Quad image / 4 display mode: the Quad image mode magnification value is shown in the databar and stored /
printed with an image.
• Polaroid 5”: Polaroid film width is handled. A recalculated magnification value is shown in the
databar and stored / printed with an image.
• User device width (set by a user via the edit box): the recalculated magnification value is shown in
the databar and stored / printed with an image.
The Keep Screen and File / Print settings synchronized check box keeps both settings identical.

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Low Vacuum
The specimen chamber manual purging procedure (see Chapters 2) can be customized in this section.

FIGURE 3-21: Low Vacuum settings

For highly outgassing samples the procedure can take very long time. In this case the Fast Low Vacuum Pumping
Through High Vacuum check box must be cleared; the specimen chamber is then pumped to a pressure slightly
lower then a desired LoVac pressure (see custom settings bellow) and proper purging ensures good water vapor or
gaseous atmosphere in the chamber.
Purge Mode area contains following radio buttons:
• No Purge – the purging is switched off and the chamber pressure goes directly to the set Low Vacuum mode
value. The gas mixture in the chamber slowly changes to the new gas type.
• Automatic – all purging parameters are set automatically, according to the mounted Low Vacuum detector
(Cone).
• Custom – custom settings (see below) are used.
Purge Settings area contains following Custom settings and controls:
• Minimum Pressure / Maximum Pressure / Number of cycles
Set the above three parameters to the desired values for the procedure.
• The Purge button enables starting to purge manually (using the actual Purge Settings) when the system is
already pumped to Low Vacuum; otherwise, the button is disabled. When purging is running, the Purge button
becomes highlighted. Clicking on the highlighted button stops the purging procedure and returns the system to
operation in Low Vacuum.
Note
During the purging procedure, the chamber pressure is not ready for SEM operation (the vacuum status is Pumping).
Therefore, clicking the Purge button automatically switches off the accelerating voltage.
The Purge Settings are not remembered separately for each user. If the Purge settings are important, please check these
Preferences before starting the Low Vacuum operation.

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Pattern Applications
It is possible to enable / disable visibility of pattern applications in the Patterning page / Property module /
Application item by checking the check box next to an application name.

FIGURE 3-22: Pattern Applications settings

The Default button sets the original settings.

MUI Sensitivity
The preset sliders control the sensitivity of the Manual User Interface (MUI – option).

FIGURE 3-23: Sensitivity settings

All MUI controls are represented except Magnification. The Default button sets the original settings.

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File Saving
The image files saving settings can be done here.

FIGURE 3-24 File Saving settings

The Working Folder area sets automatic files storing destination. Clicking the Create subfolders for Displays check
box stores images from each imaging display to the dedicated subfolder with optional Subfolder Name.
Clicking the Custom File Naming check box sets the custom file naming structure.
Moving items from the Available Items area to the Selected Items area (grab & drag) selects them to be included to
the file name. The same functionality is to double-click the item to move it from the available to selected items and
vice versa.
Items listed under the Options can be custom edited and influence the file name (see the Preview: line).
• Sample name – the core of the files name
• Custom Text – file name widening
• Numeric Seed – the image number value; it is automatically increased with each saved image
• Separator for the custom file name values can be selected (Underscore, space, dash)

Movie
For a detailed description see Chapter 5.

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Units
allow a user to change the Units of Measure, Pressure and Temperature. The choices affect the Stage module input
boxes, the databar display, the status bar and so on.

FIGURE 3-25: Units settings

Possible choices are:

• Measure: millimeter [mm] / micrometer [µm]
• Pressure: Pascal [Pa] / torr [Torr] / millibar [mbar]
• Temperature: Kelvin [K] / Celsius [°C] / Fahrenheit [°F]

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Alignments
It is possible to enable visibility of alignments in the Alignments page / Alignments list by checking the Visible check
box next to an alignment name.

FIGURE 3-26: Alignments settings

Sounds
Use the Sounds section to set system sound notices for selected tasks.

FIGURE 3-27 Sounds settings

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General
contains a variety of user settings for both the UI behavior and microscope operation, that do not logically belong
to any other Preferences section.

FIGURE 3-28: General settings

Each item in General Preferences is represented by a single line shown in the property editor. Clicking on the
corresponding Value shows a drop-down list with the settings available for that item.
Note
Some of the items are model dependent, and some are intended for options.
To make navigation among the number of preferences easier, they are divided into three groups.
Confirmation Dialogs
• Request confirmation when saving reduced color information
(Yes / No)
When saving an image with reduced colors, confirmation can
be switched on / off.
• Show confirmation dialog on xT Microscope Control closing
(Yes / No)
When Yes was selected, confirmation is needed to close the UI.
• Request confirmation when unpausing navigation view (Yes / No)
When releasing (unpausing) a window with a navigation image, confirmation can be switched on / off.
• Request confirmation when Link Z to FWD is required (Yes / No)
When starting Link Z to FWD functionality, confirmation can be switched on / off.

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UI Appearance
• Spot size / Beam current control (Spot / Current)
Provides a choice of methods for showing values in the toolbar
list box and Column module.
• Image dimensions control (Magnification / HFW)
Selects the method of magnification representation
and control.
• Frame active display (Yes / No)
Switches on / off additional highlighting of the active
display.
• Enable zooming on mouse click-and-drag (Yes / No)
Set an option of mouse zooming.
• Switch sample tracking on mouse wheel click (Yes / No)
Switches the stage movement (tracking) control between the wheel-click and move and the wheel-click & drag
modes.
• Spot Size Step: (0.1 / 0.01 / 0.001)
Enables setting the accuracy of the spot size value.
• Show workspace name in title bar (Yes / No)
Shows / hides the workspace name in the UI title bar.
• Show context help per module (Yes / No)
Shows / hides the question mark button in the module header.
• Pause stops immediately (Yes / No)
The Pause function acts instantly / waits for the complete scan.
• Source Tilt Adjustment

• Show status message pop-ups (Yes / No)

Switches the status messages pop-up on / off.
• Open Patterning page after pattern is drawn (Yes / No)
When a pattern shape was created with the use of a toolbar icon and Yes is set, the patterning page activates
automatically.
Image and Graphics
• Restart average filter when magnification changes (*)
• Restart average filter when scan rotation changes (*)
• Restart average filter when beam shift changes (*)
• Restart average filter when stage moves (*)
* – (No / Yes)
These items enable choosing whether imaging averaging should be
restarted when the indicated parameter changes. Restarting the
averaging filter causes the imaging to blink and get noisier; averaging
slows down the imaging response to the changed parameter.
• Blinking pause icon during image integration (Yes / No)
If Yes is selected, the blinking Pause symbol is shown in displays that are being stopped. Otherwise, the Pause
symbol appears only after image acquisition has actually stopped.
• Hide rotation controls when not used (No / 10 seconds / 30 seconds / 60 seconds)
Specifies if and when the on-image Scan / Compucentric Rotation control should be automatically switched off.
• Show scan rotation in Camera displays (Yes / No)
This item specifies whether the Scan rotation indicator and value should be permanently shown in the optical
display(s); only non-zero values are shown.
• Show Stage Map in Navigation display (Yes / No)
shows saved positions in any navigation image, that is available (Nav-Cam, Navigation Montage, Navigation
Alignment).
• Save digitally zoomed image as (Entire image / Zoomed area)
When saving an image, this option enables saving only the zoomed area or the entire scanned area.
• Show legacy scanning resolution (Yes / No)
enables showing of old format screen resolutions in the toolbar drop-down list, scanning presets and Photo /
Snapshot presets.

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Microscope Operation
• Interactive Databar (On / Off)
Causes the image databar fields to be active (directly editable
when possible) / inactive.
• Scan rotation sensitivity (0.1 /0.01)
Choose the Scan rotation setting sensitivity.
• E-Beam Working Distance databar precision
(0.1 millimeters / 0.1 micrometers)
It is possible to set the precision of the WD setting.
• Lower stage when venting the chamber
(No / By 10 mm / Full down)
Specifies whether the stage should automatically lower when
venting the chamber. This is recommended, because it greatly
diminishes the chance of hitting the final lens when closing the
chamber doors after mounting a taller specimen.
• Change magnification when pumping
(No / Set to 100× / Set to 200×)
Specifies whether the magnification for electron imaging
should be automatically set to a low value when the chamber is being pumped (presumably after replacing the
specimen).
• Switch off camera automatically (No / 1 minute / 10 minutes / 30 minutes / 1 hour / 2 hours / 6 hours)
Specifies if and when the CCD camera and infrared LED’s should be automatically switched off. The countdown
starts when resuming optical imaging and continues regardless of operator activity.
• Pause beam displays when switching off HV (Yes / No)
Specifies whether electron imaging should be automatically paused when switching the High Voltage off.
• Allow Beam Shift in Get mode (Yes / No)
Enables / disables automatic using of Beam Shift when a user requires very small point-to-point movements
(double-click on the sample point at high magnifications).
• Blank E-beam during long stage moves (Yes / No)
Specifies whether the electron beam should be automatically blanked during long software controlled stage
movements. This may protect extremely sensitive samples from exposure to the beam in undesired areas.
• Delete image data when user logs off (Yes / No)
If Yes, any live and/or paused imaging in all displays is deleted when user logs off.
• Unpause CCD camera for large Z movement (Yes/No)
Specifies if the optical camera should be automatically released during large Z-axis stage movements. This may
prevent a collision between the stage and final lens pole.
• Reverse joystick movement (Yes / No)
Normally the joystick movement direction corresponds to the stage movement, so the imaging moves in the
opposite direction. This setting changes the direction of the stage response to joystick movement.
• Auto switch stage measurement system (Yes / No)
Automatically switches the stage measurement systems off when not used to avoid light interference with 3rd
party equipment (EDS detectors, etc.).
• Retracted detector will be replaced with a standard detector (Yes/No):
If Yes, retracted detector will be replaced with system standard one, if No, imaging will be replaced with the
system message “Detector retracted”.
• Chamber illumination (Yes / No)
If Yes and the in-chamber Nav-Cam is installed, inner chamber illumination is on when the chamber is vented.
• Show sample exchange window on pump/vent (Yes / No)
When starting to pump or vent the chamber, the Sample exchange window opens automatically.
• Venting valve opening time (value)
prolongs the venting time (default value is 180 s) to eliminate residual vacuum, which makes it impossible to
open the chamber door, or shortens the venting time.
• Default display for Nav-Cam image (Display 1 / Display 2 / Display 3 / Display 4 / Active)
This option sets the default Nav-Cam imaging display, which is automatically activated when taking the Nav-
Cam photo.

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Holder
Select the holders to be shown within the Sample Exchange dialog / Holder list.

FIGURE 3-29: Holders settings

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EDS
Use this section to change the Settings for site Presets within the Point, Region, Line and Elemental Mapping tabs.
• Name – set the preset name
• Number of Points (Line site) – set the number of points along the line
• Termination Criteria (Time / Number of Counts) – set the parameter to stop the data acquisition
The Elemental Mapping Live preset is used continuously scan the displayed area.
The Elemental Mapping site scans entire display area with the set Acquisition Parameters:
• SEM Resolution – microscope display resolution
• MAP Resolution – resolution of the elemental maps should be smaller than SEM resolution
• Acquisition Time – the time to analyse the area
• Number of Frames to be covered to the summarized results.
The Dwell Time, Frame Time parameters, are not editable, they are computed from the setting of parameters above.

FIGURE 3-30 EDS settings

Click the Add button to add new value and confirm the entry; the new value is sorted into the list. Click the Delete
button to delete selected value. The Default button sets the factory preset values.

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CleanConnect
The CleanConnect Loader Flushing procedure (see Chapters 7) can be customized in this section.

FIGURE 3-31: CleanConnect settings

Flushing Cycle Mode area contains following radio buttons:

• No Flushing – the flushing is switched off and the CleanConnect chamber pressure goes directly to the set
Vacuum Trip Level value. This is convenient for samples not sensitive to air to save the Ar supply.
• Automatic – all flushing parameters are set according to Flushing Cycle Settings / Automatic column.
• Custom – custom settings (see below) are used.
Flushing Cycle Settings area contains following Custom settings and controls:
• Vacuum Trip Level – after reaching the set pressure level, pumping of the CC Loader stops.
• Overpressure Trip Level – after reaching the set pressure level, venting (gassing) of the CC Loader stops.
• Number of Cycles – number of pump / vent actions to clean the CC Loader inner environment.
Note
During the Flushing procedure, the chamber pressure is not ready for SEM operation (the vacuum status is Pumping).

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Account Manager application

The Account Manager application allows to a Supervisor (accounts manager) to organize user accounts. It allows
the creation and removal of user accounts, settings, passwords, as well as their descriptions. User accounts ensure
admission to the Microscope Control software and to store user individual settings and data.

Password policy
After the software installation there are initial credentials to access the operating system for all microscope users:
• User: User / Password: user
To access the Microscope Control software / Account Manager, use your individual credentials created via the
Account Manager. For the first access use following credentials:
• User: Supervisor / Password: supervisor

Accounts control
You can start the software by clicking the thermoscientific menu / Service Tools / Account Manager icon:

The application window appears.

The Supervisor (default) account can not be deleted; it has the right to create and delete user’s accounts and to
change all their settings. Particular users has a limited right to manage only theirs own accounts.

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The File and Manage Accounts menus contains the same controls (with a
few exceptions), as the buttons placed at the right side of the window.
Some actions are intended for supervisor only.
Clicking the button / menu item starts the action for a selected
(highlighted) account.
• Log on – logs on a new user (an actual user is logged out)
• Exit – exits the application

• Change Password / Description – sets a new password / account description.

• Reset User Settings – restores user account setting to the factory default.

• Copy User Settings – select a user account from which settings are copied.

• Add (Create) / Remove Account – enter information to create a new user account.
To remove user account the confirmation is needed.

• User Sessions – shows the login (.CSV) file for all user accounts.

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• Import / Export – imports selected user(s) from a previously exported (.REG) file.

User Logins and Account Settings

Each user login account stores a variety of configuration data in the registry. These values are then restored when
that user logs back into the system.

Overall layout and settings for the UI

Overall stored settings:
• Electron beam settings (HV, current, HFW)
• Dwell, resolution, position for each beam in full frame, reduced area, line, and spot modes
• Detector settings (bias voltages, etc.)
• Preferences
• Workspace (toolbar, side pan – pages, keyboard – short cuts)
Stored settings for each display:
• Active beam (electron, optical)
• Image save file path
• Image save settings (databar or overlays included)
Stored settings for each beam in each display:
• Active detector
• Detector subsettings for all detectors (is CDEM in SE or SI mode)
• Detector mixing settings
• Digital brightness/contrast/gamma settings
• Databar text
• Zoom and pan (shift) values for digital zoom mode
Others
• Various patterning settings

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4
Alignments

On the Microscope Alignments page select an alignment procedure available from the list box. Always follow the
instructions given in the Instructions module. The Step shows the present control step number and the total number
of steps. You can find some additional explanations in this chapter.

Common Rules
Alignments should be performed in the display 1. Using different display does not ensure the correct functionality
of the Contrast, Brightness and Auto functions within the Microscope Alignments page.
Before aligning the Electron column, be sure that the final lens aperture is clean.
During adjustment procedures, changing the magnification and the scanning speed are allowed, as is using a
reduced area and optimizing image contrast / brightness. It is also possible to correct astigmatism and to focus an
image (for a particular alignment this is forbidden).
During adjustment procedures changing the Vacuum Mode, the Spot size and High Voltage are not allowed. Do not
use the Beam Shift at any time during the adjustment procedures, as this is set to the zero value at each alignment
section. All specimen movements can be made using the stage where appropriate.

Buttons and Control Elements

The following buttons and control elements have the same behavior for all alignment procedures, when available:
• Start button – starts the procedure and proceeds with subsequent dialogs.
• End button – moves a user to the last step (after clicking on the Next button) to enable finishing the alignment
procedure.
• Finish button – saves new settings, ends the procedure and closes the dialog.
• Save button – saves new settings at that point without closing the dialog.
• OK button – applies all changes made in the dialog and closes it.
• Apply button – saves and applies new settings at that point without closing the dialog.
• Cancel button – discards all changes made from the last save and closes the dialog. It has the same effect as closing
the dialog with the cross (Alt + F4).
• Next button – moves a user to the following dialog after necessary settings have been done.
• Previous button – moves a user to the previous dialog when settings need to be changed.
• Contrast / Brightness adjusters – enable optimizing the image quality during alignment.
• Auto button – executes the appropriate alignment action automatically for a particular voltage / spot / direction
(whatever suitable) with the use of the Image Recognition software. If this utility does not recognize image
features well, the procedure is aborted and a Warning message appears onscreen. In this case, change the
imaging conditions (better focus, slower scanning, or lower magnification) and try again.
• Crossover button – activates the Crossover mode, where the onscreen image
shows an aperture projection instead of a sample.
• Modulator button – starts automatic parameter oscillation to facilitate the process.

Recommendation
Some procedures may influence others. Therefore care should be taken to monitor
the influence of any actions taken.
Alignment procedures, which can be carried out whenever necessary during normal
operation:
• Tools menu / Auto Contrast & Brightness, Auto Focus, Auto Stigmator, Auto Lens Alignment, Auto FLASH
• Direct Adjustments / Beam tab / Source Tilt / Auto button
Other alignment procedures can be carried whenever necessary.

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Alignments module

Grouped alignments lists are possible to roll down / up by clicking

the triangle sign to overview alignments accessible for a user.
Clicking the Collapse All button makes all lists collapsed.
Electron Beam
• E-column: Emitter Startup
This procedure enables electron source switching On / Off. In
cases of emergency shut down, it allows starting the IGP’s (Ion
Getter Pump) to pump the electron source space.
• Magnification Correction
See Beam menu / Magnification correction item.
Enhances factory calibration accuracy under particular user
selectable conditions.
• E-Column: Aperture Selection
Enables selecting a second set of final lens apertures in case
the image quality deteriorates (one or more actually used
apertures are worn out).
If an imaging is poor, try to select an alternative aperture.
• E-Column: Preventive Maintenance
– Tip Drift Compensation
– Switch Electron Beam Off
• E-Column: Alignments
– Sample Alignment: allows a user to find appropriate sample
locations within the sample holder and save them. These
positions are used in the following procedures.
– Aperture alignment
– Source Tilt / Shift: electron beam centering within the column.
– Stigmator Centering: corrects imaging shift when correcting
an astigmatism.
– Stigmator Centering
– Switch Electron Beam Off
Stage
• Stage Alignments
– Stage Rotation Center – sets the stage rotation center for the
compucentric rotation.
The stage rotation has a mechanical center. It is controlled by
the Stage module / R value: the stage moves around its
mechanical center. In some cases, this is not desired, because a
rotation around the field of view center would be more useful.
Others
• Automatic Diagnostic Test
• External Plasma Cleaning / Plasma Cleaning
Enables chamber plasma cleaning and sets the duration of the
specimen plasma cleaning.
If a longer plasma cleaning time is needed, we recommend
using several shorter plasma cleaning cycles separated by
pumping the chamber down to HiVac mode. Residuals created
during plasma cleaning are pumped away, and the following
plasma cleaning is more effective. Adjust the Cycle duration,
Clean cycles and Pumping time between cycles.
Note
If there is an external Evactron plasma cleaner, follow the External
Plasma Cleaning alignment instructions and the Evactron user manual!
• Manual Loader Alignment
• EDS pulse processor alignment
• Vacuum Actions

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WA R N I N G !
Do not use Chamber cleaning when the EDS / WDS / EBSD system is mounted! If you need to clean the system with an
EDS detector mounted, use a 1 mm collimator and do not exceed 30 minutes once a week at most.
Do not exceed 30 minutes of chamber cleaning once a week at most when the DBS detector is installed.
Do not leave sensitive samples (including Au-C resolution test samples) in the chamber during the Chamber Cleaning
(they may be damaged).
• Vacuum Actions – set of utilities:
– Start / Stop IGPs – enables starting / stopping vacuum pumps in case of power failure, emergency or service
actions
– Pump / Vent Actions: enables pumping / venting particular vacuum system sections.
– Pump Buffer: enables immediately pumping down the vacuum buffer.
– Water Bottle Venting: enables venting the water bottle to allow refilling it.
• GIS Alignment (option)
Resets the GIS crucible filling lifetime counter after its exchange, sets the GIS heating temperature, and
performs GIS mechanical alignment.
• Quick Loader Alignments (option)

Model difference
Apreo 2 High Vacuum has a slightly modified alignments list.

Selected alignments list

Tick the particular alignment check box to select it to the Selected alignments list. Use the Move Up / Move Down
buttons to change the alignments order. Click the Run button to start the selected alignments execution. Click the
Clear List button to remove selected alignments from the list.

Automatic / Manual Alignments

Some alignments have to be run manually, some run automatically and some offer both approaches; for the latter
tick the Automatic check box to use the automatic procedure.
Running alignment has a bottom tab with choices to Cancel,
Switch to Automatic mode or to proceed with Next alignment
within the list.
Any automatic alignment can be stopped at any time during the
procedure by right-clicking above the red circle and selecting
Stop # item.
If there is an alignment procedure running or paused (waiting for
a response), you must Finish or Cancel it first before running
another one; a confirmation dialog appears.
When interrupting any alignment, nothing is saved, the
alignment windows disappears and the Stop Execution dialog
appears.
Caution!
Read carefully the instructions provided by the system before proceeding with any alignment!
The last page of some alignment offers one or more of the following choices:
• Restore old values and finish: undoes the adjustments; nothing will be saved.
• Save new results and finish: keeps the new adjustment values and saves them.

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Results
Accessible informational windows can be turned on / off by clicking the Show Results / Hide Results button.
Selected alignment shows list of all its steps execution information with Status.

The status for the alignments within the Selected alignments list is expressed by an icon:

• Grey circle
The alignment procedure was not run yet.

• Green tick
The alignment procedure was finished with success.

• Orange square
The alignment procedure was cancelled.

• Red sign
The alignment procedure was ended with errors.

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5
Operating Procedures

This chapter describes how to use the Microscope system from an application point of view. The following subjects
are covered:
• Specimen preparation and handling
• Optimizing imaging
• Standard detectors
• Capturing and handling a Single image
• Recording movies (saving multiple images)
• Stage control
• Measurement and annotation functions
• Patterning & milling
Caution!
These procedures assume you are familiar with the xT microscope Server and Microscope Control software (see
Chapter 3), which are necessary to start and operate the microscope.

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Specimen Preparation and Handling

The sample material must be able to withstand a high vacuum environment without outgassing. It must be clean
and conductive. Oil, dust, or other materials may cause sample charging or contaminate the chamber, which could
hinder or even prevent evacuation.
Note
Always wear lint- / powder-free clean room gloves when handling anything inside the specimen chamber to minimize oils,
dust, or other contaminant pollution of the chamber environment.

Needed Items
• Class 100 clean-room gloves
• Specimen stubs and conductive adhesive material
• Tweezers
• 1.5 mm hex wrench
• Prepared sample

Natural Specimen
If no coating is desired, the Low Vacuum mode can be used to stabilize the specimen for observation. This mode is
useful if there is a suspicion that a coating might alter the specimen.

Coated Specimen
If the specimen is nonconductive (plastic, fiber, polymer or other substance with an electrical resistance greater
than 1010 ohms), the specimen can be coated with a thin conductive layer. This conductive layer reduces beam stir
due to sample charging and improves imaging quality.
For successful imaging, rough surfaced specimens must be evenly coated from every direction. Biological, cloth and
powder specimens may require carbon or other conductive painting on portions of the specimen that are hard to
coat.
Coating makes the imaging sharper and reduces beam penetration. It may mask elements of interest for X-ray
analysis (thus the use of carbon for geological and biological specimens).
For more information on specific preparation techniques, see Scanning Electron Microscopy and X-Ray Microanalysis,
3rd ed., by Joseph Goldstein et al., Springer, 2003.

Mounting Specimen on Holder

Wafers and PGA devices have individual sample-mounting procedures. If you are using a wafer piece or other
sample, attach the specimen to the specimen holder using any suitable SEM vacuum-quality adhesive, preferably
carbon or silver paint. The specimen must be electrically grounded to the sample holder to minimize specimen
charging. If you are using another method to mount a specimen, make sure the specimen is conductively attached
to the holder.
Note
The sample holder is not directly grounded to the chamber ground because it is connected to the BNC feed, allowing
measurement of the specimen current.
Caution!
Store samples and sample holders in a dry nitrogen storage cabinet. Dust on samples can get drawn into the electron
column, degrading performance and requiring an Thermo Scientific Customer Service call to correct the problem.

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Specimen Baking Unit

The Specimen baking unit is intended to bake out the microscope specimens (up to 60 mm diameter) mounted on
the specimen holders.
Caution!
Read and follow all following instructions carefully!
Read and follow instructions stated in the Apreo 2 User safety manual carefully!
(installed with your Microscope control software)
Place the instructions in a safe place for future reference.
Note the safety labels and engravings on the baking unit. Read them and be careful to understand their meaning!
Do not allow anyone who has not read and understood these instructions and who cannot follow them to operate
and/or service the Specimen baking unit!
Failure to comply with the precautions and instructions provided with this unit can result in bodily injury and property
damage from hazards of fire or burn.
WA R N I N G !
Do not leave the unit unattended when it is ON!
Do not open the lid when the unit is ON! Be extremely careful to avoid bodily injuries from burning.
When opening / closing the lid, always use the plastic knobs, otherwise there is risk of burning!
When replacing the halogen bulb, always wear protective gloves and safety goggles!

Wa rranty disclaimer
The unit must not be used for any other purposes than what it is intended for. Otherwise the warranty claims cannot be
accepted.

FIGURE 5-1: Baking unit / Baking unit with opened lid

Installation instructions
The unit should be placed away from flammable materials.
Do not put any objects on top of the unit – the unit becomes warm when in operation.
The unit is supplied with 12 V DC. The adaptor has a replaceable plug to fit in various mains sockets. Connect the
supply voltage cable connector to the unit and plug the adaptor into the mains voltage of 110 – 230 V AC.

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 Operating Procedures: Specimen Preparation and Handling

FIGURE 5-2: Power supply adaptor with removed plug / with mounted plug

Operation
The inner surface of the unit is polished and vacuum-clean. Avoid contamination of the inner surface otherwise the
specimens may become contaminated during the baking cycle.
Caution!
Always wear clean lint-free gloves when handling the unit and the specimens! Be sure the working desk is free from
impurities that can cause the unit or specimen contamination.
The working desk must be covered with a material with a melting temperature higher than 250 °C!
WA R N I N G !
Do not look directly at the operating bulb for any period of time! Doing so may cause serious eye injury.
Risk of burning! For support tray manipulation (sample loading, for instance), always use the special tool delivered!
Never touch the inner surface of the baking unit, including the trays and specimens, with bare hands or hands in gloves.

FIGURE 5-3: Support tray Handling tool / Removal of the Support tray

1. Open the lid and remove the support trays from the unit using the
special tool.
2. Put the support tray on the working desk and put one or more
specimens on it so that the specimen stub pin enters the hole in the
tray.
3. Put the tray back in the unit and close the lid.
There are two possible slots for tray insertion. The specimen will be
exposed to a temperature of 160 °C in the upper position and of
120 °C in the lower position.

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FIGURE 5-4: Support tray mounting positions

4. Press the rocker switch on the unit to switch the unit ON.
5. Wait at least 3 hours. Switch OFF the unit by pressing the rocker switch.
6. Carefully open the lid, remove the tray with the specimens, and put it on the working desk.
7. Carefully hold the specimen with a pair of tweezers and mount it in the microscope chamber while hot.
8. Start the pumping cycle right after mounting a sample into the microscope chamber.
To make the baking process most efficient, we recommend mounting the sample in the microscope chamber
immediately after stopping the baking cycle. Let it cool down to the room temperature inside.
Note
For high resolution observation, let its temperature stabilize for approximately 30 minutes.

Maintenance
The unit does not require any maintenance except necessary cleaning. When cleaning the unit, use vacuum
compatible cleaning agents (isopropyl, ethanol) and lint-free tissues. The support tray can be cleaned in an ultrasonic
bath.
Caution!
Do not clean the Baking unit in the ultrasonic bath!
Halogen bulb replacement
WA R N I N G !
The bulb operates at extremely high temperatures that can cause serious physical injuries and property damage!
Never touch bulb when it is on, or soon after it has been turned off, as it is hot and may cause serious burns!
When replacing the halogen bulb, always wear protective gloves and safety goggles!
Caution!
The bulbs are very fragile. Do not drop, crush, bend or shake them!
Vibration or impact will cause filament breakage and short bulb life.
Do not touch the bulb surface with your bare hands! Use clean gloves or lint-free cloth for installation and removal.
Oils from skin can lead to breakage or shorten the life of the bulb.
Do not use any other type of the bulb than specified, as it could cause overheating of the baking unit or inefficient
sample baking.
1. Press the rocker switch on the unit to switch the unit OFF. Wait until the bulb is cooled down completely.
2. Remove the bulb from the baking unit.
3. Insert the new bulb into the baking unit.
You can use spare bulb delivered together with the unit. Always use only bulb with the following specification:
Type: Low voltage halogen bulb, G4, 12V, 20W
Supplier: OSRAM
Product ID: 64428

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Microscope Control

It is assumed that the microscope is in its Full operation state (see Chapter 2).

Operation Pre-Check
To ensure correct operation check the following list before continuing. After obtaining a preliminary image, you can
then experiment with your own settings.

Table 5-1 Apreo 2 setup conditions

Adjustment Electron Beam Setting

Vacuum mode High Vacuum: conductive samples
Low Vacuum: nonconductive, mixed or contaminating samples
Column Use Case Standard
Accelerating Voltage Select voltage relative to the specimen type:
- low kV for surface imaging, beam-sensitive samples and slightly charging samples
- high voltage for conductors, high resolution, composite info (BSE, X-ray)
Examples:
- biological samples HV = (1 – 10) kV
- metal samples HV = (1 – 30) kV
Beam Current 100 pA at 30 kV
Spot size High Vacuum / Low Vacuum: 5 – 6
Scan rate High Vacuum: fast scan (dwell time 0.1 - 0.3 µs)
Low Vacuum: slow scan (dwell time about 3 µs)
Working Distance Set the highest specimen point to approximately 10 mm (yellow mark in an optical
(FWD) imaging display), tilt to 0° and press Ctrl + F (set FWD to 10 mm function).
Eucentric Position 10 mm
Magnification Set to lowest, from 20× to 200×
Standard Detector High Vacuum: ETD (SE)
Low Vacuum: LVD
Filtering High Vacuum: Average (2-4 frames for fast scans)
Low Vacuum: Live
Contrast With contrast at the minimum value, adjust the brightness to just show a change in
and Brightness intensity on the screen. Increase the contrast to produce reasonable imaging. Increasing
brightness and decreasing contrast produce softer imaging and vice versa.

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Inserting / Exchanging Specimen

1. Click on the Vacuum module / Vent button.
The confirmation dialog appears.
After switching High Voltage off, the vacuum
system switches off the pumps and opens
appropriate valves to vent the system. After a
specified venting time, the venting valves will
close.
Note
If the venting valve closes before the chamber is
at the atmospheric pressure (it is not possible to
open the door), click on the Vent button once more to open it again.
2. When vented, open the specimen chamber, and using lint-free gloves or tweezers, place a specimen into the
specimen holder.
3. Close the specimen chamber door and click on the Vacuum module / Pump button.
Instructions for a sample exchange are also shown within the informational window by clicking on the
toolbar icon.

Selecting Vacuum Mode

Tick the Vacuum module / High Vacuum or Low Vacuum mode radio
button.
In case the Low Vacuum mode is selected and a detector with no
PLA is used, the X-Ray Cone must be used when:
• Chamber pressure above 50 Pa is needed
• OptiPlan column Use case is needed
When EDS analysis takes place, the X-Ray cone is recommended
To automatically install the cone on the final lens pole (the
specimen chamber must be evacuated), click the X-Ray Cone /
Insert button. To remove the cone, click the Retract button.

X-Ray Cone ERROR procedure

In case of the X-Ray Cone insertion is not successful, follow the procedure:
1. Vent the specimen chamber and release the X-Ray Cone from the incorrect position (final lens pole or
Multipurpose holder).
2. Attach the cone to the Multipurpose Specimen Holder (Auto PLA) so the corresponding cone and holder sloping
surfaces match.

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3. Click the Pump button and select the PLA Accessories dialog / No
Accessory item.
4. Run the Stage menu / Home stage procedure.
WA R N I N G !
The system can be damaged by using the Low Vacuum mode without an
appropriate PLA. Do not select a PLA Cone that is not actually being
used (see Chapter 2)!

Imaging Onscreen
Continue the procedure:
5. When the vacuum status is PUMPED (see the status bar), click
on the Column module / Beam On button to ramp up the electron
beam acceleration voltage.

6. Select an appropriate column Use case, detector and release the active display (if paused), where the image
appears.
7. Focus the imaging and Link Z to FWD.
8. Adjust to a suitable magnification. Optimize the imaging using the Contrast & Brightness, Focusing, Astigmatism
Correction etc.

Optimizing Imaging

Principles of SEM Imaging

All scanning beam microscopes share the same fundamental
technique. The primary beam is scanned across the specimen
surface in a regular pattern called raster. Normally, this raster
consists of a series of lines in the horizontal (X) axis, shifted
slightly from one another in the vertical (Y) axis. The lines are
made up of many dwell points and the time of each dwell point
can be shortened or prolonged (dwell time). The number of
points per line can be increased or decreased as well as the
number of effective lines. The result is a picture point (pixel)
array. Low or high resolution imaging can be obtained by
changing these factors. The larger the pixel array, the higher
the image resolution. The image is created pixel-by-pixel in the
computer memory and shown on a monitor screen.
The signal emitted by the specimen surface as it is illuminated
with the primary beam is collected by the detector, amplified
and used to adjust the intensity of the corresponding pixel.
Because of this direct correspondence, the pixels shown on the monitor are directly related to the specimen’s
surface properties.
The raster consists of many (typically one million) individual locations (pixels) that the beam visits. As the beam is
scanned, the signal emitted by the sample at each beam position is measured and stored in the appropriate digital
memory location. At any time after the beam scan, the computer can access the data and process it to change its
properties, or use it to generate an image.

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Magnification
Magnification is calculated as the shown dimension (L) divided by the sample scanned dimension (l).
If the observed sample area is made smaller while the monitor size remains constant, the magnification increases.
At low magnification, one gets a large field of view. At high magnification, only a tiny sample area is imaged.
It is possible to set a corresponding databar magnification readout in the Quad Image and Single Image modes and
in the saved image (see the Preferences / Magnification section).

Changing Magnification
• Keyboard control (+ / - / *) – the numeric pad plus key (+) / the minus key (-) increases / decreases the
magnification 2× and rounds the value. The star (*) key rounds the magnification value (e.g. 10 063× becomes
10 000×).
• Mouse wheel control – coarse / fine control can be operated by the Ctrl / Shift key and rolling the mouse wheel
up / down to increase / decrease the magnification.
• Toolbar list box – used to choose from predefined values
• Selected Area Zooming In / Out – a quick way of zooming in / out on an area of interest. Click
inside the imaging area & drag to make a dotted box over the area of interest (the cursor
changes to a magnifying glass with a + sign). Release the mouse button, and the selected
area increases to fill the whole imaging area with respect to the sides ratio. Clicking on &
dragging + Shift consecutively reverses the above described technique (the cursor changes to
a magnifying glass with a – sign). The Esc key cancels the operation at any time.
• Magnification module
• Digital Zoom module

Scan Speed
To obtain a good imaging with acceptable signal to noise ratio it is necessary to find a balance among scan speed,
sample charging and/or damage.
A noisy image can be improved by decreasing the scan speed. If sample charging and/or damage is the limiting
factor(s), it is better to use a higher scan speed in combination with noise and charge reducing tools like Average or
Integrate filter, Line Integration or Scan Interlacing.

Contrast & Brightness

The contrast and brightness can be set manually either by
adjusting the Detectors module controls, using the mouse (Ctrl +
click on & dragging – horizontal / vertical direction adjusts the
contrast / brightness) or by using the MUI (option):
1. Select a medium scan speed in an active display.
2. Reduce the contrast to zero. Adjust the brightness to a level
corresponding with the last gray level detectable by eye before
the screen goes black.
3. Increase the contrast until the image of the observed structure appears.
4. If necessary, adjust the brightness level to improve the image.

Videoscope (F3)
This tool can facilitate contrast and brightness optimization to utilize the full grayscale imaging range.
Three yellow horizontal lines (placed over the display) indicate white (top line), gray (middle line) and black
(bottom line) levels. The oscillogram signal amplitude / central position reflects the contrast / brightness of the
line just scanned. If the oscillogram is cut by the bottom / top line, the signal level is clipped in black / white. This
should be avoided, because imaging details are lost in the clipped areas.
Tuning the oscillogram exactly between the top and bottom lines for a feature of interest (using a reduced area)
results in full detailed imaging. Signal clipping may be used to obtain harder contrast conditions when more black and
white is needed. Lowering the signal amplitude decreases the contrast, i.e. the imaging looks softer.
1. Select a slow scan in an active display.
2. Activate the Videoscope in an active display (F3 / clicking on toolbar icon / Scan menu) or in all live displays
(Shift + clicking on the toolbar icon).

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3. Reduce the contrast to zero and adjust the brightness level to the lower dashed line (black).
4. Increase the contrast so that the signal level just touches the upper dashed line (white).
5. If necessary, adjust the brightness level so that the average signal level is roughly in the middle.
6. The high and low peaks should just touch the dashed lines.
Repeating the contrast & brightness optimization helps improve the image quality.

Note
Use also the following functions to optimize the Contrast / Brightness: Auto Contrast Brightness (F9), Display Saturation
(Shift + F11).

Focusing
Find a feature of interest with distinct edges on a specimen. Use a combination of contrast, brightness and
magnification adjustments to optimize the imaging quality.
1. When the mouse cursor is over an imaging area, right-click on & drag (the mouse cursor changes to a 2-
ended arrow). Move the mouse from side to side until the observed object is sharp, then release the
mouse button.
2. The focus function uses the whole screen without any interference from other controls. If the full
mouse motion is not sufficient to get the focus, release the mouse button at one side of the screen,
move the mouse cursor to the opposite one, and right-click & drag again over an imaging area to
continue focusing.
3. If necessary (for example when new specimen was loaded), run the Link Z to FWD function.
Focusing at a higher magnification makes the result more precise. For example, for an output at the 2 000×
magnification, focus at 4 000× – 8 000× magnification.
To avoid scanning too long and contaminating or even damaging the sample before you take the final image, move
away from the feature of interest with the X and Y stage controls, and focus until the image is sharp on an adjacent
area.

Focusing with MUI (option)

Use coarse and fine focus knobs. The imaging immediately responds to the MUI.

Note
Use also the following functions to focus: Reduced area (F7), Auto Focus (F11).

Correcting Astigmatism
This optical aberration is caused by different focal lengths for rays of various orientation, resulting in directional
imaging blur (“X and Y rays” are not focused to the same plane). It is best seen on the edges of observed sample
structures. Stigmator serves for correction of this imperfection, which is usually better seen at higher
magnifications (3 000× or more).
When imaging conditions are changed, use the following procedure to correct astigmatism:
1. Focus an image.
2. Bring the imaging just slightly out of focus. The image appears to become sharper in one direction whereas in a
perpendicular direction, blur increases (blurring or stretching).
3. Bring the image just slightly out of focus in the other direction to observe the opposite directional blur.
4. Focus to the midpoint between the two directions, where the blur is visible.
5. Use the Beam module / Stigmator 2D control.
Mouse: shift + right-click on & drag while in the active display. This results in a 4-ended arrow cursor
appearing in the screen’s center. Move the cursor around the screen to achieve maximum sharpness.
When you are satisfied, release the mouse button.
The MUI (optional): adjust imaging sharpness with the stigmator X and Y knobs until the best result is
achieved.
6. Repeat steps 1–5 as necessary.
If astigmatism is severe and the cross is close to the edge of the screen when nearing correction, release the mouse
button and reposition the cross in the center of the screen. Then repeat the procedure above to perform further
astigmatism correction. You can advantageously use a reduced area.
If astigmatism cannot be corrected, there may be some other reason. Usually it is that the final lens aperture is

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dirty (see Chapter 4 – E-Column: Aperture Selection), the magnification may be too high for the beam spot size, or
the sample is charging (apply a conductive layer or use the Low Vacuum mode).

Note
For normal astigmatism correction use the automatic procedure (Ctrl + F11).

Auto Flash Predefined / Customized

This functionality is based on the set of acquired images; it enhances the image quality by correcting focus,
working distance, lens alignment and astigmatism in one go.

Predefined
Selecting the Tools menu / Auto Flash Predefined item or clicking the toolbar icon starts the automatic
functionality (reduced area and parameters are factory preset).

Customized
Selecting the Tools menu / Auto Flash Customized item starts the customized automatic functionality. To customize
settings set user defined reduced area in the imaging display, and right-click above the toolbar Flash icon and
select the Customize item.

Set imaging parameters: the number of Steps, Dwell Time and screen Resolution.

Manual
User can use also the manual procedure by making accessible another toolbar icon (from the workspace
Customization / Toolbar / Column area).
Follow the procedure:
1. Start imaging with the dwell time about 300 ns and the screen resolution 768 × 512, or start a reduced area.
2. Click the toolbar Flash icon to start the process (icon is highlighted in orange), or press and hold the Ctrl + Shift
key simultaneously.
The orange Flash icon appears in the active display top right corner.
3. Right-click and move the mouse above the active display with a live imaging from left to right so, that imaging
shifts from de-focused, through focused, to de-focused image state in one go.
The display Flash icon changes from orange to green when number of acquired images is sufficient for
computing the settings.

4. Release the mouse button to apply new imaging settings.

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Direct Adjustments
This control page serves for fine-tuning the beam geometry to achieve the best focus and brightness.

Electron Beam tab

• Source Tilt 2D box – serves for correction of signal intensity by
changing the effective angle of the beam coming from the
source into the electron column.
Move the crosshair in order to get the electron beam spot into
the display center.
• Clicking the Auto button sets the Source Tilt automatically.
• In the Crossover mode (activated with the button), the image
shows the electron source position instead of the sample surface.
• Crossover Zoom slider – set the Crossover image magnification.
• Lens Alignment 2D box – optimizes the primary beam passage
through the final lens so that image shift during focusing is
suppressed.
Try to minimize the image shift by the crosshair movement.
• Lens Modulator (useful for HV > 3 kV) / HV Modulator (useful
for HV ≤ 3 kV) button – starts automatic objective current /
accelerating voltage oscillation (periodically under- and over-focuses imaging in a narrow range) to facilitate the
above mentioned optimization.
When the accelerating voltage is above 3 kV, Lens Modulator
is automatically selected, otherwise the HV Modulator is. You
can choose either one manually.
• Amplitude slider – sets the modulation amplitude.

Electron Stigmator Centering tab

• Stig. Center X / Y 2D box – serves for minimization of image
shift during astigmatism correction. The crosshair indicates
the actual stigmator setting.
Try to minimize the image shift by the crosshair movement.
• Modulator X / Y button – starts automatic modulation of the
respective stigmator to enable the stigmator centering
procedure. Modulation occurs in a narrow range around the
current stigmator setting.
• Amplitude slider – sets the modulation amplitude.

Electron Focus tab

• Focus Centering 2D box – serves for minimization of image
shifting during focusing if HV ≤ 3 kV. It is a complementary
function to Lens Alignment and it is not applied for HV > 3 kV.
Try to minimize the image shift by the crosshair movement.
• Modulator button – starts modulation of the corresponding
electron optical components to enable the focus centering
procedure.
• Amplitude slider – sets the modulation amplitude.
• Apply Focus Centering check box – if selected, the result of the
focus centering procedure is applied.

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Digital Imaging Enhancement / Imaging Mixing / Coloring

The Enhanced Image module offers various digital imaging enhancements.
Note
When saving an image with the digital enhancements applied, be sure to choose the correct Digital file format (see
further).
LUT (Look-Up-Table) tab module
enables monitoring and modifying gray level distribution
(histogram).
• Presets list box – enables selecting the Digital Contrast, Digital
Brightness and Gamma values using pre-defined or custom
presets.
• D. Contrast adjuster – sets digital contrast in the range from -10
to +10 (negative values lead to an inverse image).
• D. Brightness adjuster – sets a digital brightness in the range
from -2.0 to 2.0.
• Gamma adjuster – corrects image brightness non-linearly in
the range from 0.1 to 10.
• Auto Levels button – sets the three above mentioned parameters
automatically according to the image / image quality.
• Graph area – graphically shows the applied modification via the
gray line. Horizontal / Vertical axes represents the input /
output values.
• Auto Levels button – sets automatically D. Contrast, D. Brightness and Gamma to optimize the actual imaging.
• Histogram button – switches on / off the gray level distribution (corresponding to the live imaging) illustration.
The left / right side corresponds to black / white original image pixels. The height of the blue line is proportional
to the number of pixels with the corresponding gray level.
• Save button – saves the actual setting as a custom preset.
• Default button – restores the default values.
Mix 3 / Mix 4 tab module
The Mix feature operates in display 3 / display 4 and is
automatically enabled when clicking the 1 + 2 / 1 + 2 + 3 button.
Any combination of live and paused images can be mixed
together, providing all mixed images have the same pixel
resolution. However, there are some logical limitations and
behaviors related to the Mix display:
• Average and Integrate filters are disabled.
• Pause / Activate functionality influences the mixed imaging
only, not its sources. The Mix display is always paused
immediately regardless of the actual scanning status.
• Optical imaging is not mixed.
Note
In the Mix 3 tab the Source 3 controls and the 1+2+3 button are not
available.
• 1 + 2 / 1 + 2 + 3 button – switches on / off mixing of the
corresponding displays. It also restores detectors or automatically selects suitable ones in appropriate displays.
• Presets list box – enables selection of the mixing ratios and colors using pre-defined or custom presets.
• Source 1 / 2 / 3 adjuster – tunes the mixing ratio of display 1 / 2 / 3 imaging. The adjuster % value
correspondingly influences the resulting image, and the others change automatically to reach the 100% sum.
• Clicking on the Color control areas (below each Source adjuster) enables selecting of a color, replacing the
source image black (left) / white (right) one. The image grayscale is linearly transformed to a new color
spectrum before it is mixed with other image(s).
Note
A colorized image (see the Color tab) is converted to a grayscale one before mixing.
• Invert check box – inverts a corresponding source spectrum. It has the same effect as exchanging the left and
right colors selections.
• Save button – saves the actual setting as a custom preset.

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Color tab module

enables colorizing a grayscale image. An image already colored
with the use of the Mix 3 / Mix 4 tab cannot be colored again; the
Color tab is disabled.
• Presets list box – enables selecting the color profile using pre-
defined or custom presets.
• Coloring Control area – shows the active display histogram and
enables editing a color profile.
Clicking on the histogram area adds the vertical borderline
with a divided triangle at the top (right-clicking on an existing
one removes it). Clicking on & dragging a borderline changes
its position along the histogram. Clicking on the left / right
part of the triangle selects the left / right border color. The part
of the histogram between the two borderlines is linearly
transformed to a new color spectrum.
• Reset button – sets the modified color profile to its original
state.
• Save button – saves the actual setting as the custom preset.
Process tab module
Here a user can set parameters, that adapt an image.
Note
This functionality works only with grayscale images (not colored via
the Mix3, Mix 4 or Color tab), images that are paused, or with loaded
saved ones.
The Preset list enables to select the image postprocessing using
pre-defined or custom presets. Changes in the custom presets
must be saved manually.
Clicking the “…” button opens the menu with choices:

• New – to create new preset

• Save / Save As – to save updated preset / the preset with new name
When any preset(s) is/are not saved, and actual user logs off, the system asks to save new settings.
• Visible to All Users – presets are visible within other user accounts
• Delete – to delete selected preset
Within the Processing Pipeline area list of filters selected within the active preset is shown. Filters with cleared check
box are not processed. Selecting any filter line (greyed) shows individual filter controls in the bottom of the
module.
• Add button shows all filters available to be added to the Processing pipeline
list.
• Remove / Remove All button – clicking the button removes selected filter / all
filters.
• Original button – clicking the button toggles original and processed image
imaging.

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Accelerating Voltage and Beam Currents

The choice of accelerating voltages – in the UI named High Voltage (HV) – and
beam currents for the active display is possible via the toolbar dropdown list
boxes. The electron beam current and HV are independent, so any change of
voltage will not influence the current.
Changing High Voltage
Besides a normal list box’s behavior an intermediate value can be
entered into the toolbar editable HV text box or set by the Column
module / High Voltage adjuster on the Beam control page. This
provides a calculated range of beam current / spot values. Default
values in the list box are set in the Preferences dialog / Presets
section.

Electron Beam Current / Spot size

This is one of the basic operating parameters. Functionally, it represents the electron beam diameter (usually
presented as the Spot size, expressed as a relative number from 1 to 20), the final lens aperture diameter, and its
opening angle as set by the condenser. It is considered to be close to ideal when a spot’s edges just touch its
neighbouring ones. If the spot is too large, overlaps occur and the image appears out of focus. If it is too small,
electronic noise appears in the image.
A suitable beam current value for a particular magnification can be determined easily when good focus and
astigmatism correction are achieved.

Table 5-2 Spot sizes and recommendation of their use

SEM column Use case Spot size Best use

Standard / OptiPlan / Immersion 1–4 Very low currents, charging and sensitive samples
Immersion 3–7 Ultra high resolution
Standard / OptiPlan 4–6 High resolution
Standard / OptiPlan / Immersion 6 – 12 Standard imaging
Standard / OptiPlan / Immersion 12 High current imaging, X-ray analysis with SDD detectors
and more
Standard / OptiPlan 10 – 17 High current imaging, X-ray analysis, EBSD detector,
cathodo-luminiscence
Standard / OptiPlan 18 – 20 Very high currents, fast analysis

Changing Electron Beam Current

Either electron Beam Current or Spot Size can be shown within the User Interface. This can be set
in the Preferences dialog / General section or by right-clicking on the toolbar text box and
selecting the desired context menu proposal.
An intermediate value can be set by the Column module / Beam current/Spot size adjuster on the
Beam Control page. Default values in the list box are set in the Preferences dialog / Presets
section.

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 Operating Procedures: Optimizing Imaging

Column Use cases

The electron column can be operated in different Use cases
optimized for specific applications. To select the desired Use
case, use the Use cases module drop down list box.
You can immediately switch from one Use case to another. If high
voltage or beam current is out of the operating range of the new
Use case, it is set automatically to the closest possible value. If
the newly set conditions do not allow imaging, (e.g. it is not
possible to focus), transition is not allowed, and a warning is
shown in the application status window.
• Standard
This is the survey mode ideal for navigating and reviewing sites at lower magnifications. The A-Tube is on the
ground potential, and the default detector is the ETD in the Secondary Electron mode. Maximum probe current
is limited to 13 nA.
Probe currents above 13 nA are available for analytical applications such as EDS, WDS or EBSD. It should be
used when higher probe currents are required. Currents can be as high as 400 nA; the accelerating voltages
above 13 nA are available within 5 to 30 kV. The A-Tube is on the ground potential, the ETD detector should be
used for secondary electrons and T1 or DBS (optional) for backscattered electron imaging.
• OptiPlan
Here primary electrons are accelerated by the potential of the
Acceleration tube (A-Tube) and pass through the column at
high energy. They are decelerated back in between the T1
detector and the sample. Secondary as well as backscattered
electrons are also collimated into the final lens by the A-Tube
electrostatic field and detected by the Trinity detectors (T1, T2,
T3).
This mode is used for ultrahigh resolution electron imaging of
the sample at short working distances (1 – 2 mm). The A-tube
is at the highest potential and the T1 and T2 detectors should
be used. The full range of the Beam Deceleration mode (if
installed) is available for this Use case.
In this mode, the maximal working distance depends on the
landing energy (Beam Deceleration mode). It ranges linearly
from 5 mm (at 200 eV) to 70 mm (> 10 keV). It is possible to
use overview imaging at the maximal field of view, so there is
no need to switch the Use Case for navigation purposes.
Note
For detailed high resolution electron imaging, see the Help menu /
User Guidance item / High Resolution Imaging.
• Immersion
This Use case is available only with the Immersion lens
(option). The primary electrons are accelerated by the
potential of the A-Tube (Acceleration tube) and pass through the column at high energy. They are decelerated
back in between the T1 detector and the sample. Moreover, immersion magnetic field is applied in between the
pole piece and the sample to form the smallest possible beam diameter. The secondary as well as backscattered
electrons are collimated into the final lens and detected by the Trinity detectors (T1, T2,T3). Described
combination of the electro-static and magnetic lenses is called Compound lens (see Chapter 3 – Compound
Lens Filter module).
The Immersion Use case should be used to reach the ultimate performance – the best resolution. The optimal
working distance for ultra-high resolution imaging is suggested to the user by the Working distance indicator,
typically the lower the landing energy the shorter the optimal working distance. The maximal working distance
depends on the landing energy. It ranges linearly from 5 mm (at 200 eV) to 70 mm (> 10 keV). The maximal
field of view is working distance dependent and it ranges from one hundred micrometers to three millimeters.

Model difference
The low Vac mode can be used only with OptiPlan and Standard Use cases depending on the PLA (pressure limiting
aperture) installed on the pole piece.

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 Operating Procedures: Standard Detectors

Standard Detectors

The Detectors menu and Detector Settings module / Detector list box show all installed
detectors; the selected one has a tick mark next to its label. When a Detector Settings
module / Mode is selected, its acronym is shown beside the detector label in the
Detectors menu. The availability of detectors (full color label) depends on the actual
conditions.
Detector selection is related to the display and to the selected beam – the system
always reverts to the last detector used for that beam in that display and remembers its
Contrast & Brightness settings.
Detector exchange and modification of its conditions made via the Detector Settings
module are immediate.
During the patterning (option) process the Detector Menu is still in use, but modifications
will not become active until Patterning has stopped or has been interrupted. A typical
circumstance under which changes can be made during a patterning session is Snapshot
or image acquiring. These facilities can be set up in advance. When patterning is stopped,
the last scan detector and scan conditions will be set.
Note
If a detector that is not compatible with the actual vacuum mode is selected, imaging cannot
be started.
Images from individual segments / detectors can be acquired simultaneously in up to four
different displays.
In addition to the standard detectors available, there may be optional ones available for
your system (see Chapters 2 and 7).

Retractable detectors control

When any retractable optional detector is installed in the system,
the appropriate Insert / Retract button is added to the Detector
Settings module / Detector CCD to enable control of the equipment
while observing the optical imaging display. The same button is
also present in the appropriate detector module.
To insert any retractable detector, a confirmation dialog appears.
When insertion is not possible, tooltip gives a reason why.

Infrared CCD Camera

Imaging obtained with this camera assists in overall sample and
stage orientation by viewing the inner space of the specimen
chamber (an optical imaging display). It helps protect the
objective lens and retractable detectors against collision when
moving (especially in the Z-direction) or tilting the stage. IR LED’s
are used to light the specimen chamber’s interior.

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Everhart Thornley Detector (ETD)

The Everhart Thornley Detector is a scintillator photo-multiplier
type detector that collects electrons generated by the primary
beam interaction with the specimen surface. It is permanently
mounted in the chamber over and to one side of the sample. It
works in Modes:
• Secondary Electrons (SE)
• Backscattered Electrons (BSE)
• Custom
ETD Settings
The Detector Settings / Mode list box enables choosing an SE /
BSE mode (the Grid Voltage is set to +250 V / -150 V) or a Custom
mode, for which the Grid Voltage can be set by the adjuster in a
range from -240 to +260 V. When the voltage is negative (use a
range of -25 to -240 V), SE are repelled from the ETD detector
and only BSE are detected.

Low Vacuum Detector (LVD)

This detector is standard and optimal for general imaging in Low
Vacuum mode over the entire pressure range from 10 – 500 Pa
(0.08 to 4 Torr). Its signal contains both secondary and
backscattered electrons. The LVD detector limits the field of view
to about 1 mm at the 10 mm working distance. The minimum
working distance is limited to about 3 mm.

FIGURE 5-5: Low Vacuum Detector (LVD)

LVD Settings
After the pump down and purge processes, switch on the
accelerating voltage. The modified Detectors module / Bias slider
is automatically activated.
Adjust Bias if necessary to increase the signal or to stop possible
discharges. At the lowest possible magnification, adjust the
Contrast and Brightness, if necessary, until the bright circle of the
LVD cone can be seen in the center of the image. Increase
magnification and adjust Contrast and Brightness more precisely.

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Trinity Detectors T1 / T2
Electrons generated by a primary beam can be collected by the
in-lens Trinity detectors T1 and T2, which are located inside the
final lens.
Note
Whenever the T1 or T2 is selected, the optical display is paused (the
CCD camera infra-red LED’s are switched off to keep emitted photons
from supersaturating the detector).

T1
The T1 detector is primarily designed to collect backscattered
electrons. It provides composite sample contrast. In the OptiPlan
and Immersion column Use cases, it detects backscattered
electrons throughout the whole range of accelerating voltages
thanks to the A-Tube at high potential that accelerates the BSE
towards the detector. In the Standard column Use case, the T1
provides strong BSE contrast at accelerating voltages of 5 kV and
higher.
The Compound Lens Filter is optimized for this detector
especially.

The functional detector area is split into two halves, and the
detector can be operated in four modes. Apart from the
composite mode A + B, the detector can be operated in the
topographical mode A - B, where a pseudo-topographical imaging
with suppressed atomic number contrast and maximum
topographical contrast is obtained. Signals from each half can be
also collected separately in modes Segment A / Segment B.

T2
The T2 detector is primarily designed to collect secondary
electrons and provides information of the sample topography in
the OptiPlan and Immersion column Use cases. Thanks to the
high potential of the A-Tube, the SE are accelerated and
collimated to the T2 detector. It can be operated with the
grounded A-tube as well - Standard column Use case. In this
case, backscattered electrons are collected, but the accelerating
voltage must be at least 5 kV. The intensity of the signal in the
Standard column Use case is dependent on the beam current and
working distance – the higher the beam current and the shorter the WD, the higher the T2 signal.

T3 (option)
Electrons generated by a primary beam can be collected by the in-column Trinity detector T3, which is located
inside the column just below the aperture strip (see Chapter 7).

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 Operating Procedures: Beam Deceleration

Beam Deceleration

The Beam Deceleration (BD) mode is based on a negative voltage

(bias) applied to a stage (i.e. a sample). An electrical field is
formed between the sample and the nearest surface over it (a
column bottom or a detector). This field acts as an additional
electrostatic lens. Its power is described by the Immersion Ratio
(imRatio) parameter.

Detection Principles
Beam Deceleration influences both primary and detected
electrons.
As the sample is at a negative potential with respect to the
ground and detectors, the initial SE and BSE energy (when leaving
the surface) is accelerated by the Stage Bias before the detection.
The higher the Immersion Ratio is, the lower the difference
between SE and BSE energies is when detected.
Signal electrons are accelerated upwards and deflected towards the column axis.
The SE’s have a low initial speed. They are usually absorbed into the detector central hole, continue through and
can be detected by in-column detectors (T2 and T3).
Conversely, the BSE, heading nearly parallel to a surface (which normally cannot be detected), are driven to a
detector.
By changing the Stage Bias, the output angle of electrons leaving a surface can be changed.

FIGURE 5-6: Typical trajectories of secondary (red) and back scattered (green) electrons

Detectors most convenient for Beam Deceleration are BSE detectors placed closely under or directly inside the
column. Their efficiency depends on their active area – the smaller the inner diameter of the active area is, the
better. The standard ETD can also be used, but its efficiency is low.

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 Operating Procedures: Beam Deceleration

Beam Deceleration module

The Beam Deceleration module has the following features:
• On button – switches the BD mode On / Off. This is available
only in the HiVac mode and with the Beam On. When
switching the beam off, the BD mode switches off
automatically.
• Stage Bias adjuster – reflects the voltage applied to a stage
up to –4 000 V.
When the BD mode is on, a hook mark is placed behind the HV. In this case, the value
represents the energy of electrons reaching a sample surface (it is also stored within the
TIF file header).
imRatio = (HV + bias) / HV

Beam Deceleration Mode Imaging Procedure

1. Put the sample into the chamber and pump down to HiVac.
In the BD mode, a sample becomes the electrode. Its position, size, tilt and surface roughness influence imaging
quality. At optimal conditions the sample should be symmetrical, planar, have a size comparable to the detector
size, and be placed perpendicular to the column axis. Under other conditions, distortion, astigmatism and
blurring caused by chromatic aberration appear. This is even worse when the Immersion Ratio is higher.
2. Select the suitable HV and find an area of interest. Set the Eucentric Position and tune an image with the Direct
Adjustments module / Beam and the Stigmator Centering tabs. Using various displays, get the SE and BSE images
so you can observe different images simultaneously.
3. Click the On button. Gradually raise the Stage Bias (lower voltage); the SE / BSE image gets dark / light.
At low magnifications, an ETD image should become dark symmetrically around the window center. In other
cases, the sample can be tilted.
When a dark area is shifted with a Stage Bias change, the sample is possibly not parallel with the detector. With
the use of the Compucentric stage rotation / stage tilt, try to keep the dark area in the center of the screen.
Note
When a retractable detector is inserted, stage tilt is restricted via the UI. Overcome it manually (confirmation is necessary)
to keep the dark area in the center of the screen.
An image shift when changing the Stage Bias can be caused by imaging near the sample edge or any other edge.

4. Set the Stage Bias, considering the sample material (charging compensation, material contrast) and optimizing
the signal. Set the brightness, contrast and WD as required.
5. Tune the Direct Adjustments module / Beam and the Stigmator Centering tabs (both factors remember the HV and
Stage Bias last used).
6. Repeat steps 4 and 5 to get the best results.
Note
For the column Use case application suitable for the Beam Deceleration mode, see the Help menu / User Guidance item.

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 Operating Procedures: Beam Deceleration

Applications
The Beam Deceleration mode provides the following features:
• Enables detection of the BSE when the electron energy is under the detection limit of the detector.
• Expands the electron energy range under the minimum HV limit.
• Improves the microscope resolution at low accelerating voltages. A conventional microscope resolution is
limited by chromatic aberrations at low electron energies. The higher the Immersion Ratio, the smaller are the
aberrations and a loss of resolution at low electron energies is well compensated.
• Enables detecting of electrons heading nearly parallel to a surface, which accentuates surface roughness.

Restrictions
In the LoVac mode, the chamber environment is rather electrically conductive, and the BDM is not available.
Sample preparation and limitations
In general, all types of samples can be imaged using the Beam Deceleration mode. However, there are several types
with certain limitations that should be mentioned:
• Tilted samples
Tilted samples, such as non-horizontal fractures, may cause distortion of the electrical field deformation, which
adds non correctable aberrations and an image distortion. In general, the flatter the sample the better for the
resolution and also ease of use (fewer corrections of astigmatism and lens alignments).
An acceptable sample tilt is about a few degrees; for higher immersion ratios, it is preferably less.

FIGURE 5-7: Signal Distortion and Image Aberrations for Tilted and Rough Sample (Tin balls) at high Immersion Ratio

• Particulate samples
All samples consisting of small (micro- or nano-particles) particles must be prepared to minimize presence of
volatile particles on the stub when loaded into the chamber. The sample can be prepared either from solution
(dilute the powder in ethanol or isopropylalcohol, disperse and put few droplets on a clean stub or piece of
wafer) or fixed by carbon paste or tape. When pumping and venting, keep the sample at long working distance
(10 mm) and ideally off the pole piece. Imaging can be done on any working distance.
For the systems with T1 detector, the shortest working distances are interlocked by the software.
• Non-conductive particles, fibers, wires and rods
These samples are very sensitive to charging induced by an electron beam. When charged, they have tendency
to be attracted by the electric field of the Beam Deceleration, and move around the stub or travel towards the
final lens pole piece. Therefore, these samples have to be securely fixed to the stub. Longer working distance or
lower Stage bias is another way that prevents the column from the particle contamination. Decreasing of a
sample exposition to the electron beam (by setting of low voltage, low current and short dwell time) is
recommended.
Caution!
Always use a dust off, compressed air or nitrogen to blow all loose particles from the stub / sample before inserting into
the microscope chamber!

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 Operating Procedures: Electron Channeling Pattern

Electron Channeling Pattern

Electron Channeling Contrast Imaging (ECCI) is a mode of the

microscope allowing observation of dislocations (point or line
defects) in metals or semiconductors as well as at the interfaces
of thin layers.
Since those defects can be located below the surface, it is
necessary to find optimal conditions leading to the enhancement
of the dislocations contrast, such as optimal mutual orientation
of the sample with respect to the primary beam.
In order to find the optimal orientation, the Electron Channeling
Pattern (ECP) can be used. ECP is a diffraction (Kikuchi-like)
pattern (diffraction of the primary beam on the crystal lattice),
representing the crystal lattice in a reciprocal space.

Sample preparation
The procedure demands high surface cleanliness, so samples
have to be either mechanically polished or electrochemically
etched.
Mechanical polishing starts with wet grinding using silicon
carbide abrasive paper (grain size is 10 µm). In the subsequent
steps the abrasive papers with smaller grain size are chosen to
reduce the sample surface roughness. As the final step, the fine
sample surface polishing using colloidal silica suspension
(nanoparticles size is below 60 nm) takes place.
Alternatively, the electrochemical etching can be applied using
appropriate chemicals.

Sample loading
1. Attach the sample to a stub using silver or carbon glue, carbon or copper tape or other means suitable for
vacuum.
2. Vent the specimen chamber and mount the stub on the holder.
Note
Central holder position is recommended for electron channeling contrast imaging.
3. Run the Sample top surface positioning procedure (see below).
4. Tick the Sample Exchange dialog / Take Nav-Cam Photo check box to take Nav-Cam photo during pumping the
specimen chamber to the HiVac mode. Mount no final lens accessory (the PLA Accessories dialog / No Accesory).
5. Navigate to the region of interest using the NavCam image in third quad
6. Use the mouse wheel in the CCD image in the forth quad to move the sample in the Z axis at the 10mm
indicator.

Set imaging parameters

It is comfortable (but not mandatory) to start the Optiplan use case with conditions:
Accelerating voltage: 20 kV, Beam current: 3.2 nA, Detector: T1 (Display 1), ETD / T2 (Display 2),
Image resolution: 768, Dwell time: 200 ns, Filter: Average (4).
ECCI mode requires the Compucentric rotation and stage tilt. Therefore, the stage should be properly aligned
(Stage Alignments / Stage Rotation Center) and the Eucentric position must be set (see below).
Optimize an imaging.

Entering ECCI mode and taking ECP image

Use the T1 detector, alternatively the retractable CBS detector.
1. Increase the magnification and navigate to an area of interest.
2. Click the Electron Channeling Pattern module / ECCI button.
Note
Since the ECCI mode uses different optical model, the user can experience an image shift after entering the ECCI mode.

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 Operating Procedures: Electron Channeling Pattern

3. Focus an imaging and run the Stage menu / Link Z to FWD procedure, when the Link Z to FWD and move to
eucentric position reminder appears within the module.
4. Position the feature of interest (grain) center under the display center cross.
5. Click the Electron Channeling Pattern module / ECP button and set parameters to acquire the ECP pattern:
Image resolution: 1536, Dwell time: 10 µs, Filter: Average (1) (adjust the contrast and brightness if necessary).
6. Use the Compucentric rotation and stage Tilt to find appropriate diffraction condition. Optionally tick the Show
Tilt & Compucentric Rotation in overlay check box to use the controls within the display.

Note
If the rotation and/or tilt is/are significant, click the ECP button to stop image acquisition and check if the feature is still
under the display center cross.
While rotating and tilting, the incident angle (electron beam vs. sample surface) is changing. Thus, the mutual contrast of
individual grains can change as well.
Since the ECP pattern is a representation of a crystal lattice in a reciprocal space, the distance units transform into angular
units. Therefore, the horizontal field of view transforms into angular field of view. In addition, the scale bar is recalculated
into angular units as well.
7. Acquire the ECP pattern again with parameters:
Image resolution: 3072, Dwell time: 20 µs
Note
If the scanning is paused once the ECP pattern is acquired, it is visible within the module even when leaving the ECP mode.

ECCI imaging (dislocations observation)

In general, if the sample is oriented so that the display center cross lays on the diffraction line in the ECP pattern,
then dislocations have a proper contrast. However, the optimal alignment (i.e. selecting appropriate diffraction
condition) requires sufficient level of knowledge.
1. Stop image acquisition by clicking the ECP button.
2. Optimize an image.
3. Take an image with parameters:
Image resolution: 1536, Dwell time: 5 µs,
Filter: Line Integration (8) (see Preferences dialog / Scanning section / Snapshot, Photo preset).

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 Operating Procedures: Stage Control

Stage Control

Eucentric Position
Establishing the eucentric position is an important part of setting up a sample for observation or modification.
At the eucentric position, the stage tilt and the beam axes intersect. When the stage is tilted or rotated in any
direction, this point remains focused and almost does not shift. At the eucentric position, one can use various
system components in a safe and optimal way (e.g. GIS).
The eucentric position should be adjusted after loading any new sample, as the sample loading clears all position
information.
Note
For electron imaging of a non-tilted sample, the eucentric position adjustment is not necessary. But it is still necessary to
run the Link Z to FWD procedure.

FIGURE 5-8: Eucentric Position Principle

Beam Beam

Eucentric position
Eucentric position
Point of interest
Point of interest

Stage
Stage Tilt

1) The point of interest is focused below the Eucentric 2) Tilting the stage moves the point of interest out of
point. the beam.

Beam Beam
Eucentric position
Feature is at and Point of interest
eucentric position.

Stage
Stage Z adjustment
3) The point of interest is focused at the Eucentric 4) Tilting the stage does not move the point of interest
point. out of the beam.

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 Operating Procedures: Stage Control

Sample top surface positioning

The distance between the observed sample and the stage rotation head surfaces must be properly set to bring the
stage to the eucentric position. This procedure also prevents the specimen from touching the final lens when
moving the stage in the Z-axis direction.
With the single stub specimen holder, it is possible to move the sample (its top surface) up / down along the Z-axis
if required (holder movement). This allows the flexibility of loading large height specimens onto the stage.
1. Load a specimen onto the specimen holder.
2. Adjust the Z so that the highest specimen point is approximately 10 mm below the lens by using the optical
display.
3. Close the chamber and pump it down.
4. Switch on the beam, focus the specimen top surface and run the Link Z to FWD function.
The FWD is now recognized by the system as the Stage module Z value.
The Z coordinate can now be changed via the software Z control around the eucentric
position and further, but not less than 1 mm from the lens for safety reasons.

Eucentric position setting

1. Apply the Stage menu / Auto Beam Shift Zero function.
2. Show the Window menu / Center Cross (Shift + F5).
3. Focus an image. Link Z to FWD and go to 10 mm WD.
4. Set stage tilt to 0°.
5. Using the Z-control, coarsely focus the image.
6. Set the magnification to 1 000×, find a recognizable feature, and center it under the yellow cross by moving the
stage.
7. Watching the feature, change the stage tilt to 10°. Using the Z-control, bring the feature back under the cross.
8. Change the stage tilt to 30°, and bring the same feature back under the cross using the Z-control.
9. Change the tilt to 0°. The feature should not shift significantly. If the shift is > 5 µm, repeat steps 6 to 9.

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 Operating Procedures: Stage Control

Software control
The Navigation page contains the Stage, Stage Z and Tilt Correction modules, which control the stage movements
that locate the position of the specimen by reference to coordinate points.

Stage module
Three modes are possible via the list box:
• Actual mode (default) – shows actual position coordinates in
the edit boxes.
• Target mode – activates when clicking on a stored position or
when editing a coordinate value.
• Relative mode – used to move the stage by a given value and to
repeat it several times if needed.
Clicking on the Go To button drives the stage to a new location.
This only acts on just-edited coordinates (with a tick mark).
Pressing the Enter key after editing any coordinate value works as
clicking the Go To button. Double-clicking on a stored location
moves the stage to the desired position immediately.
During stage motion, the Go To button changes to the Stop button,
which stops the stage immediately.
Coordinates X, Y, Z, R, T
Edit boxes for X, Y, Z, R and T coordinates are filled with the selected
or actual position values. The changed value is automatically ticked.

Caution!
Danger of hitting the final lens! The Link Z to FWD procedure did not
pass. The red up arrow next the Z axis alerts that the positive Z-axis
stage movement direction is up. It means raising a value in the Z axis
edit box causes moving the stage up towards the final lens.
After running the Link Z to FWD procedure the symbol and the
stage movements direction change. The black down arrow next
to the Z axis indicates the positive Z-axis stage movement
direction is down.

The units of measure follow the Preferences / Units setting, unless

the Stage menu / User Units function is active, in which case UU is
shown for X and Y.

The software locks prevent inadvertent stage movement of

selected axes during particular applications. The edit boxes for locked axes are disabled
and the stage does not move in these directions. When any or all axes are locked, the
Status bar shows the closed lock icon.
When any axis is locked and stage movement
is required in that direction (trying to move to
the stored position), a warning dialog appears.
• When the Compucentric Rotation check box
is ticked, the R coordinate operates as the
Compucentric Rotation function (see
further) and does not physical rotate the
stage.
• When the Z-Y Link check box is ticked and
the stage is tilted, the system
compensates for the observed point of
interest shifting during stage movement, which allows making a Z-axis move with a tilted stage while keeping
the point of interest in the field of view. This makes it much easier when imaging with the electron beam at
shorter working distances to accurately switch to the eucentric position.

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 Operating Procedures: Stage Control

Location list
This list shows stored stage positions. When expanded the scrollbar is available. The Last Position (the stage
position before latest movement), which is updated during stage operations, is in the list by default.
The position selected becomes the actual active position and it is highlighted in the list and also in the map area (12).
Clicking on a position name allows a user to edit it. Pressing the Enter key or clicking on a different item confirms
the new name; pressing the Esc key restores the old name.
It is possible to load / save stage positions (.stg file) with the use of the File menu / Import / Export functions.
• When the Touch Alarm Enabled check box is ticked, stage movement is stopped, and the Touch Alarm warning
dialog appears whenever the stage or a conductive specimen touches the objective lens or any other equipment
conductively connected to the chamber. This functionality is also used when the stage engines rise their power
above a determined level.
Map area
In the map area, the stage schema is represented showing all stored positions, which are listed in the Location list.

FIGURE 5-9: Map Area Elements

5
7 10

2
6

11
5 10
9 5

8
11
12

1
3

6
4
3

Table 5-3 Map Area Elements

Number Function
1. Light gray rim (dashed line): physical limit of the stage movement along the X and Y axes
2. Dark rim (continuous line): the sample holder outline
3. X / Y scroll bar: to move the map area at different magnification factors
4. Magnification factor of the map area (1× – 100×)
5. Stage rotation overlay: Chamber door / ETD / CCD camera
6. Notch (black triangle): rotation marking (active control within the Radar view)
7. Radar view X / Y / Z (perpendicular lines): stage axes
8. Gray +: mechanical stage center: X = 0, Y = 0
9. Blue +: map area center
10. Red + in a red circle / Red + (Radar view): actual stage position
11. White × on a red background: a stored location (rotation noted by the black triangle)
12. Black  on a green background: a stored position selected (highlighted in the location list)

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 Operating Procedures: Stage Control

Double-clicking anywhere in the circle area marks a new location (10) and moves the stage to that position.
Right-clicking on the Map area provides a context menu.
• Add Current Stage Position – adds a new Location list entry, using
the actual position. The new entry is named Position (X) (X = 1,
2, 3…). When renaming and the name already exists, a number
increment is added after the name.
The Add button has the same functionality.
• Update to Current Stage Position – stores the (edited) coordinate
values under the selected name (an overwriting confirmation
dialog appears).
The Update button has the same functionality.
• Remove Selected Position – deletes the selected location(s) from
the map and from the Location list.
The Remove button has the same functionality.
• Magnification – provides a menu allowing the Map area
magnification factor (4 – from 1× to 100×) to be selected. Scroll
bars (3) appear if necessary to move over the whole Map area.
• Center view – brings the actual stage position (10) to the map
area center (9).
• When the Auto Center on Target item is ticked, the actual stage position (10) remains in the map area center (9).
• Show Radar View (7) – switches the radar view show in the map area On / Off.
• Zero Radar View – resets the Radar view X / Y axes rotation representation to 0°.
The radar view conveys the stage rotation at any time either by the stage axes or by the notch.
To rotate the stage, click on the notch (black triangle), drag it around the radar view perimeter,
and release the mouse button at the desired position – the stage rotates accordingly.
• Stage Location Overlay (5) – toggles the representation of the detector(s), chamber door, and
CCD camera in a mutual relationship.
• Show Notch on Map (6) – switches representation of the black triangle in the map area On / Off; it gives quick
information about the stage rotation.
• Show Nav-Cam Image on Map – switches representation of the Nav-Cam image in the map area On / Off
• Show Sample Holder Image on Map – switches the sample holder schema representation in the map area
• Show Stored Positions in Navigation Displays – switches representation of stored positions in navigation displays
On / Off.

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 Operating Procedures: Stage Control

Stage Z module
This module enables slowly moving of the stage in the Z-axis
direction. The more the slider is pushed to the each side, the
faster the stage motion is. Clicking on the slider bar moves the
stage by a small step.

Tilt Correction module

When the appropriate check box is ticked, the function becomes
active.
• Dynamic Focus check box ticked – the focus automatically
changes as the beam scans from the image top to its bottom,
trying to follow the change in the working distance of the tilted
specimen.
• Tilt Correction check box ticked – the flat specimen
foreshortening compensation is on (in one direction, at a
known tilt angle, when the tilt axis is parallel to the stage XY
plane).
Because the image is a two-dimensional representation of a three-dimensional object, certain distortions occur.
For instance, a square grid image appears rectangular when you tilt the specimen. This function corrects the
aspect ratio and restores the square appearance.
• Tilt Angle list box – enables choosing among 3 modes.
In the Automatic mode, the Tilt Angle is equal to the stage tilt plus the Specimen Pre-tilt adjuster value (a Tilt
Angle correction in case the specimen is not parallel to the stage XY plane).
In the Automatic mode, 90° is added to enable observing the cross section perpendicular to the sample surface.
When in the Manual mode, the adjuster enables manually setting of the Tilt Angle from -90° to +90°. It is useful
when the Dynamic Focus with Automatic Tilt Angle does not give satisfactory results (or cannot be used at all
because the specimen is tilted in a direction different from that of the stage Tilt).
When switching from Automatic to Manual mode, the actual Tilt Angle is not changed. When switching to
Automatic mode, the Tilt Angle is set to the actual stage tilt.
Note
Both Dynamic Focus and Tilt Correction work properly only if the specimen (scanned area) is tilted around the X-axis (in
the same direction as the stage Tilt). Therefore they cannot be used with Automatic Tilt Angle in combination with a non-
zero Scan Rotation. If the specimen is tilted in a different direction, you have to align the tilt axis horizontally using the Scan
Rotation, and then optimize the image focus by tuning the Manual Tilt Angle.
Both functions are also disabled (check box cleared) in the Crossover mode.
Due to the limited range of dynamic focusing, the overall conditions should be within certain limits. If the dynamic focus is
out of range, an information sign next to the check box becomes visible. Leaving the mouse over this sign calls up a tooltip
giving advice with information about what must be done to enable it again (usually increase the dwell time or the
resolution).

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 Operating Procedures: Stage Control

Stage Related Functions

Stage Movements – Keyboard Shift

The stage can be moved by 80% / 40% of the field of view in a perpendicular direction by
pressing / Shift + pressing the appropriate keyboard arrow key.

Stage Movements – Track mode

This functionality allows continuous directional stage movements at a variable speed
(see the Preferences / General section / Switch sample tracking on mouse wheel click on
item):
• Wheel-click & drag mode – the yellow dot appears onscreen in an active display at the
mouse cursor point. Move the mouse to the direction intended for an observation – a
yellow arrow appears onscreen denoting the direction of the stage motion. The
motion speed increases with the distance between the arrow and the dot. The
direction can be changed by moving the mouse. When you come to the place of
interest, release the mouse wheel – the action stops.
Note
When a yellow line perpendicular to the moving direction appears, the stage approaches the
movement limit in that direction; when a yellow cross appears, the limit was reached.
• Wheel-click & move mode – the mouse wheel does not need to be held; just click on
the desired direction to start the Track motion and click again to stop it.
In the optical imaging display, clicking the mouse wheel activates the stage
Z movement, which can be seen live.
• Wheel-clicking & dragging the mouse up / down – moves the stage
up / down (Z-coordinate).
• Ctrl + Wheel-clicking & dragging the mouse left / right – tilts the stage left / right.
The direction is indicated by a yellow arrow, either pointing up / down from the
horizontal line or left / right from the vertical line.

Stage Movements – Get mode

This function brings an image point of interest to the screen’s center.
Double-click anywhere within the imaging display; this point is mechanically centered
onscreen by moving the stage, which is suitable for lower magnifications. When
working at higher magnifications, beam shift can be also employed (see the Preferences
/ General section). In this case, the point is electronically centered onscreen by moving
the electron beam. When the beam shift comes to a limit in any direction, its value resets,
and the necessary stage movement adapts the observed point position.
Beam Shift
When you want to employ the beam shift only (which is suitable for higher
magnifications), shift + click on an image point. Drag the Hand cursor to move the
imaging area in any direction.
When the limit of the beam shift has been reached, either the Stage menu / Auto Beam
Shift Zero or the Beam Shift Reset function needs to be applied. In this case, the beam
shift is reset, and the observed point position is adapted by the stage movement.
Releasing the mouse button stops the action.

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 Operating Procedures: Stage Control

Align Feature
This utility is designed specifically for long features that extend off the
screen at the magnification required for an observation. It applies the
mapping process by bringing the long feature either to the horizontal or
vertical stage axis to make navigation easier. This can be performed at any
point within the stage field limits. It takes into account the stage rotation
offset.
Note
Align Feature works best at the eucentric position (see above). Longer distances result in greater accuracy.
Caution!
Watch for obstacles extending significantly from the sample plane, as these may interfere with equipment under the lens.
1. Find a long feature of interest on the sample.
2. Click on the Stage menu / Align Feature.
3. Choose Orientation, either Horizontal or Vertical, that relates to the desired final orientation of the feature.
4. Click on the first point along the feature. The Position 1 coordinates update.
5. Moving the mouse continuously updates Position 2 coordinates; clicking anywhere along the feature stores them.
The Angle shows the value that is used to correct alignment of the feature along the horizontal / vertical axis.
Right-clicking anywhere on the image area deletes points, enabling them be defined again.

6. Drag any point to change its position if needed. Click on the OK button to finish the setting.

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 Operating Procedures: Stage Control

Compucentric Rotation (F12)

Clicking on the Stage menu / Compucentric Rotation places a
green circle in the image window. The green triangle on its
perimeter denotes by its position the sample rotation relative to
its original position when mounted on the stage. Initially, this is in
the 12 o’clock position.
The readouts shown at the image window bottom provide
information about the Actual Rotation (original position) and the
Target Rotation (the selected position).
Click on & drag the triangle around the circle to choose a new
sample rotation. Releasing the mouse updates the stage position
to bring the original field of view (rotated to the Target Rotation
position) onscreen. With a sample at the eucentric position this
can be performed at any sample point irrespective of the
mechanical stage center.
Clicking on the written angles around the circle perimeter (0° /
90° / 180° / 270°) or the perimeter anywhere drives the stage to
that rotation position, and the green triangle updates onscreen.
Clicking on the framed + / – sign increases / decreases the rotation
angle by an incremental value.

User Units
Clicking on the Stage menu / User Units item (a tick mark appears
next to it) activates user defined units as the basis of the stage
coordination system. The UU appears in the Stage module next to
the X and Y values and the stage coordinate system activates the
last defined user units.
Define User Units Procedure
This procedure assigns user-defined points to stage points. The
stage coordination system can be anchored to either 1, 2 or 3 points, depending on the sample management or
application. For example, if you choose a (0,0) position, you can drive the stage relative to that origin using user
defined units (0,1 / 1,0 points), which may equal to some repeated sample structures, etc.
It is possible to end the procedure by clicking the Finish button when point(s) (0,0) / (1,0) / (0,1) are defined. An
overview of the point(s) just defined is shown. The Details button shows the actual coordinates with the possibility
of browsing them (Go to button) and editing their values.
1. Find a sample surface feature and view it at an appropriate magnification to check its relation to other structures.
2. Click on the Stage menu / Define User Units item. The
dialog appears to alow choosing the desired operation:
• Define new User Units – defining of new User Units
• Redefine User Units – changing or updating User Units
• Redefine User Units with shift – as above, with the use of
the Beam Shift
• Reset User Units so that they are equal to the Stage Units
3. Click on the sample user point (0,0) and its coordinates
appear in the Details module. Proceed by clicking the
Next button.

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 Operating Procedures: Stage Control

4. Repeat step 3 for the sample user point (1,0) and (0,1) if needed.

Using 1 / 2 / 3 Point(s) Alignments

Table 5-4 Alignment Type Differences

Use 1 Point Alignment 2 Points Alignment 3 Points Alignment

Major Use Aligning to new point Aligning the stage axes with Transforming to nonstandard
directly offset from the specimen X-Y orientation units on dies or RAM arrays;
the existing location to correct any distortion to correct any distortion
Change in Scale None Scales the axes together X can be scaled differently from Y
Change in None Rotates both axes with a fixed X and Y orientation
Orientation 90° angle between axes can be different

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Sample Navigation
The Stage menu / Sample Navigation (Ctrl + N) software feature
enables navigating along the sample surface when the field of
view is smaller than desired (limited by an aperture, for instance).
For this purpose various sample navigation images can be
dynamically and independently selected, regardless of their actual
content and status (paused, saved, loaded).
As soon as the active display is paused, the Sample Navigation icon appears in the upper
right display corner to indicate its functionality. This indicator is green, and the paused
display can be used to navigate along the live one. Otherwise it turns red and indicates no
functionality in the respective display.
A green rectangle showing the actually selected field of view (in the active display) appears with the size
corresponding to the magnification. In display(s) using Sample Navigation, the Selected Area Zooming and the Get
features can be used.
To employ the Sample Navigation there are three possible techniques to acquire (or use) a Navigation image:
• Navigation Montage
• Navigation Alignment
• Nav-Cam (option)
Navigation Montage
Set the Target HFW (Horizontal Field Width) by the slider,
which influences some information field values:
• Map Size – the number of tiles
• Single Image HFW – HFW of each tile
• Remaining / Elapsed Time – time still needed for the
procedure completion / elapsed
• Target Resolution – navigation image pixel resolution
• Use actual HFW check box – when ticked, the system does
not automatically use the HFW according to the hardware
configuration, and sets the user one.
This is convenient when the image corners are rounded
and imaging does not cover an entire area.
• Switch off the beam when finished check box
This is convenient to use in case a large Target HFW and
long dwell times are used to capture the Navigation image,
because the process can take a significant amount of time
to complete.
Click the Start button to run the procedure. After process
completion, Sample Navigation is then automatically set to on.

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Navigation Alignment
This procedure, in comparison to the Navigation
montage or Nav-Cam (option), enables using any
loaded or paused Navigation image that is
calibrated according to the live Reference image.
Follow the instructions given within the process
(6 dialogs) and calibrate 4 image points. If 2 points
are sufficient for the desired purpose, click on the
Compute 2pt alignment button to finish the process
after setting 2 alignment points.
When any point setting does not satisfy system
requirements, a Warning message informs the user.

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Scan Rotation (Shift + F12)

The Scan menu / Scan Rotation function activates the onscreen
tool to rotate the scan and align the image. Because it is solely a
functionality of the electronic optics, it has no effect on stage
movements. It is used to orient the image relative to mechanical
rotation and detector direction.
Clicking on the Scan menu / Scan Rotation places a green circle in
the image window. The green triangle on its perimeter denotes,
by its position, the sample rotation relative to its original position
when mounted on the stage. Initially, this is in the 12 o’clock
position. Click on & drag it around the circle perimeter to choose
a new sample rotation.
The readouts shown at the image window bottom provide
information about the Actual Rotation (original position) and the
Target Rotation (the selected position).
Clicking on the written angles around the circle perimeter (0° /
90° / 180° / 270°) or the perimeter anywhere drives the stage to
that rotation position and the green triangle updates onscreen.
Clicking on the framed + / – sign increases / decreases the
rotation angel by an incremental value.

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 Operating Procedures: Capturing and Handling Single Image

Capturing and Handling Single Image

After acquiring a quality image, it can be paused (F6 or the toolbar icon) and saved (the File menu / Save item).
Setup the file name label and hard drive destination for the image to be saved using the next available label /
number prior to the capture session. Set the databar information important for the archiving by right-clicking on
the image databar.
The conditions for good image quality are:
• Slow scan speed (longer dwell time or fast dwell time together with line or frame integration) of the beam.
• Select a pixel resolution from the drop down list box to suit the detail in the image, i.e. no tearing pixelated edges.
• Move the stage next to the area of interest, increase the magnification at least 2× above the desired value, focus,
correct the astigmatism and lens alignment (using the reduced area), then return the magnification and stage
position back to their desired parameters.
• Use the Videoscope to set the Contrast and Brightness accurately; otherwise use the Auto Contrast Brightness
procedure.
• Use the Pause / Snapshot / Photo / Scanning preset / filtering functions.

Image Types
A computer perceives an image as a two-dimensional array of numbers – a bitmap. Each array element is called a
pixel and is represented as an integer value. Frequently, the pixel is represented as an unsigned 8-bit integer in the
range [0, 255], with 0 / 255 corresponding to black / white and shades of gray distributed over the middle values.
A 16-bit representation produces up to 65 536 different shades of gray (it is not possible to distinguish them
onscreen), which may be crucial for obtaining accurate data in analysis.
The raw scanned image is always a grayscale bitmap. Colors can be added digitally as a result of particular features.
The UI is able to show and save images with various bit depths:
• Grayscale 8 / 16 bit image – offers 256 / 65 536 levels of gray.
Live / Averaged and Integrated images are scanned as 8 / 16 bit ones. For the Mix display images a selection
between the 8 or 16 bit mode is possible.
• Color 24 bit image – offers 256 levels of each primary color (red / green / blue).
Digital colors come from the Display Saturation feature, Enhanced Image module / Color tab, and Mix display
with color mode set to change image bit depth, so the image must be saved as a color one. When the user wants
to acquire the image without these color enhancements, it is necessary to turn off the respective UI functions.
An image can be saved with / without colored digital overlaid graphics (Measurements, Annotations, Patterns,
Videoscope) (see the respective checkbox in the Save As dialog). Other types of overlaid graphics over an image
are never saved (icons, controls, etc.).

Digital File Formats

The image captured can be saved in various
digital formats, depending on the color and
bit depth needed. Generally there is no reason
to save an image with a higher bit and color
depth than what is available in the original
image. Saving an image with a lower bit and
color depth than what is available in the
original leads to a loss of information. In this
case, this message is shown onscreen.
• TIF 8 / 16 file – grayscale only image type,
full data format
• TIF 24 file – color image type, full data
format
A file contains active processing information, which can be utilized for a databar setting.
• JPG file – color image type, compressed data format
A lossy compression algorithm is used, resulting in the smaller file size with a little loss of information. The amount
of loss depends on the particular image appearance and the compression level (factory preset is 80%). The 8 /
24 bit depth is automatically selected when saving a grayscale / color image file.
• BMP file – color image type, full data format. The 8 / 24 bit depth is automatically set when saving the grayscale
/ color image file.

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Saving / Opening / Printing

The following universal file handling functions can be used:
Image Capturing
1. Select the area of interest and set the Magnification, Scan condition,
image pixel Resolution and the Databar information that are required
in the saved image.
2. Make the best image using any suitable method you are familiar with.
3. Use the Pause (F6) / Snapshot (F4) / Photo (F2) / Active Preset Snapshot
(Ctrl + F2) / Scanning Preset function. The scan makes one display
pass (or several passes when the number of integrated frames is
larger) and pauses.
Note
When applying the Shift key together with above mentioned acquisition
functions, the effect simultaneously works in all displays with the same beam.
Image Saving
• Save (Ctrl + S): stores the image to the predetermined location with the last used filename, including an
incremental number.
• Save As: opens a dialog for saving images (this provides an opportunity to change the file name, its location, and the
possibility to also save Databar and overlaid graphics).
• Save All: (Ctrl + Shift + S) behaves the same way as the Save As functionality, but enables saving the images from
all four displays at once.
• Open: opens a single image file into the active display. The dialog shows, by default, the location used in the last
Save As utilization.
Image Printing
1. Capture the image or open a saved one.
2. Click on the File menu / Print (Ctrl + P), the printer setup dialog
appears. The choice of printer and settings can be established
to print the active display.
3. Complete the print setup and click the OK button to activate
the printer and print an image.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Recording Movies (Saving Multiple Images)

This function captures dynamic experiments performed with the microscope and creates the digital video files (AVI).
Up to 4 imaging displays (not the optical one) can be recorded simultaneously with a synchronized start. It is possible
to switch between single and quad image mode while the video is recording. The movie has the following embedded
features:
• Resolution 768 × 512 or 1536 × 1024 (512 × 442 or 1024 × 884 for the 4:3 view)
• Databar image optionally included in the video
• Average or Integration are changeable during recording
• Scan speed is changeable during recording
• Reduced area pauses recording of all displays
• Remaining time indicator
• Single frame TIF images are recordable during the video sequence
• Compressed AVI (*.avi) formats
• Start, Stop and Pause onscreen indicators
• Preferences set-up dialog
Note
For the display(s) with the Enhanced Image module / Color tab / Enable check box ticked, if Movie recording is paused, the
colored TIF files are stored anyway if selected.

Movie Settings Dialog

The Preferences / Movie provides selections to set-up conditions for timing and save conditions for the resultant
movie.

FIGURE 5-10: Movie Preferences

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Movie Timer
The parameters in this section can be changed when the digital video is inactive, but are disabled during recording.
The digital video is recorded asynchronously to the scanning.
• Save AVI Movie check box – Period list box:
After the Period time, the image of each active display is stored immediately
(even in the middle of the frame) as a new frame in the video stream.
• Save TIF Images check box – Period list box:
After the Period time, series of each active display images are stored at the
end of the running scan in TIF format.
If both TIF and Movie check boxes are ticked, AVI and also TIF files are stored.
In this case, the AVI file is not reconstructed from TIF files, which means the
directly recorded movie could be different from the movie reconstructed from
TIF files.
Note
In many cases it is better to save TIF files, as they can be built into a faster AVI and
the databar display can be customized when building an AVI file.
If both AVI and TIF are recorded, the AVI may be jerky due to delays when writing
TIF files to a disk. TIF delay must always be equal to or longer than the Movie delay.

File Settings
Names of Movie [TIF] files are composed as follows:
File name, (display name), Numeric seed, [- series number].avi [tif]
For example: MovieName (Channel1) 015 [- 00023]. avi [tif]
[The series number always has a five digits form with leading zeros.]
• File Name – enter a generic file name here. Do not use punctuation, dashes or other non alpha-numeric
characters, otherwise the movie maker would not be able to build an AVI.
• Save in – enter a path to an existing folder here. Use the Browse button to find the location.
• File Type – the list box with supported video compression format types. Try to change the format if the resulting
movie files are too big or if the system is overloaded during movie recording.
• Numeric Seed – enter any number from 1 to 999, which is converted to the three digit form with leading zeros.
The numeric seed is automatically incremented after the recording has stopped or the video file size limit has
been reached.
• Video File Size – the maximum AVI video file size (lower than 2 000) in MB must be entered here, otherwise the
Movie section cannot be closed. After reaching this size, the video file is closed and a new one is automatically
created without interruption of the recording process. A warning dialog appears if the hard drive lacks sufficient
free space.
• Record Databar check box – allows the databar to be included in the video (tif files).

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Movie Procedure
The File menu / Record Movie item (Ctrl + Shift + M) starts / stops recording of all active displays at
the same time – no video / images are stored for paused imaging. When an image in any display is
paused during video recording, storing video frames is interrupted, but the video streams keep
synchronization for the next recording. The File menu / red dot icon changes to a red square when
movie recording starts and vice versa. Video recording is stopped in all displays and all video files are closed.
The red dot with the timer (shown in the top right-hand corner) indicates that
recording is running in this display. The Pause symbol indicates that the recording
is paused and the data from this display are not stored.
The timer indicates the time estimation (in the hh:mm:ss format) remaining to the
end of the video. This is calculated from the average disk space consumption and
disk free space.
1. Open the Preferences / Movie section. In the Movie Timer module, tick the Save AVI Movie and/or Save TIF Images
check boxes and select the desired Period (time between stored frames).
2. In the File Settings module, fill in the File Name and give the Save in folder path. Fill in the Numeric Seed value and
the Video File Size. Select the File Type and choose whether to record the databar with the Record Databar check
box.
3. Pause those images that you don’t want to record. Set up the imaging parameters.
4. Select the File menu / Record Movie, or press the keyboard key
combination Ctrl + Shift + M, to start movie recording. When the scan
resolution is higher than 1536 × 1024, the following dialog appears.

5. Choose either of the offered Resolution values, at which the movie starts to record.
6. Select the File menu / Record Movie again, or press the keyboard key combination Ctrl + Shift + M, to stop the movie
recording.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Movie Creator
This is a separate program that creates a single AVI movie file
from a sequence of TIF images. Click on the Thermo Scientific
menu / Movie Creator to activate the tabbed dialogs.
The following items are common for all tabs:
• Databar Preview – shows the databar created within the Databar
tab.
• Status – shows the progress of the movie creation process.
• Create Movie button – opens the Movie Creator dialog.
• Stop button – stops the movie creation process.
• Close button – closes the Movie Creator program.

File Tab

FIGURE 5-11: Movie Creator dialog / File tab

• Name Prefix – click on the … button to browse the TIF files (with the desired sequence prefix) folder. It is not
necessary to choose the first file in a row.
• Time Period – click the [ms] radio button to select a custom timing for the movie playback.
One may experiment for instance: 200 ms/per image (good for most movies to speed it up) for 100 images
results in 20 second total movie duration.
• Time Period – click the TIF Time radio button to select a timing for the movie playback.
• From / To – enter the number of the starting / ending frame. This field is filled automatically with the first / last
frame available.
• Save in – enter the path where the AVI file should be saved. Click on the … button to browse it.
• File Name – enter the resulting AVI file name. This field is filled automatically with the first image file name.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Databar Tab
Settings made in this dialog does not affect the databar or units settings used in the UI.
Note
The Databar Preview does not show any item until you enter the File tab / Name Prefix field.

FIGURE 5-12: Movie Creator dialog / Databar tab

• Available / Displayed items: lists – all items that can be entered in the databar / are already present in the
databar.
• > / >> (< / <<) button –add one / all item(s) from the Available list to the Displayed list (removes one / all
item(s) from the Displayed list back to the Available list).
Since there is a finite amount of databar space, the area expands or contracts as other items are added to or
removed from the Databar. Items exceeding the allowable space are ignored.
• Move Up / Move Down / Top / Bottom button – moves a position up / a position down / to the top / to the
bottom in the Displayed list (a position to the left / a position to the right / to the left / to the right in the Databar
Preview).
• Label / Show Beam Icon / Micronbar check boxes – set the show of the appropriate items in the Databar. The
Micronbar scales to the magnification.
• Units button – sets the Units of Measure / Pressure / Temperature used in the movie Databar display.

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 Operating Procedures: Recording Movies (Saving Multiple Images)

Preview Tab
Once the movie is set-up, opening the Preview tab automatically shows the first image of the movie sequence.

FIGURE 5-13: Movie Creator dialog / Preview tab

• Start / Pause / Stop button – starts / pauses / stops the movie play back. By dragging the adjuster, one can run
forward or backward through the movie.

Playing a Movie
The AVI file movie can be played in Windows Media Player or any another more advanced movie editing or playing
program that recognises the *.avi file type.

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 Operating Procedures: Patterns / Measurements / Annotations

Patterns / Measurements / Annotations

The toolbar Patterns / Measurement / Annotation items give a user many

capabilities to draw pattern shapes, to measure distances, angles, diameters
and areas and to locate and label items that are of significant interest on the
sample area.
The selected tool is shown as the toolbar icon. Clicking on it activates
(drawing mode – orange background) / deactivates (white arrow cursor –
normal background) the tool. Clicking on the down arrow icon opens the list of
available tools. The one chosen is activated from that time on, and the object
can be drawn onscreen. To deactivate the drawing mode at any time, press the
Esc (keyboard).
Each tool shows its description as a tooltip.
• Patterns – enable creating various pattern objects, which are prepared for
subsequent processing.
• Measurements graphics – enable gaining dimension information about a
specimen feature by overlaying it with a measurement object of different
shapes. When changing the magnification, these objects resize accordingly.
• Annotations graphics – enable graphical highlighting and labeling of the items of interest with different shapes.

Shape Creating
1. Choose the suitable Patterns / Measurements / Annotations graphic tool.
2. Draw the graphic over the area of interest.
This can be done by:
• clicking & dragging the cursor in any direction – this creates a rectangle shape
• Shift + clicking & dragging the cursor to any direction – this creates a rectangle shape that starts to grow from
the point where you have clicked as its center.
To create a text label, click the T annotation tool, create a rectangle area into which a text should fit, and start writing.

Shape Editing
Once a Pattern / Measurement / Annotation object has been drawn, it can be adjusted in size and position over
the area of interest. A number of appropriate properties are available in the Property editor, which can be changed
by a selection from a drop down list or by direct precise editing of a text or a value.
To select all objects in the active display, press Ctrl + A. To delete selected object(s), press the Delete key.
The selected object is denoted by the addition of resizing handles (white
rounded or square points) to the graphic outline. Moving mouse point cursor
in the vicinity of these points forces the cursor to change:

• Moving: click inside the boundary of the object and drag it.
Note
Holding the Ctrl + Alt keys while hitting any arrow key moves the pattern
in a corresponding direction by a fixed distance.
• Rotating: click on the object rotation control (white point in the middle
above the graphic) and drag it.

• Resizing: click on & drag the resizing handle until the desired size is reached
(horizontal / vertical / diagonal resizing cursor). Holding the Ctrl key while
dragging forces the dimensions to be changed proportionally.

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6
Maintenance

This section describes necessary microscope maintenance procedures that can be carried out by the microscope
user. The user maintenance is at a minimum due to source and column design providing the long uptime. Therefore
a complicated maintenance is normally a part of a service contract to be performed by a qualified service engineer.
Caution!
Read and follow all instructions within the Apreo 2 User safety manual carefully!
Caution!
Before any maintenance action, check the vacuum interlock status in the Sample
exchange window / Vacuum tab / Sensor States area. The circle in the
Chamber Pressure HiVac and Chamber Pressure LowVac lines must be red!
Caution!
- Parts that operate in vacuum should be handled carefully using clean powder-free
gloves. Parts not in use should be stored in suitable containers or packed in aluminum foil.
- The EDX window (option) is very fragile and must be protected from large pressure
oscillations. It is also recommended to remove the detector before major cleaning
activities.
- Be aware of removing the chamber door locking screws, used during instrument transportation (labeled REMOVE)!
If these are installed, an overpressure over 20 kPa (150 Torr, 0.2 bar) can arise inside the chamber during the vent
procedure (N2). If installed, the overpressure is harmful to the EDX window.
Note
Gas back fill (N2) should be maintained while the specimen chamber is at ambient pressure. However, to avoid gas waste
it is recommended that the chamber be left vented no longer than necessary.

Cleaning procedures overview

Caution!
Be aware of the electrical, thermal and mechanical hazards. Refer to the User safety manual for the details.
Frequency of cleaning is, in most cases, determined by necessity. The need for cleaning is shown by poor image
quality or gross astigmatism levels. Recommended cleaning procedures are given below for parts that operate in
vacuum and that are subject to possible contamination.

List of applied cleaners

• De-ionized or distilled water – H2O
• Ethanol – C2H5OH
• Ethanol p/a (Pro Analysis: 99.8% pure) – C2H5OH
• Isopropanol
• Neutral pH cleaning fluid (soap solution)
• CIF or Soft Scrub (fine abrasive household cleaner) or 0.05 µm aluminous powder

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 Maintenance: Cleaning column parts

Table 6-1 Household Cleaners

Country Name Country Name

Austria CIF Italy CIF
Australia CIF Japan CIF
Finland CIF Netherlands CIF
France CIF Switzerland CIF
Germany CIF UK CIF
USA Soft Scrub

WA R N I N G !
The cleaning solvents ethanol and isopropanol are highly flammable! Do not use open flames and do not smoke while
cleaning. Ventilate the room properly.

Cleaning column parts

All column parts are polished before the instrument is delivered. For this reason, only occasional light polishing is
required to remove contamination that may build up on components in the column and specimen chamber as part
of normal operation. Any part that is exposed to the electron beam should be highly polished, and free of
contamination and/or scratches that can charge and thus degrade the image.
Caution!
Users are allowed to clean the final lens pole only from the outside!
Gold plated parts should not be polished with abrasive.

Materials and technique

To polish components, place a lint-free cloth on a flat surface (a glass block is ideal) and apply a small amount of
Soft Scrub or CIF and distilled water to the cloth.
Place the part to be cleaned on the polish and rub with a circular motion until all contamination is removed. For
inner surfaces, use a cotton swab or wooden dowel as an applicator. A toothpick can be used for small holes.
Lint-free nylon (not cotton) or latex surgical gloves should be worn while handling parts to avoid contaminating
just-cleaned surfaces. Tweezers should be used to hold small parts.
After the part has been polished, remove the Soft Scrub/CIF cleaner by washing in hot water. Inspect the part
under a stereo microscope at 20× magnification to ensure that there is no remaining contamination or polish
residue. Wash the part in de-ionized or distilled water in a beaker with an ultrasonic cleaner for several minutes.
Transfer the part to a clean beaker with alcohol or isopropanol and clean ultrasonically again for several minutes.
When the components are dry (a compressed air “duster” can speed drying), reassemble and return them to the
column. If a part is stained, heat it with hot water and immediately rinse with alcohol and dry using compressed air.

Cleaning tips
Parts exposed to the electron beam require periodic polishing. This will ensure maximum performance of the
instrument for many years.
Do not use metal polishes such as POL or WENOL to clean parts, as these can leave outgassing material. Be aware
that threaded surfaces should not be polished, as these do not contact the beam and are a source of outgassing if
polish is trapped. Wash threads with alcohol or isopropanol if absolutely necessary.
After cleaning, inspect all parts for residue and stains using a light microscope.

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 Maintenance: Cleaning stage mechanics

Cleaning stage mechanics

Checking the condition of the stage should be a weekly exercise, as many different samples may be exchanged in
this time period. Some samples may be powders or composite materials that inadvertently drop particles on or in
the stage. If a silicon wafer breaks in the chamber, it can shatter into hundreds of pieces. In this case the stage
should be thoroughly mechanically cleaned, if there are any visible pollutions before attempting movement again.

Cleaning stage parts

Abrasive and solvents must not be used on the moving stage parts. Cleaning by a suction is the ideal method. If not
available, cleaning should be done by using dry nitrogen gas bursts around the stage mechanics to blow out any
foreign materials. Make sure the final lens and detectors are protected from the turbulence. Do not use sharp metal
objects to scrape away debris. A fine pair of plastic tweezers can be used to pick up difficult particles. Spillage on
the stage should be wiped up using a lint-free cloth, followed by suction or blowing with clean gaseous nitrogen.
Caution!
Do not perform mechanical cleaning of the stage nearby the encoders to prevent its damage.

FIGURE 6-1: Sensitive stage encoders placement

Cleaning Multipurpose stub holder

Recommended cleaning procedure is given below for parts that operate in vacuum and that are subject to possible
contamination. Frequency of cleaning is, in most cases, determined by necessity (image quality or astigmatism level).
1. Loosen the holder with the use of 2.5 mm allen key.
The bolt is hidden under specimen position No. 9. Hold the holder with hand to
eliminate rotational force coming from loosening the bolt and applying stress
on stage mechanics.
2. Clean the holder using a lint free cloth and a mild abrasive according to the list
of applied cleaners (see above).
3. Rinse in tap water.
4. Clean in an ultrasonic cleaner for 5 minutes using distilled water.
5. Clean in an ultrasonic cleaner for 5 minutes using alcohol p/a or isopropanol.
Caution!
Do not place parts together in the beakers. Wash separately as damage can occur to the metal surfaces.
6. Rinse in alcohol p/a.
7. First blow dry with a compressed air canister, then dry thoroughly under an infra-red lamp (from 15 min to 1 hr)
at a temperature between 80 °C and 100 °C.
Caution!
Do not bake the Multipurpose stub holder in an oven!

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 Maintenance: Refilling water bottle

Refilling water bottle

The water bottle in the instrument typically needs to be filled about once a
month if the instrument is used on a regular basis in the Low Vacuum mode.
The water reservoir is located on the left side of the microscope console,
behind the cover. To fill the bottle, do the following:
1. Run the Vacuum Actions / Vent Water Bottle alignment procedure (see
Chapter 4).
Caution!
Be aware of the gas type connected to the gas inlet before the Vent water bottle
button is clicked! If you are not sure, disconnect the gas pipes from the gas inlet
coupling.
2. Open the Water bottle chamber cover.
3. Pull out the water bottle and remove the threaded cap.
4. Refill the bottle with distilled water (not de-ionized) until 1/3 full.

FIGURE 6-2 Refilling water bottle procedure (steps No. 2–4)

5. Mount the cap and install the water bottle in the reverse order of that described above.
6. Pump the chamber. Switch to LoVac mode to force automatic purging to flush any air out of the bottle and
connecting tubes.
Note
The first time the system is pumped to LoVac mode after filling the bottle, Auto-purging may be erratic until the bottle
pressure has steadied. The removal of all the gas from the liquid must be accomplished before good imaging is possible.
This has been done correctly when no bubbles are produced in the water when increasing the pressure in the chamber.

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 Maintenance: Water chiller

Water chiller

The ThermoCube chiller is placed in the vicinity of the microscope console. It is used for cooling the temperature
stages.

FIGURE 6-3 Water chiller / Display & controls

The mains rocker switch is placed on the left side of the box.
The front control panel has a 16-character LCD display and four input keys:
• UP – raises the parameter value displayed
• DOWN – lowers the parameter value displayed
• ENTER – momentarily enters the parameter changed
Pressing and holding the ENTER key for 3 seconds causes the chiller to change the display menu.
Do not change any setting otherwise you know the consequences.
• START/STOP – turns the chiller on (cooling “-” / heating “+”) / off (Standby “*”)
Recommended coolant temperature for temperature stages is 20° C. If the cooling is not sufficient, lower the value
by pressing the DOWN key (minimum is 5° C).

Troubleshooting
Multiple system alarms are shown on the display.
• Tank Level Low: Liquid reservoir level is too low.
Remove the cap and refill coolant (distilled water only) until the alarm disappears.
If this error happens often, contact service.
Note
When the water hoses start to bloom (green inside), exchange the water and also the hoses, if necessary.
• Fan Fail: The flow of plant cooling water is insufficient to cool the coolant by the thermoelectric heat exchanger.
The coolant is still flowing, the system can still operate, but it can cause system error if lasts for a long time.
Therefore check the chiller status regularly (once a fortnight at least).
Run the procedure:
1. Switch off the ThermoCube (main rocker switch), wait for 3 seconds and switch it back on.
2. If the Standby mode (*) is on, press the Start/Stop button.
If any other error appears contact the Thermo Fisher service.

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 Maintenance: Water chiller

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7
System Options

This chapter covers hardware and software that is an option either integrated in, or accessory to the Apreo 2
system (not all options are described here).
• Support PC – connects your workspace to the network and can hold some other software utilities.
• Manual User Interface (MUI) – provides direct manual control of microscope parameters such as focus,
magnification, contrast, brightness, beam shift and correcting astigmatism.
• Joystick – brings another possibility for controlling the basic stage movements.
• Electron Beam Current Measurement
• External Scan Interface
• Quick Loader
• ColorSEM – integrated EDS analysis
• Nav-Cam
• Patterning
• Gas Injection System – Platinum Deposition, Tungsten Deposition, Insulator Deposition II, Delineation Etch,
Insulator Enhanced Etch, Enhanced Etch, Carbon Deposition, Selective Carbon Mill, Gold
• Uninterruptible Power Supply
• Mains Matching and Isolation Transformer – provides a galvanic isolated AC-regulated power source with the 115 /
230 V, 50 / 60 Hz output.
• Compressor 120 V / 230 V, 50 / 60 Hz 4-litre Tank
• Thermo Neslab Water Cooler 50 Hz / 60 Hz
• Acoustic Enclosure for Pre-vacuum Pump
• Specimen Holder Kit
• Set of 20 Specimen Stubs for SEM’s
• UMB Stub Holder Kit
• CryoCleanerEC + spare vessel – anti-contamination device
• Plasma Cleaner
• Annular STEM detector – allows detection of electrons transmitted through the sample. The regular voltage
range which of course is dependent on the sample thickness, is from 30 kV down to around 5 kV.
• Universal Lift-out Holder for STEM observation
• Trinity detector (T3) – In Column detector especially suitable for the Beam Deceleration mode
• Directional Backscattered Detector (DBS) – Angular (ABS) / Concentric (CBS)
• Thermal Printer Kit
• Remote Control / Imaging
• VolumeScope
• SIS Scandium Image software
• SIS Scandium desktop license
• Scandium Solution Height software – enables creating of a topographic map of a sample
• SIS webRacer – allows regular users with ID / passwords to view and retrieve worldwide database data, using any
internet browser and any computer system (PC, Apple, Sun…).
• ResolveRT
• DualBeam Course – Acht
• Apreo 2 Course – Hillsboro, Oregon / China / Japan
• Advanced Course DualBeam – Acht
• DualBeam Short Course - Acht
• On-site Training / Support - 1 day – North America / China / Japan
For further up-to-date information on system options please contact your local Thermo Scientific representative.

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 System Options: Manual User Interface

Manual User Interface

The Manual User Interface (MUI) provides knobs to perform functions that can also be performed with the
software. It is connected to a USB connector located on the Microscope computer.

FIGURE 7-1: MUI

The MUI offers additional flexibility for controlling magnification, beam shift, focus, astigmatism, contrast and
brightness.

Joystick

The Joystick provides knobs to perform stage functions that can also be performed by the software. It is connected
to a USB connector located on the Microscope computer.

FIGURE 7-2: Joystick

• Up / Down lever motion – moves the stage in the Y axis

Left / Right lever motion – moves the stage in the X axis
Clockwise / Counterclockwise lever rotation – rotates the stage clockwise / counterclockwise
• Button 1 – not used
• Button 2 is used together with the lever motion:
- Up / Down moves the stage up / down (regardless of the Link Z to FWD status)
- Left / Right tilts the stage (available for stages with motorized tilt axis movements)
• Button 3 speeds up the stage motion:
- 10× in X / Y axis
- 5× in Z axis
- 2× in R / T axis

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 System Options: Uninterruptible Power Supply (UPS)

Uninterruptible Power Supply (UPS)

If power failures occasionally occur, using the microscope UPS is recommended. It maintains the electron source
section.
In case the microscope system is powered by the UPS and a mains power failure happens, the system starts a 10
minute countdown to switch to the safe mode. The user is informed of the countdown progress in the application
status window. If the mains power is recovered within this time, the countdown is cancelled and nothing happens.

After 10 minutes of continuous power off, a shutdown to the safe mode with the following actions is activated:
• FEG emission is gently switched off
• Chamber is vented
• UI is stopped
• xT Microscope server is stopped
• Microscope console is switched off to Standby mode
• Microscope controller and the support computer (if present) are switched off
WA R N I N G !
Because the Emitter IGP’s are supported by the UPS, some parts of the microscope are still under power.
To return the system to operation, follow the startup procedure (see Chapter 2). When the xT microscope Server is
launched the first time from the safe mode, a dialog is shown to inform a user.

Note
If the Startup procedure fails after a longer power failure, contact Thermo Scientific Service Engineer.

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 System Options: Optional Detectors

Optional Detectors

It is possible to extend the Apreo 2 microscope system with some detectors, depending on user needs.
See also Chapter 5 – Retractable detectors control.

Optional detectors connection

Detectors are connected to the feed-through connector board.
Connectors have printed names and are used to connect the
following detectors (UI representation):
• GAD: Directional GAD (GAD–ABS / GAD–CBS)
• DBS: Directional BackScattered (ABS / CBS)
• STEM: Scanning Transmission Electron Microscopy
(STEM 3 / STEM 3+)
Caution!
Connector insertion is a service operation!

Trinity Detector T3
Electrons generated by a primary beam can be collected by the
in-column Trinity detector T3 that is located inside the column,
just below the aperture strip. It is useful in the OptiPlan column
Use Case.
It is ideal for use together with the Beam Deceleration mode (BD)
and Standard Use case and with/without BD in the OptiPlan Use
case, when standard off-axis secondary electron (SE) detectors
fail.
In BD mode with stage bias above 2.5 kV, the detector detects SE; without BD the detector collects the BSE signal.
Optimum WD should be from 3.5 to 7 mm to achieve maximum detection efficiency. Due to geometrical restrictions,
higher probe currents and HV over 4 kV should be used.

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 System Options: Optional Detectors

RGB Cathodeluminescence detector (CLD)

CLD is a high sensitivity photomultiplier sensor dedicated for detection of light induced by primary beam. It is
provided as a retractable optional detector. CLD is primarily used in HiVac, basically it can be used in any vacuum
mode.

FIGURE 7-3 CLD inserted

Detector Settings
When a detector insertion is not allowed, tooltip is given.

CLD offers following basic modes which can be run in parallel:

• Red mode (red part of the visible light spectrum is detected)
• Green mode (green part of the visible light spectrum is
detected)
• Blue mode (blue part of the visible light spectrum is detected)
• Panchromatic
Additionally following summing modes are supported:
• Green+Blue
• Red+Panchromatic
Finally, following settings are provided, which helps the operator
to set all four displays with one button:
• Total Signal
• Color Imaging

• When Color Imaging is set (button highlighted in yellow), the True Color check box can be ticked – in this case
display 4 shows balanced color imaging of the sample (RGB channels contrast and brightness for the highest
values are set to give white color).

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 System Options: Optional Detectors

Directional Gaseous Analytical Detector (GAD)

This is a lens mounted low voltage silicon diode with an active area of approximately 100 mm2, that can be used at
pressures above 10 Pa. It is positioned directly over the sample to obtain maximum detector efficiency.

FIGURE 7-4: Directional GAD Diode

The GAD can be used down to a high voltage about 1 kV and works best with slow scan conditions.
It can be used for HiVac, but because it limits the minimum achievable WD, it is disadvantageous for high
resolution imaging. It has a 500 µm PLA cone for LoVac operation, especially the X-ray analysis. The cone extends
down from the unit to 7.5 mm, which reduces the gas path length for electrons to an efficient 2.5 mm at the
standard WD = 10 mm.

Installing / Removing
When not used, the GAD is placed at its parked position (inside the chamber
at the bottom right side) in the protective plastic box to prevent it from being
polluted. The cables are permanently connected to the feed-through
connector board by Thermo Scientific service.
1. With your gloved hand grasp the detector in the protective box.
2. Push the mounting collar gently up to the objective lens cone. The part
with the connector cables faces towards the chamber door.
3. Push the sides of the protective box and release the installed detector.
When removing the detector, proceed in reverse.

FIGURE 7-5: Directional GAD detector installation

1 2 3

Caution!
The diode is sensitive to mechanical damage. The active area (shiny diode) should never be touched.
The GAD is mounted close to the (optional) X-ray detector collimator, which must not be touched when changing
detectors. It is advisable to retract the EDX collimator when mounting / removing the detector on / from the objective
lens.

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 System Options: Optional Detectors

Detector Settings
• Select the GAD–ABS from the Detector Settings module / Detector
list box / GAD–ABS or GAD–CBS detector.
Choose the required diode segment(s) by clicking the relevant
radio button:
• All is the normal BSE image with suppressed topographical
contrast and maximum atomic number contrast.
• Inner / Outer uses shadows to create strong topographical and
atomic number contrast.
• A / B / C is the pseudo-topographical image with suppressed
atomic number contrast and maximum topographical contrast.
• Custom 1 / 2 can be set by a user by clicking the selected
segments to add signal to (+ yellow background) / subtract
signal from (– blue background) the overall detector signal.
Clicking on the same (+ / -) sign again turns the segment
background gray; this segment sends no signal.
Note
Setting segments to subtract signal is allowed only for Custom 2.
Set combination remains stored under the particular user.
• The Contrast button equalizes signals (contrast) from different
segments so they do not to override one another and have the
same contrast in different displays in which the GAD–ABS /
GAD–CBS detector is used.
Distribution of electrons collected by detector segments
changes with setting the working distance, lens mode and Beam
Deceleration mode.
It is also possible to set different segments in particular displays
and thereafter to use the Enhanced Image module / Mix 3 or Mix 4
tab to mix color coded signals to create color images.
Note
Whenever the GAD is selected, the optical display is paused (because
the CCD camera infra-red LED’s are switched off so as to not emit
photons that might supersaturate the detector diode).

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 System Options: Optional Detectors

Directional Backscattered Detector (DBS) –

Angular Backscattered Detector (ABS)
Concentric Backscattered Detector (CBS)
The ABS uses angular segmentation of the detector diode to
distinguish topographic contrast from different signal directions.
The CBS uses concentric segmentation of the detector diode to
distinguish between BS electrons scattered close to the beam
axis – inner segment (preferentially composite contrast) and
electrons scattered far from the beam axis – outer segment (more
topographical signal).
Caution!
Be aware of sample and final lens collision when tilting large samples!

Detector Settings
• Select the Detector Settings module / Detector list box / ABS or
CBS detector.
Choose required diode segment(s) by clicking the relevant radio
button:
• All is the normal BSE image, with suppressed topographical
contrast and maximum atomic number contrast.
• Inner / Outer uses shadows to create strong topographical and
atomic number contrast.
• A / B / C is the pseudo-topographical image with suppressed
atomic number contrast and maximum topographical contrast.
• Custom 1 / 2 can be set by a user by clicking the selected
segments to add signal to (+ yellow background) / subtract
signal from (– blue background) the overall detector signal.
Clicking on the same (+ / -) sign again turns the segment
background gray; this segment sends no signal.
Note
Setting segments to subtract signal is allowed only for Custom 2.
A set combination remains stored under a particular number and user.
• The Contrast button equalizes signals (contrast) from different
segments so they do not to override one another and have the
same contrast in different displays in which the ABS / CBS
detector is used.
The distribution of electrons collected by the detector segments
changes with the setting of the working distance, the lens mode
and the Beam Deceleration mode.
It is also possible to set different segments in particular displays
and thereafter to use the Enhanced Image module / Mix 3 or Mix 4
tab to mix color-coded signals to create color images.
When the detector is retracted, the information text is shown in
each display that uses it.

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 System Options: Optional Detectors

Retractable Annular Scanning Transmission Electron Microscopy Detector

(STEM 3 / STEM 3+)
This is a solid-state diode mounted on a retractable arm. It works
best at a slow scan conditions.
Note
There are several hardware variations of the STEM 3 / 3+ detector
depending on number of diode segments (8 or 11) and modes (radio
buttons) which are available within the Detector settings module. All
these variations have the same handling and control as described.

Inserting and retracting STEM 3 / 3+ detector

Before insertion of the retractable STEM 3 / 3+ detector, the
chamber must be pumped, otherwise the Insert button is not
active (a tooltip occurs under mouse cursor).
When the STEM 3 / 3+ detector is inserted stage movements are restricted automatically for the safety.
Caution!
Always take care of any stage movement that can cause a collision with the STEM 3 / 3+ detector.
Any collision can cause damage to the detector!
When clicking on the Insert button, the Select your sample holder configuration dialog requires determination of the
correct sample holder configuration to enable safe detector insertion. When the stage is not in the correct position
for insertion, another dialog appears requiring confirmation of moving it to the safe position.

In case the Horizontal holder or µHeater Holder configuration is selected and the EBSD extender is installed on the
system, dialog appears to confirm the EBSD extender is not mounted on the holder, alternatively followed by the
safe position confirmation dialog (see above).

Caution!
In case the EBSD extender is installed on the Multi-Sample holder at the µHeater or Horizontal positions, the STEM
detector must not be inserted!
The EBSD extender is not supported in 3D party applications (Autoscript for instance), be aware of stage movements.

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 System Options: Optional Detectors

Note
In case the X-Ray cone or the GAD detector with integrated cone is mounted, insertion of the STEM detector is not allowed
by the system.
Retraction of the STEM 3 / 3+ is automatic when Stopping /
Starting the server or venting the chamber. Otherwise a user can
use the Retract button. When the detector is retracted, this
information text is shown in each display that uses it.

Settings for STEM 3 / 3+ Detector

1. Position the desired sample grid in the field of view using the
ETD. Focus and link Z coordinate to FWD.
2. Select the Detector Settings module / Detector list box / STEM 3 /
STEM 3+ detector.
3. Insert the STEM 3 / 3+ detector.
Bright Field
1. Click on the Bright Field radio button.
2. Adjust the contrast and brightness. An image should be visible
at low magnification.
3. Change the voltage to suit the contrast necessary over the sample.
For example, light materials (poly-silicon or silicon oxide) may
work better with 5 – 10 kV to create contrast, while dense
materials (metals) might require 10 – 20 kV or higher.
4. Set the desired magnification, fine focus and correct the
astigmatism.
Dark Field 1 / 2 / 3 / 4
In this mode, it is possible to use separate segments by selecting
the appropriate radio button.
1. Obtain a Bright Field image first.
2. Click on the Dark Field 1 / 2 / 3 / 4 radio button.
3. Adjust the contrast and brightness.

HAADF (High Angle Annular Dark Field)

This mode may require higher voltage to create a suitable image, as
the angle subtended to the detection diode can be wide. Choosing 2× the value used for Bright field is a good guide
level. HAADF segments cannot be combined with DF or BF.
1. Obtain a Bright Field image first.
2. Click on the HAADF radio button.

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 System Options: Optional Detectors

Custom Annular 1 / 2 / 3 / 4
These buttons uses separate variations of segments adjustable
by clicking any segment:
• Click on the Custom Annular 1 / 2 / 3 / 4 radio button.
+ sign – segment signal is added (yellow color)
– sign – segment signal is subtracted (blue color)
no segment signal (gray color)
The combination set remains stored under the particular user.
Custom Angular
• Click on the Custom Angular radio button.
You can select / deselect any combination of outer segment
partitions by clicking on them in the detector diagram. Selected
segments are highlighted in yellow.
The entire area of the selected segments can be “rotated” using
the circle arrow buttons to view orientation contrast changes.

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 System Options: Nav-Cam

Nav-Cam

Besides the Sample Navigation / Navigation Montage feature, this functionality represents a fast method to
navigate across a large stage movement area. It provides a quality Navigation image quickly and easily, which is
convenient when investigating large area samples or several samples with the use of any multi-sample holder.
Note
Nav-Cam operation is restricted for highly shiny and simultaneously planar specimens (Si wafers, mirrors etc.).

Capturing Navigation Image Procedure

1. Vent the chamber, open the chamber door, insert a sample and pump the chamber.
2. Select the Stage menu / Move Stage to Nav-Cam function to
move the stage to the Nav-Cam position.
At this moment, the beam and the detector change to Nav-Cam
and a live image from the navigation camera is obtained in the
active display (with a resolution of 768 × 512 pixels only). Set
the Detectors module / Brightness slider in case the imaging is
not satisfactory.
WA R N I N G !
Retract all retractable detectors to prevent equipment damage!

Note
Run the Stage menu / Take Nav-Cam Photo (Ctrl + Shift + Z) item to
run steps 2, 3 and 4 automatically at once. It is possible to cancel this
procedure with the Abort button at any time; the stage then remains
in its present position.
3. Capture the Navigation image (with the high resolution of
3072 × 2048 pixels) by using the Snapshot / Photo function.
The image can be saved or adjusted like any other image taken
from the microscope (image enhancement, process, etc.).
It is possible to capture the Navigation image after the
Home Stage procedure has been run. For better image quality
and navigation accuracy, running the Link Z to FWD is also
recommended.
Note
Wait until image capturing is finished (about several seconds).
4. Click on the Stage menu / Move Stage to Nav-Cam function
again to move the stage to the previous stage position.
A green rectangle (or just a cross) represents the spot where
the electron beam is aimed.
Besides a navigation image the Digital Zoom module can be applied
to navigate the stage.
When the Preferences / General section / Show Stage Map in
Navigation displays item is set to Yes, saved stage positions are
shown in the Nav-Cam photo.
In case a user logs off and the sample and its stage loading position did not change, use Stage menu / Restore Last
Nav-Cam Photo.

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 System Options: External Current Measurement (Keithley Picoamper Meter)

External Current Measurement (Keithley Picoamper Meter)

When the Stage menu / External Current Measurement is ticked,

the system expects to have the Keithley picoamper meter
connected to the External Connectors panel / SPECIMEN CURRENT
connector, which is located on the back of the microscope console.

FIGURE 7-6: External Connectors Panel

In this case, the Status bar / Specimen Current shows N/A and the Keithley meter readout shows the actual
specimen current.
Note
When this functionality is not used, switch the picoamper meter off or disconnect it!

Energy Dispersive Spectroscopy (EDS)

The EDS is a technique used for identifying the elemental composition of the specimen, or an area of interest
thereof.
EDS analysis can be performed by using the ColorSEM option which is an integrated feature of the scanning
electron microscope (see below). Alternatively, the user can perform the EDS analysis using the Pathfinder
software package or 3rd party EDS detectors.
The specimen is bombarded with an electron beam inside the
microscope column. These electrons collide with the specimen
atoms' own electrons, knocking some of them off in the process.
Positions vacated by ejected inner shell electrons are occupied by a
higher-energy electron from an outer shell, while giving up some of
its energy by emitting an X-ray. The amount of energy released
depends on which shell it is transferring from / to. The atom of
every element releases X-rays with a unique amount of energy.
This identifies it.
The output of an EDS analysis is an spectrum, which is just a plot
of how frequently an X-ray is received for each energy level. The
higher the peak in a spectrum, the more concentrated the element
is in the specimen.

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 System Options: Energy Dispersive Spectroscopy (EDS)

In ColorSEM, the observed spectra are processed to provide the user with a ColorSEM image in real time, or with a
conventional elemental map (see below).

EDS analysis and microscope configuration

High Vacuum
HiVac operation gives the most accurate X-ray results, but the
sample must be electrically conductive.

Low Vacuum
The LoVac mode allows observation of electrically insulating
samples, but care must be taken when using this mode to collect
X-ray results.
Some of the electrons are deflected due to interaction with the
chamber gas. The deflected electrons form a “skirt” around the
main beam. The skirt electrons will hit the sample at points that
are remote from the area of interest, and generate X-rays from
these points.
The number of skirt electrons increases with chamber pressure and the distance that the beam travels through the
gas. The effect of these skirt electrons can be minimized by reducing gas pressure, or by shortening the distance
between the sample and the final PLA.
X-ray analysis in LoVac mode is possible in combination either with the standard LVD detector or with the optional
GAD detector. The GAD is recommended for achieving the best signal-to-noise ratio, especially when using lower
accelerating voltages, because the long GAD cone minimizes the primary beam path and therefore the beam
dispersion in the gaseous environment of the chamber. On the other hand, the LVD detector offers the largest field
of view for the LoVac operation. The CBS is compatible with EDS.
The X-ray analysis should be performed at the lowest possible gas pressure to minimize interaction of the electrons
with the chamber gas. Normally, it is performed with a relatively high beam current so that there will be enough
signal for a good LVD image even at very low gas pressures.

LVD EDS Analysis

EDS analysis should be performed at the lowest possible gas
pressure, so it should be done with the LVD. Normally, X-ray
analysis is performed with a relatively high beam current so that
there is enough signal for a good SE image even at very low gas
pressure.
The Hot Stage cone can also be used with the LVD for X-ray
analysis, it has a field of view twice as large as the X-ray PLA.

GAD EDS Analysis

Maximum detector response is around the 8,5 mm WD,
providing an atomic number contrast, when the resolving power
is better than 0.1 (in the Atomic number range around 20).

STEM EDS Analysis

Set the sample surface to 7 mm WD.
Select the area of interest in the STEM mode and perform X-ray analysis, mapping or line scans as appropriate.
Because the samples are not bulk in nature, the beam spread normally associated with SEM samples is greatly
reduced, and therefore higher spatial resolution can be obtained with the STEM detector. This also provides less
background in the spectrum and allows better separation of peaks as well as more accurate lower count rate
mapping. The high voltage chosen for the analysis still depends mainly on the composition of the sample.

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 System Options: ColorSEM

ColorSEM

ColorSEM is an integrated EDS system functionality that provides the user with a colorized image on the fly and
with a set of tools for detailed EDS analysis. Image colors are simulated according to elemental composition for a
quick overview. To obtain more accurate results proceed with the Analytical layout (see below).

Hardware
To start the ColorSEM functionality the detector must be inserted. There are two hardware detector configurations:
• Manual – knob on the ColorSEM detector on the microscope chamber front side
Rotate the knob clockwise / counterclockwise up to the stop to retract / insert the detector.
• Motorized – Detector position control box on the microscope table
Press and hold the INSERT / RETRACT button to insert / retract the detector.

FIGURE 7-7 ColorSEM: Manual insertion knob / Motorized insertion control

Pathfinder
In case the ColorSEM is a part of the Pathfinder analytical tool, the Pathfinder computer (placed in the vicinity of
the microscope) must be on before starting the ColorSEM functionality, otherwise the detector temperature
readout is not correct. Push the black On button (the Active diode shines) to start the computer and wait about
5 minutes to start the ColorSEM.

FIGURE 7-8 Pathfinder computer control panel

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 System Options: ColorSEM

Software
Click the ColorSEM toolbar icon to start colored imaging in an active display; the functionality starts automatically
when activated and it is available for all displays with different detectors except CCD display – selecting the CCD
display pauses the ColorSEM display and vice versa.

The ColorSEM bar at the display lower left corner enables to configure the layout:
• Clicking the ColorSEM button switches the ColorSEM imaging on or off.
• Clicking any colored element icon switches contribution off this element to the composite
color imaging; the icon becomes just outlined to depict element elimination. The same
functionality is to right-click the element icon and to select Do Not Show check box.
• Double-clicking any element icon selects just this element to contribute to the color
imaging. Removing the contribution of an element to the ColorSEM image in the legend
does not exclude the element from the analysis. The element can be excluded from the
analysis in the periodic table (see below).
• Clicking the left arrow shows / hides the bar.
• Right-clicking over the element icon shows the menu for specific color selection. The icon
is then marked by the white star, which indicates that the color was chosen manually by
the user and should not be changed automatically.
• Clicking the circle arrow icon automatically changes colors for all elements, except the
ones marked by the white star (see above).
• Clicking the cursor icon changes the cursor to the crosshair one and shows the
tooltip with approximate elemental composition of the sample point under the
cursor.
• Ticking the AutoID check box switches the automatic elements identification on
(see below).
• Clicking the … button shows the periodic table with depicted analysed elements
(see below).
The periodic table depicts which elements are chosen for the analysis either by
the user or by the AutoID functionality, and allows the user to exclude elements
from the analysis.

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 System Options: ColorSEM

Analytical layout
Clicking the Analytical toolbar icon switches UI to the analytical layout. Active display is shown at the display 1
position.

Note
Switching to the Analytical layout does not require the ColorSEM functionality to be on.
Next to the activated Analytical Layout icon, four additional icons appear that represent the tools available for
detailed EDS analysis: point analysis, region analysis, line analysis and elemental mapping.
See the Chapter 3 – Preferences dialog / EDS item to configure each site type.
Click the appropriate toolbar icon, select the live operation or a preset from the list, and choose the sample region
to be analyzed in the active display. The point, region or line icon that was selected for the analysis is highlighted
(orange) and the corresponding spectrum is shown below (Spectrum tab). The chemical composition can be
viewed in the Composition tab (see below).
Point analysis
Select one point to be analysed.
Region analysis
Select the region to be analysed.
Line analysis
Draw the line with set number of points spread regularly along the line.
The chemical composition at individual points of the line is plotted in the graph within the Line Plot tab. The user
can change the type of information shown and the scale of the vertical axis:
• Y Value – weight or atomic percentage
• Y Range – Maximum value or Full range
Exact composition for selected point (highlighted within the Line – orange, and Plot area – grey vertical line) is
available at the bottom of the Plot area.

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 System Options: ColorSEM

Elemental Mapping
The entire display area is analysed – analysis is dependent on the magnification set.
The display 1 shows a composite color image obtained by combining individual elemental maps shown within the
Maps tab. Each elemental map depicts the relative intensity of the given element over a pixel of a fixed size (see
Preferences), and can be selected (highlighted by orange borders) / deselected from the composite image by
clicking it. As opposed to a ColorSEM image, the elemental maps are not based on quantitative EDS information
but merely on gross EDS counts measured for a given spectral line (see below).

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 System Options: ColorSEM

Periodic Table tab

Chemical elements are arranged in the form of periodic table.
• AutoID On – clicking this button starts (highlighted) / stops automatic element identification from this point on
(see the ColorSEM bar).
• Run AutoID – clicking this button (available when the AutoID was switched off) starts automatic element
identification procedure once and stops.
• Clear Selected – clicking this button clears all elements identified by the functionality from the periodic table; in
case the AutoID On is running, new elements identification starts immediately again.
At the bottom of the display is the color code for Selected by User / Selected by AutoID / Exluded from AutoID
elements.
Moving the cursor over the periodic table shows the spectral lines corresponding to the element under the cursor
in the Spectrum area. Vice versa, by moving the cursor over the Spectrum area, the elements which have a spectral
line at the chosen energy are highlighted in the periodic table.
When Elemental mapping is active, it is possible to select a particular spectral line for which the intensity of the
EDS events is depicted in the elemental map corresponding to the element by right-clicking above the desired
element and ticking the desired spectral line.

Composition tab
For the chemical elements selected in the periodic table, the results of the quantitative chemical analysis are
shown in the Composition tab. The chemical analysis is based on the integral spectrum acquired for the analyzed
point, region, point in a line or image. Both atomic percentage and weight percentage are shown for all selected
elements, along with the estimated error figures.

Note
The Atomic % / Weight % composition and theirs Errors values are not valid when the integral spectrum is computed over
a non-homogeneous area. To avoid this, zoom into a homogenous area or switch to the spot mode to obtain correct values.

Spectrum area
Peaks of elements identified in the sample are displayed. Moving the cursor above the spectrum depicts elements
with this peak energy in the periodic table display (see above).

• Rick-clicking above the spectrum area induces the menu with possible elements occurrence according to the
cursor position (depicted also in the periodic table).
• It is possible to Save spectrum to / Load spectrum from EMSA file.
• Clicking the Autosize item resizes the spectrum to fit the display (the same as double-clicking inside the
spectrum or clicking the spectrum area lower left corner icon).

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 System Options: ColorSEM

Mouse control within the spectrum area

• Click & Drag in spectrum area from left to down right to zoom in created rectangle to entire display.
Click & Drag in any other direction to zoom out entire display to the area of created rectangle.
• Click & Drag in axis area left / right zooms in / out corresponding axis.
• Ctrl + Click & Drag in spectrum area should zoom in corresponding axes:
X-axis: dragging left / right zooms in / out; point of the first mouse click is relative center of the zoom.
Zooming out can't go below 0 kV and above 20 kV.
Y-axis: dragging up / down zooms in / out relative to the spectrum bottom line (irrespective of a mouse click).
Zooming out can't go below 0 in Y axis.
• Shift + Click & Drag left / right in spectrum area moves the spectrum left / right.
Moving in X-axis can't go below 0 kV and above 20 kV; moving in Y-axis can't go below 0.
• Rolling the mouse wheel up / down zooms both axes of a spectrum in / out relative to mouse position.
Zooming out can't go below 0 in Y-axis.

Analytical page
To manage analyses use modules within the Analytical page.

EDS Acquisition Progress module

The point, region and line analysis can be executed for a series of locations of the sample. When the processing of
multiple locations is in progress, the current state can be observed:
• Overall Progress – Relative progress for the processing of all selected sample locations.
• Current Progress – Relative progress for the processing of the currently analyzed sample location.
• Remaining Time – The estimated time required to finish the analysis of all selected sample locations.
• Clicking the Next / Stop button proceeds with next sample location / stops analysis.

Analysis History module

The analysis history tracks the progress of the EDS analysis in a hierarchical structure. The Session contains all Sites
on the sample with each analysis (Point, Region, Line and Map – elemental mapping) that were performed over this
site. When an analysis contains more structured information, such as in the case of line analysis individual points,
this information is stored in the child items of the analysis (click the black triangle to expand the list).
New Session is started automatically by creating the first site, any other by clicking the button. New site is created
when changing the stage position or scanning conditions (magnification, beam current, strong focusing, etc.).
The outcome of the EDS analysis can be exported as the Microsoft Word document in a report by clicking the
Create Report button. The report contains all vital information on the analysis, including the spectrum, the chemical
analysis results and the location in the ColorSEM image.
Each analysis can be Renamed / Deleted from the list by use of the right-clicking context
menu.
Selecting several sites within the session from the list shows all selected sites in the
paused image (highlighted – selection is possible also directly from the image), and the
overlapped spectra in the spectrum area (see the list at upper right area corner).

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 System Options: ColorSEM

EDS Detector Status

Status of the EDS detector can be checked and monitored:
• Count Rate is the number of output counts per second. These are the counts that form the integral spectrum and
are used for the creation of composite color image.
• Dead Time is the relative portion of time over which the incoming EDS counts could not be processed due to
system bandwidth. The dead time increases proportionally with the count rate, and should generally be less
than 50%.
• Detector Temperature (Cool (green) / Warm (red)) depicts the temperature state of the EDS detector chip. If the
detector chip is too warm to perform EDS analysis (such as shortly after the system is started and the detector
has not cooled down), the Warm is shown and the user cannot perform the analysis. Please ensure the correct
operating conditions of the hardware and wait for the cooling cycle to finish.

EDS Pulse Processor Alignment

It is possible to align the system to provide relevant results. Run the automatic alignment > Validation Only to check
the state, if the results are not satisfactory, run the Full Alignment (13 steps).

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 System Options: Patterning

Patterning

With this option, the Patterning menu, the Patterning page and some toolbar icons are available within the UI to
enable control over the entire process.
Patterning is the process of moving a beam over a defined
pattern along the specimen surface (while leaving other areas
untouched) with the purpose of deposition, adding well-defined
amounts of new material. The pattern is shown in color
appropriate to the gas selected.
The Patterning menu and the Patterning Control module control
the entire process.
Caution!
When deposing a large volume of material at higher currents, we
recommend removing any detector not in use. There is a risk of
decreasing a detector’s efficiency by material deposition.
The system provides additional monitoring possibilities:
• Simultaneous Patterning and Imaging (SPI)
The SPI provides an electron imaging (in a display different from patterning) during patterning. It is strongly
influenced by secondary electrons (SE imaging), so the image quality is not perfect. Higher electron currents
(higher spot numbers) and averaging help improve imaging. In case the BSE detector is used, this interference is
less important (BSE imaging). The system remembers the brightness and contrast settings separately for SPI or
normal imaging.
• Integrated Real Time Monitor (RTM)
The RTM provides an immediate image (in the same display with the patterning) of the patterning process. The
patterned area is observed, and in case of relatively slow scanning, the scan trajectory can be inspected.
RTM is typically used as an end-pointing device by observing brightness differences in the detector signal. These
result from contrast differences when milling through layers of different composition on a stack of multiple
materials.
RTM can be used with any of the pattern types that are available in the UI. When starting patterning with the
RTM activated, the pattern in the UI will be updated with real time image information. The patterned area
information is updated based on the detector signal, which is shown in synchronization with the beam trajectory.
It is possible to grab a snapshot with the electron beam during patterning while using RTM.
Note
The acquired data are matched to the calculated positions of the corresponding milling points. The pixels shown on the
screen might not therefore directly match what is happening on the sample surface, and some imaging artefacts (due to
milling points and screen pixels mismatch) can occur. To prevent this, try to change the field of view.

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 System Options: Patterning

Patterning Control module

There are several tool icons and the progress monitoring area within
the module.

Tool Icons
Clicking on an icon activates (highlighted with an orange back-
ground) / deactivates (normal background) the tool. If no icon is
selected, the pattern selection cursor (arrow) is active.

• Pattern type selector (also see Toolbar icons) – clicking on the

down arrow next to the icon activates the drop down list to
select a pattern type:
Rectangle / Line / Circle / Polygon / Bitmap / Stream File
• Trash Can (Delete) button – deletes the selected pattern(s)
• Pattern / Exclusion Zone (overlapping area of the two patterns)
Enabled / Disabled button – sets selected pattern / exclusion
zone between two patterns to be / not to be processed
The corresponding icon and pattern graphics color change.

• Hide button – hides / shows all patterns; the button becomes highlighted / normal background
• Patterning Serial / Parallel sequence button – switches between two possibilities
• Zoom button – enlarges the selected pattern(s) to fill the entire display
• Patterning sequence buttons – sets the process order of the active display patterns
Patterns are milled in the order they are created. Numbers are shown close to the pattern and in front of its name
to indicate the actual milling order. This can be changed by clicking on the left / right arrow to move the selected
pattern one position up / down and by clicking on the left / right double arrow to move it to the first / last
position.

• Skip to a next pattern in order button

• Select All button – selects all pattern shapes within the active display
• When Finished list – When a long lasting patterning is processed, select an
action to proceed: No Action / Beam Off (sets the beam off).

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Pattern Types
Patterns are automatically assigned to one or more particular processes.
They are distinguishable by a different crosshatch within the display.
The Rectangle / Line / Circle / Polygon pattern is dedicated to both
milling and deposition.
The Bitmap pattern enables importing bitmaps as a pattern. It must be 24
bit RGB bitmap, each pixel consists of:
• Red component – actually not used
• Green component – determines if the beam is blanked.
Any value other then 0 activates the beam
• Blue component – determines the dwell time per pixel:
If the value is 0, the pixel is skipped (no milling or deposition proceeds).
If the value is 1 (border), the dwell time is the lowest (approx. 100 ns).
If the value is 255 (border), the dwell time is identical as it is set for the
pattern.
The dwell time for values in between the border values is linearly interpolated.
Note
When drawing a bitmap, we recommend using black (0 / 0 / 0) for no milling points and white (255 / 255 / 255) for milling
points.
Do not forget to optimize other properties, such as the Application file, Z size, leading edge, etc.
The Stream File pattern is created as an ASCII text or binary file that directly addresses the patterning DAC (Digital
Analog Converter) and produces custom pattern files. The 16-bit DAC is used, so the patterning field is divided into
65 536 steps in both the X- and Y-axes.
s16 96 2867 2867 96 1639 2048 96 2457 1639
40 96 1229 2457 96 2048 2048 96 2867 1639
25 96 1639 2457 96 2457 2048 96 1229 1229
96 1229 2867 96 2048 2457 96 2867 2048 96 1639 1229
96 1639 2867 96 2457 2457 96 1229 1639 96 2048 1229
96 2048 2867 96 2867 2457 96 1639 1639 96 2457 1229
96 2457 2867 96 1229 2048 96 2048 1639 96 2867 1229
The file must begin with an s, indicating a stream file. The second line defines the number of loop repeats (40×).
The third line indicates the total number of X, Y coordinates (pixels) in one loop (5 × 5 = 25 in this case). The 96
figure represents the dwell time in units of 100 ns (=9.6 µs).
Note
Stream files cannot be created directly from the UI; use any suitable text processor. There are several stream file types that
are recognizable by the first header line (s16 / s16,25ns / s16,DAC / s16,25ns,DAC).
When two patterns overlap, it is possible to join them into one by using the Build Polygon functionality.
Selected patterns can be multiplied by using Build
Array functionality. The Dimension / Pitch means
the number of repetitions / distance.
It is possible to convert any selected Annotation
or Measurement graphic to a Bitmap type
pattern shape with the use of the Convert from
Annotation item.

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 System Options: Patterning

Serial Patterning
All patterns defined on the screen are processed consecutively; milling / deposition is completed on one pattern
before moving to the next one. This is the default patterning mode.

Parallel Patterning
All patterns defined on the screen are processed concurrently; one pass of the beam is completed on all patterns
before moving on to the second pass. Parallel patterning is typically used to avoid a redeposition of material on adjacent
areas.
With parallel patterning, the mill time is recalculated to include all the patterns that are shown in the image
window.
When a user switches to the Parallel mode, the following pattern properties in the group must be the same: Gas
Type and Passes. The first selected pattern determines these values for all the other patterns.
Other properties (Application, Z size, Overlap, Saturation Sputter Rate and Refresh Time) are also all set to those of the
first selected pattern to avoid confusion, even though they can theoretically remain unchanged. Restoring Serial
mode does not undo these changes; the properties remain as in the Parallel mode.

Progress area
Information updated as the milling progresses can be found here
(captions change according to a running process):
• Total Time – estimated total patterning time
• Overall Progress – related to the total patterning time of all
patterns
• Current Progress / CCS Line Progress – related to the actual pattern in progress
Note
When patterning is paused in one display, it is possible to start patterning in another one. Similarly, when patterning
finishes, there may still be a paused patterning in another display.
It is possible to acquire an image from the signals generated during patterning. All imaging parameters are dictated
by the patterning requirements. Much better images can be acquired by a Snapshot during patterning. In this case,
patterning is paused, an image is grabbed, and patterning resumes.
Note
If the magnification is too high, creating certain patterns can use too much memory needed for the control system to run.
The pattern corners become round, and the edges become jagged. A good rule of thumb is to pick a magnification where
your pattern fills 35-50% of the screen.

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 System Options: Patterning

Patterns Processing
Once a pattern shape has been drawn, it can be modified (see Shape editing above).

Importing / Exporting patterns

User created patterns may be imported or exported (saved) via
the File menu / Import or Export / Patterns item. The saved file
(.ptf) contains all parameters found in the Patterning property
editor (Basic / Advanced) for all patterns drawn in the active
display. Six (for each beam) toolbar Pattern Presets (labeled p#)
can be individually assigned to any of these .ptf files.
Note
These buttons are hidden under the triangle down arrow, or within the
Workspace customization (see above).
Right-clicking on the selected button calls up the menu:
• Apply item – activates an appropriate button (highlighted with
an orange background) and starts the patterning with the preset
parameters (the same as clicking on the button directly)
• Edit item – opens the Assign Pattern File (.ptf) window to assign
a desired parameter file to a selected button
The toolbar Pattern Presets assignment to the particular .ptf file
can be saved or loaded by the File menu / Export or Import / System Parameters item.

Properties module
A certain pattern can be selected with many associated parameters
that can be set via the Property module:
• Application – clicking on the value slot produces a drop-down
arrow bringing a list of applications. Choosing the required one
sets the subsequent properties.
• X / Y / Z size – dimensions of the pattern
• Scan Direction –
• Dwell Time – a time the beam spends on a single pixel per pass
(rounded to a multiple of 25 ns).
• Time – required to process this pattern
• Rotation of the patterns (the positive direction is clockwise)
• Position X / Y of the pattern relative to the origin (the display
center)
• Overlap X / Y – sets the beam diameter overlap. The value of the
overlap can be positive or negative, depending on a particular
application. The overlap parameter influences the Area
Calculation and the Dose.
• Gas Type – the gas to be used to process the pattern (or None if
no gas is to be used). This determines the pattern color onscreen.
• Pitch X / Y – sets the pitch between two spots
• Area Calculation – defines how the patterning area will be
calculated in order to get the most accurate value for the Dose.
This value is related with the Overlap X/Y. The Pattern
(default) / Array are set for positive / negative overlaps.
• Dose –
• Volume per Dose – the volume of material that is removed per charge
• Saturation Sputter Rate – the maximum linear sputter rate for a given gas. For Gas = None, this is 0 (actually not
used).
• Refresh Time – the minimum loop time that must elapse before the next pass, so that the adsorbed gas can be
refreshed

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• Loop Time – the time required for a single pass (read only)
• Area – the surface area of the pattern (read only)
• ScanType – Serpentine means the beam proceeds from left to
right and back from right to left, while Raster scans from left to
right, then the beam returns to the left starting point
• Fill Style – one can choose either to mill a Solid or just a Frame
(box and circular types only)
• Passes – a number of the beam scans over the pattern
• Defocus of the beam (WD change) – influences the Total
Diameter and Area Calculation. It allows focusing above /
below (negative / positive value) the sample surface
• Blur – like Defocus, but specifying the (additional) diameter of
the blurred spot
• Interaction Diameter for an infinitely small beam – influences the Total diameter
• Total Diameter – the combination of the beam diameter and interaction diameter influences the Overlap X / Y and
Pitch X / Y values (read only)
• Maximum Dose per Area – describes the adsorbed gas layer, allowing a certain dose to be deposited at a higher
rate than the saturation current density, allowing a temporary higher rate (actually not used)
• Saturation Current Density – the current at which 63% of the saturation sputter rate is reached (actually not used)
• Total Volume Sputter Rate – the speed at which material is removed or deposited (actually not used)

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 System Options: Patterning

Gas Injection module (option)

Patterns have many associated parameters, such as the gas that
can optionally be used during patterning to deposit the desired
material. The gas is delivered by a Gas Injection System (GIS) on
the sample surface.
As different applications require different gases, there can be more
GIS’s installed on your system. One can select an Application file
for a given pattern in the Patterning property editor. It automatically
sets the appropriate GIS, the dwell time and overlap and calculates the proper dose appropriate to the beam
chemistry. A pattern must be defined before the material file is selected.
The GIS can be selected manually, but note that overlap, dwell time and an appropriate gas type should be set
carefully to avoid disappointing results.
Setting up the GIS
The Gas Injection module enables control of the installed GIS’s. A Gas
type is allocated to each GIS (several injectors may be mounted
according to the configuration, its color depends on the gas type).
A tooltip info is given about the selected GIS line:
• Port # – GIS connection position
• Lifetime – time of GIS employment
Right-clicking on the installed GIS module line opens a context
menu.
Before patterning with the GIS starts, the gas reservoir must be
heated by selecting the Heat column context menu / Warm item.
The Cold status is replaced by a progress bar, which in turn is
replaced by the Warm status when the GIS is fully heated. To cool
down a reservoir, proceed in reverse order.
To insert the GIS needle manually, click on the Insert check box (a
tick mark). A confirmation dialog appears. Clicking on the Insert
check box again retracts (clear box) the GIS.
Caution!
Confirm the needle insertion only if you are sure that nothing obstructs its travel.
Beware of stage moves while the GIS is inserted! The GIS needle can be damaged by careless stage movements!
To open / close the GIS valve, click on the Flow column / Closed /
Open status. This will not be possible until the Heat column /
Warm status has been reached.
Note
If any Property module / Gas Type is chosen, the opening / closing of
GIS valves is done automatically during patterning.
Some conditions must be fulfilled before insertion is enabled. The
user is notified by a tooltip.
When not in use, the GIS should be closed (to save lifetime), cold
and retracted. Leaving it closed, heated but retracted is also an option so that reheating is not necessary if it is to be
used over several patterns.
Caution!
Logging off an actual user does not change the conditions of the GIS’s.
It can be Warm, In and Opened even if the Microscope Control software is closed!
When the vacuum status is vented, GIS needles are retracted automatically. Despite that, retract it/them manually
before you start any activity inside the chamber (specimen exchange, detector mounting, etc.).

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Application Files
There are several application files delivered with the system that are intended for different uses. Each one incorporates
multiple parameters for particular patterning. Some of these application files use GIS’s. With multiple GIS’s
installed on your system, you can select a suitable application file for a given pattern. Processing specific materials
without gas can be done by using no application file, or more efficiently with the appropriate scanning conditions
using the dedicated Application file for that material. There are pre-defined (non-editable) and user-defined
(saved) files.
Note
A pattern must be defined before the Application file is selected. The pattern type automatically predetermines the set of
possible application files (therefore of gas type).
Within the application files compilation, there is the former Si application file with the Volume per Dose value determined
in the past, and the Si New application file with values corrected for use with silicon. Be aware of the different results from
using these application files!

Application Files Editing

A new application file can be created or an actual Application file can be edited in Windows Notepad® in case any
parameter of the process is insufficient. Application files (*.xml extension) are located in the
C:\Program Files\Fei\data\patterning application files\ folder.
Note
If any Application file is to be changed, we recommend making a copy of the original one. Server restart is necessary after
placing a new Application file in the above mentioned folder for it to be functional.
Examples
For clear arrangement, there are comment lines within xml files:
• comment line filter
<!-- Application file for milling silicon (Si) without any gas -->
In order to make the application files selection more comprehensible, several filters have been implemented:
• pattern type filter
The system only shows application files that are related to a given pattern type.
<!-- Optional type, must be "Line, Circle, Rectangle, RCS, Bitmap, StreamFile, Polygon", can be a combination -->
<PatternType xmlns:dt="urn:schemas-microsoft-com:datatypes"dt:dt="string"> CCS</PatternType>
Multiple patterns can be designated in a list separated by comas. If the command is left blank, the file is shown
for all pattern types.
• GIS type filter
The system only shows application files depending on GIS’s installed on the system.
It is possible to edit / add / remove parameters (for instance Refresh Time - for filling vias, Blur - for depositing
large areas etc.) if required for certain applications.
• Volume per Dose variable
<VolumePerDose xmlns:dt="urn:schemas-microsoft-com:datatypes" dt:dt="r8">
0.15e-9
</VolumePerDose>
The Volume per Dose is material dependent. Using any application file for milling different material substrates
results in a differnet Z size. The actual value can be measured and subsequently a new Volume per Dose value
can be defined / set.

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 System Options: CleanConnect

CleanConnect

The CleanConnect is the transfer device enabling quick loading samples destroyable by air (O2 / H2O) to the
microscope without venting the whole chamber. It uses Argon or other inert atmosphere to protect samples for at
least 10 minutes before loading them to the microscope chamber.

Mechanical Design
The CleanConnect (CC) consists of:
• CC Loader
• CC Shuttle
• CC Transfer rod
• CC Stage adapter
• CC Sample carrier
• CC Carrier holder
• Not supported by Thermo Fisher: Glove box

FIGURE 7-9 CleanConnect parts (from left): Loader / Shuttle / Transfer rod

FIGURE 7-10 CleanConnect parts: Carrier holder with Sample carrier

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CC Loader
CC Loader is a small chamber fixed to the microscope's chamber. It maintains the environment required for a
successful sample transfer, protects a sample against external atmosphere and the microscope chamber from
venting.
The CC Loader and microscope chamber are separated by the Gate valve (the one same as used on the CC Shuttle)
controlled by the tube rail with 2 defined positions: Locked (closed) / Parked (open).

FIGURE 7-11 Gate valve functionality: upper – CC Loader (with Shuttle connected): Locked (closed) / Parked (open)
lower – CC Shuttle valve closed / opened

On the outer side of CC Loader the CC Shuttle is connected. When the CC Shuttle is removed for sample exchange,
the Plug must be connected to decrease the CleanConnect Loader contamination.

FIGURE 7-12 CC Loader with / without Plug

The CC Loader and Shuttle are interfaced by the bayonet controlled by the lever:
Rotate the lever clockwise, remove the plug, attach the Shuttle and rotate the lever back (counterclockwise).

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 System Options: CleanConnect

Vacuum control
Opening and closing vacuum valves are controlled by the software with the use of Sample Exchange dialog / Pump /
Vent buttons. The CC Loader P / V buttons (illuminated when it is possible to start a dedicated action) have the
same functionality.
• P (pump) labeled button – pressing it starts the Flushing cycle according to the Preferences / CleanConnect
settings. The stage moves to a loading position at the same time. After finishing the flushing cycle, the message
appears asking to open the CC Shuttle valve. Pressing the button again pumps down the CC Loader to the
required vacuum (see procedures below).
• V (vent) labeled button – pressing it starts venting the CC Loader. The venting continues until it is terminated by
a time-out. The venting gas is usually either Argon or Nitrogen.
• OK labeled indicator lamp – lights up when required vacuum is reached. When it goes out, the vacuum has been
lost.
The control buttons do not shine when the system is recovering from vacuum status transition (e.g. immediately
after the load/unload sample, during venting the chamber…). When finishing the state transition, the control
buttons operate again.

CC Shuttle
CC Shuttle is used for transferring the sample under inert gas atmosphere. It contains the Shuttle valve (the same
one as used on the CC Loader) controlled by the tube rail as the CC Loader (see Figure 1-3) to interface the CC
Loader and Shuttle.

FIGURE 7-13 CC Shuttle (the pressure gauge is not present)

The pressure gauge on the shuttle shows the pressure status of atmosphere inside the shuttle.
The shuttle can adapt 1× 1” or 4× 1/2” sample stubs.

FIGURE 7-14 Maximal sample size for 1" / ½" sample stub

Warning!
Because the valve is fully manually controlled, users can destroy a sample (by air) if they do not operate carefully by pre-
described steps. The sample carrier with the transfer rod tip included in CC Shuttle could be pulled in by vacuum.

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CC Stage adapter and CC Sample carrier

CC Stage adapter must be installed in the chamber at 110 mm stage. MD- how is this done?) It adapts the CC
Sample carrier from the Transfer rod tip.

FIGURE 7-15 CC Stage adapter / CC Sample carrier / CC Stage adapter with loaded CC Sample carrier

CC Transfer rod
The CC Transfer rod is used to load / unload the sample carrier to / from the CC Stage adapter and also to stick out
the sample carrier from the CC Shuttle in the Glove box for a sample stub exchange. It is designed as detachable
from the CC Shuttle enabling to insert the Shuttle into the Glove box via smaller antechamber. Operating with CC
Shuttle and Sample carrier in the Glove box is then more convenient with the short rod version (a part of
accessories for the CleanConnect system).

FIGURE 7-16 Figure 26. CC Transfer rod long (left) and short (right) version

The Transfer rod tube has drilled labyrinth which works as the rail for correct loading / unloading the sample
carrier.
The CC Transfer rod and CC Shuttle are connected by the Clamp, that must be secured by pressing.

FIGURE 7-17 CC Transfer rod clamp opened / closed

The CC Transfer rod and the rod tip (inside the Shuttle) with attached Sample carrier are joined together by locking
mechanism controlled by the rod lever at the end of CC Transfer rod (both versions).
Locking (parts are joined) / Unlocking can be done only in the Default position of the rod handle (see figures 1-10
and 1-11).

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 System Options: CleanConnect

FIGURE 7-18 CC Transfer rod lever unlocked / locked

FIGURE 7-19 Sample loading and unloading movement sequence with depicted Default position

CC Port
CC Port is the modification of CC Loader with manual vacuum control. It is used at the Glove box to insert the
Sample carrier into. Flushing cycle is executed by the manual Ar valve (see Figure 1-12 red oval). It can be provided
by Thermo Fisher Scientific on request.

FIGURE 7-20 CC Port (with manual valve)

Antechamber
The antechamber is operated fully manually. This is a part of the Glove box, run the Flushing cycle manually
according to the providers manual.

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Procedures
To operate CC parts mechanisms see descriptions above.
The sample exchange between the Glove box and CleanConnect can be done in two different ways depending on
the input equipment: CC Port or antechamber.

Glove box – CleanConnect Port sample exchange

1. Turn the CC Port lever to the right and remove the plug.
2. Attach the Shuttle with Transfer rod to the CC Port and rotate the Loader lever back to the left.

3. In case the Shuttle is empty (vented by air):

Open the Shuttle valve and start manual flushing (3 cycles recommended) of the CC Port and Shuttle by manual
Ar valve (see figure 1-12).
In case the Shuttle contains a sample (flushed by Ar):
Start manual flushing only of the CC Port by manual Ar valve (see figure 1-12).
After the flushing cycle open the CC Shuttle valve.
4. Open the Loader valve and push the transfer rod with the Sample carrier into the Glove box (see Figure 1-11 the
Loading sequence).
5. Rotate the rod to position the carrier vertically, with the use of the Carrier holder grab the sample carrier and
release it by rotating counterclockwise.
6. Place the Carrier holder to the Glove box, replace/place the sample stub(s) and secure it/them by the allen key.

7. Put the sample carrier back to the transfer rod (proceed step No. 5 vise versa).
8. Pull the transfer rod back to the Shuttle, close the CC Port and Shuttle valves.
9. Remove the Shuttle from the CC Port.
10. Attach the plug.

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 System Options: CleanConnect

Glove box – antechamber sample exchange

1. In case the Shuttle is empty (vented by air), open the Shuttle valve.
In case the Shuttle contains a sample (flushed by Ar), leave the Shuttle valve closed.
2. Open the outer antechamber door and place the CC Shuttle into; close the outer antechamber door.

3. Run the manual flushing procedure of the antechamber (3 cycles recommended) not to destroy the inert
atmosphere inside the Glove box (see a Glove box manual).
4. Open the inner antechamber door and place the Shuttle into the Glove box; close the inner antechamber door.

5. Attach the short Transfer rod to the Shuttle.

6. Join the rod tip by the rod lever (see Figure 1-10). Open the Loader valve and push the transfer rod with the
Sample carrier into the Glove box (see Figure 1-11 the Loading sequence).
7. Replace/place the sample stub(s) and secure it/them by the allen key.

8. Pull the Transfer rod back into the Shuttle, close the valve and unlock the rod lever.
9. Release the clamp and remove the Transfer rod from the Shuttle.
10. To unload the Shuttle from the Glove box proceed steps 3. (only in case the antechamber was opened to air
environment) and 4 (in the said order).
11. Open the outer antechamber door and remove the CC Shuttle; close the outer antechamber door.

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Microscope chamber – CleanConnect sample exchange

The Stage adapter must be mounted to the stage (see the Apreo 2 User manual) and selected within the Sample
Exchange dialog / Holder list / CleanConnect Pre-tilted Holder.
1. Turn the Loader lever clockwise and remove the plug.
2. Attach the Shuttle with the Transfer rod to the Loader and rotate the Loader lever counterclockwise (see the
Glove box – CleanConnect Port sample exchange procedure Step 2.).
3. Click the Sample Exchange dialog / CleanConnect Loader area / Pump button, or press the CC Loader P button.
The Flushing cycle starts according to the Preferences / CleanConnect settings (see Chapter 3). The Loader is
vented with Ar / inert gas.

4. After the Flushing cycle finishes the confirmation message appears; open the Shuttle valve and click the OK
button, or press the CC Connect P button within 30 s countdown.
The CC Loader and Shuttle are pumped down.
5. Join the rod tip by the rod lever (see Figure 1-10). Open the Loader valve and push the transfer rod into the
microscope chamber (see Figure 1-11 the Loading sequence). The sample carrier is attached to the Stage adapter
(visible in the microscope UI CCD display).

6. Pull the Transfer rod out from the chamber and close the Loader valve.
7. Click the Vent button or press the V Loader button to vent the Shuttle with inert gas, or leave it under vacuum.
8. Close the Shuttle valve.
Unloading from microscope chamber
1. Run the Loading procedure steps 1.–4.
2. Open the Loader valve and push the Transfer rod into the microscope chamber (see figure 1-11 the Unloading
sequence). The sample carrier is attached to the Transfer rod (visible in the microscope UI CCD display).
3. Run the Loading procedure steps 6.–8.
4. Transfer the sample under inert gas or vacuum back to the Glove box following procedure as described above.

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 System Options: CleanConnect

Manual Loader Alignment

In case the Sample carrier does not attach to the Stage adapter correctly, run following alignment procedure; follow
the instructions within the module.

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 System Options: MAPS Mineralogy

MAPS Mineralogy

Mineralogy workflow is described within the MAPS User manual.

To work with this workflow, the dedicated sample holder must be selected in the Sample Exchange dialog and
installed on the stage. Stage movements are then restricted to protect a collision of the holder with any in-chamber
component.
Caution!
Mineralogy holders are higher than Multipurpose holder, so users must take care to lower the stage sufficiently during its
installation not to hit the final lens pole when closing the chamber door.
When any mineralogy holder is installed, it is forbidden to use the final lens PLA and LM GAD!
When EBSD (ColorSEM) and/or any 3rd party equipment is used users are responsible for not hitting any in-chamber
component.

FIGURE 7-21: Mineralogy holders 16 × 25 / 10 × 30

When mineralogy holder is used and the X-axis coordinate is >39 mm, the rotation is limited to a few degrees;
when rotating more, Touch alarm is activated. When the stage is rotated, it is not possible to reach entire stage
area (diagonal corners).

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 System Options: μHeater

µHeater

The µHeater is used to control the sample temperature from 40 °C to 1 200 °C (under recommended chamber
pressure 400 Pa) while observing a sample with the use of the Thermo Scientific electron microscope.
WAR NI N G!
Venting the microscope chamber switches off the heating, but it is possible to operate the stage with limited
temperatures even when vented.
Be aware of the thermal hazard. Refer to the User safety manual for the details.
When operating the Heating stage, please be aware that neighbouring surfaces can become hot; stage temperature is
displayed in the Temperature Stage module /Temperature tab / Actual Temperature item.
Caution!
For the correct initialization of the temperature stage, the xT microscope Server must be fully started when connecting
the cable connectors to the corresponding feed-through plate connectors.
The µHeater consists of the following parts:
• µHeater assembly (Base, Multi-sample holder, µHeater Holder, µHeater Chip)
• Chamber feed-through plate
• MEMSC (Micro Electro Measuring System Controller)

FIGURE 7-22 Multi-Sample holder / µHeater Holder (top view) / µHeater Holder installed

FIGURE 7-23 µHeater Holder EBSD extender

This option is used with the EBSD system enabling component analysis of heated samples.

Caution!
In case the EBSD extender is installed on the Multi-Sample holder at the µHeater or Horizontal position, the STEM
detector must not be inserted! See the Inserting and retracting the STEM detector above.

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µHeater consumables

FIGURE 7-24 µHeater chips package (10 pcs.) / data sheet

µHeater installation

Caution!
Use dust free gloves when manipulating with µHeater and within the microscope chamber!

µHeater Base installation

1. Install and fix the cable lock (1 – 1 screw) and plastic dovetail with a cutout (2 – 2 screws) on the stage (if it is not
there). Position the cable according to the picture and secure the lock.
2. Install the 6 mm thick washer (3) on the stage so its bottom pins fit the dedicated stage holes. This is necessary
to not collide with the STEM, DBS and CLD detectors!
Step 1. Step 2.
2 3
1

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3. Install the µHeater Base so its bottom pins fit the dedicated washer holes and also the plastic dovetail, and
tighten it by the screw in the middle of the Base together with the washer.
4. Rotate the top gray part of the µHeater Base to be positioned as depicted on the figure.
Step 3. Step 4.

5. Put the Multi-Sample holder (with the µHeater holder connected) on the µHeater Base so the two differently wide
dovetails fit. Tighten it by the allen key.

6. Connect the µHeater connector to the chamber feed-through placed inside the chamber at the rear side.
7. Let the cable on the chamber bottom so it does not obstruct the stage movements.

To remove the µHeater proceed in the reverse order – remove also the plastic dovetail with a cutout and the cable
lock. The µHeater Base can be left connected on the chamber bottom, but be aware of securing it and its cable not
to obstruct stage movements!

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µHeater Chip installation

To install the µHeater Chip into the Holder use the µHeater Test tool.

FIGURE 7-25 µHeater Test tool

1. Press the black button on the µHeater Test tool; the Bat OK diode lights.
If the diode does not light, exchange batteries.
2. Place the µHeater with the Chip shutter (placed at the bottom of the µHeater holder) opened.
3. Insert the µHeater holder to the Test tool; if the contacts fits, the Holder diode lights.
steps 1. & 2. step 3.

4. Put the µHeater Chip to the µHeater Holder so the contacts on the chip meets contacts on the Holder.
5. Secure the latch by the tweezers; if the Chip is alright, the Chip diode lights.
step 4. step 5.

6. Insert the µHeater Holder into dedicated position of Multi-Sample holder (see Figure 7-30 above).

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Sample exchange

Caution!
Do not heat samples like powders and materials producing fume and/or vapour! This can damage detectors inside the
electron column.

Software control
The µHeater is software controlled using the xT Microscope Control software / Temperature page (added when
µHeater is installed) / Temperature Stage module. If the stage is installed and detected, the type is indicated at the
top of the module and controls are available.

Calibration
When a µHeater Chip is replaced (or after xT Microscope Server
restart), click the Temperature tab > Manual Control > Calibrate
button to open the µHeater Calibration dialog for editing Chip
parameters, that are enclosed in the µHeater Chip package.
After completing the Calibrate button changes to the On button; to
repeat the calibration process at any time, use the Advanced tab >
Calibrate button.
• Identifier – Chip serial number
• R0 – Room Resistance
• TCR – Temperature Coefficient of Resistance
• Description – user chip description
It is possible to store parameters for several chips. To maintain
data, use the Add, Update, Remove, Remove All buttons.

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Temperature tab
The Manual Control is available when no Temperature Profile is
running.
• Clicking the Manual Control > On button activates (highlighted in
yellow) / deactivates (grey background) the temperature stage
software control; a confirmation dialog appears.

• The Actual Temperature shows temperature measured by the

temperature stage hardware (the same value is used in the
databar). The arrow can point up / down / horizontally (double
arrow) to point up the temperature rise / descent / constancy.
• The Target Temperature edit box sets the target temperature.
• The Ramping Speed sets the speed of the temperature change.
• Clicking the Set button starts to proceed to the target temperature. Clicking it during the temperature ramp
stops ramping and holds the actual temperature; clicking it again continues to ramp the temperature.
The Temperature Profile edit boxes are used to define a temperature profile. Edits are active when the profile is not
running. Each point (row) pertains to a single heating cycle; it is highlighted when the Profile is running.
• Profiles are possible to Import from / Export to a file (.trp) by clicking an appropriate button.
Note
Exported temperature values are represented in K.
• Time – schedule column is calculated automatically according to values entered.
• Temp. – target temperature
• Ramp – speed of a temperature increase / decrease
• Soak time – specifies time [seconds] for how long the target temperature should be held after it is reached
Note
Edited values are checked for limits, values out of limits are not accepted.
By right-clicking above any point the menu appears enabling to Insert point / Delete
point / Delete all points.
• Clicking the Start Profile / Stop Profile button starts (highlighted in yellow) / stops
the Temperature profile. The profile starts with step one.
• Clicking the Hold button (highlighted in yellow) stops cycle and holds actual
temperature. Clicking it again continues running the profile.
• Clicking the Next button bypasses an actual cycle and continues with next one. The button is disabled when the
Hold button is active.
• Ticking the Repeat profile check box causes the profile to start again and again from the beginning when it is
finished.
Caution!
When the Temperature profile ends, the heating keeps on (last temperature), until stopped manually.

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Advanced tab
The Advanced tab shows Actual Temperature of the µHeater and the
heater Power.
• By ticking the Direct Output Control check box the heating power
starts to be controlled by the Output Power slider; a user can
apply desired percentage of power directly to the heater.
This functionality is useful when sample temperature should be
monitored precisely, for example during a phase transition like
quenching or melting.
• The Sample Bias slider applies potential from -40 V to +40 V to a
sample.
Potential is applied to contact pads on the chip, to which the
sample needs to be connected (for example by means of the GIS
deposition).
• Ticking the Sample resistance measurement check box shows the
Sample Resistance value calculated from the measurement on the
chip contact pads. Resistance ranges from 1 mOhm to 1 kOhm
(from 10% to <1% rel. error).
• Clicking the Calibrate button enables to repeat the µHeater
Calibration process.

Graph tab
It is possible to graph running temperature, power and/or sample
resistance profiles.
Clicking the Set Up Recording button opens the dialogue with
selections of desired data and parameters to be recorded:
• Actual Temperature and/or Power values to be plotted
with period set
• Sample Resistance value to be plotted with period set
• Stop data recording after elapsing of set time period
• File path template – storage of the saved plots .

Clicking the Record Data button starts graph recording.

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Right-clicking above the graph area shows the graph Settings

context menu:
• Plot mode > Auto-Scale: the minimum and maximum of both axes
are computed automatically so that the graph is completely
visible. As points are added the graph may rescale to achieve
this.
• Plot Mode > Auto-Pan: the graph is recorded within the interval
set in the Graph time span.
• Ticking the Plot Temperature / Plot Power check box plots the
temperature / heater power within the graph.
Clicking the black rectangle next to the Graph tab header enlarges
the graph in separate window. The control buttons within the large
graph window at the bottom left have the functionality:
• Zoom In / Zoom Out enlarges / reduces graph scale;
• Pan mode enables to scroll around in the enlarged graph;
• Reset returns the zoom and pan to default;
• Explore data point on Each plot is used to browse and to explore data points on each plot.
A tool tip is given when leaving the mouse cursor above the button.

Clicking the Save Graph button opens the Save dialog to save the graph to file (.bmp format).

High vacuum heating stage

The High vacuum HS is used to control sample temperature from 40 °C to 1 100 °C while observing a sample with
the use of the Thermo Scientific electron microscope.
WAR N IN G!
Venting the microscope chamber switches off the heating, but it is possible to operate the stage with limited
temperatures even when vented.
Be aware of the thermal hazard. Refer to the User safety manual for the details.
When operating the Heating stage, please be aware that neighbouring surfaces can become hot; stage temperature is
displayed in the Temperature Stage module /Temperature tab / Actual Temperature item.
Caution!
For the correct initialization of the temperature stage, the xT microscope Server must be fully started when connecting
the cable connectors to the corresponding feed-through plate connectors.

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Be aware of the limitation! The presence of water hoses and cables inside the chamber causes a risk of High vacuum HS,
and further the vacuum system damage (when hoses were pulled out of the stage and water is spilled into the vacuum
port on the chamber bottom). Once the High vacuum HS assembly is installed, it should be moved only by ±10 mm in X- /
Y-axis direction from the home position. Rotation and Tilting are locked automatically. Tilt can be released by a user in
the Stage module / Coordinates tab / Tilt check box (see Chapter 5).
The Heating stage consists of the following parts:
• High vacuum HS assembly
• Chamber feed-through plate
• PHSC (Peltier & Heating Stage Controller)
• Water chiller, Flow controller and water hoses
• Heat shields

FIGURE 7-26 High vacuum heating stage system block diagram

The HS assembly is mounted onto the microscope stage using the mounting adapter (see below). It is provided
with 2 Heat shields (see below).

FIGURE 7-27 High vacuum heating stage case / Accessories case

FIGURE 7-28 High vacuum heating stage / Installed

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PHSC (Peltier & Heating Stage Controller)

This microprocessor-controlled board provides accurate and stable automatic temperature control of the cooling
and heating stages and interfaces with the xT microscope Control software.
The temperature measurement accuracy is determined by the thermistor and the controller. Additionally, accuracy
of a temperatures readout depends on sample conductivity, thickness, shape and general thermoelectric
properties that vary by sample and mounting method.
Temperature measurement
• HS sensor accuracy: ±1 °C
• HS normal operating range / limit temperature: up to 1 100 °C
This board provides voltages used for the following features:
• A heat shield bias voltage (0–300 V) draws the electrons from the sample through a small opening in the heat
shield.
Note:
The safety interlock causes the bias voltages to switch off whenever the specimen chamber is vented; however make sure
the supply is turned off before changing any connection.

Chamber feed-through plate

provides feed-through connectors for the temperature stage cables and water hoses.

FIGURE 7-29 Chamber feed-through inside / outside connection

Power connector

Water hoses flanges

Stage connector

Water chiller
An external chiller is provided to efficiently remove excess heat from the temperature stage. See the Chapter
Maintenance for the control and troubleshooting.

WAR N IN G!
The temperature stage Water chiller is powered directly by the individual power cord. The hazardous voltages may be
present even when the microscope power plug is disconnected!

FIGURE 7-30 Water chiller

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Flow controller
The Flow controller is installed between the Water chiller and the chamber feed-through plate. It monitors a water
flow via a sensor on each line and closes both solenoid valves if a failure is detected to protect the system against a
water leak into the chamber.
Note:
It is important to keep the Water chiller away from the microscope console to prevent vibrations.

FIGURE 7-31 Flow controller

Heat shields
This temperature barrier protects the HS neighbourhood from overheating and/or burning. The black Heat shield
has larger opening and it is used together with the EBSD detector. The metallic Heat shield has small circular
opening. The Heat shield sits on the HS assembly top and it creates an “oven” effect helping to keep the
temperature consistent throughout the sample.

FIGURE 7-32 EBSD heat shield / Top-down imaging heat shield

High vacuum HS installation

1. Remove an actual (if any) sample holder adapter.
2. Install the mount adapter included onto the stage rotation base (if it is not in place).
3. Set stage coordinates (Installation position): X = Y = 0; R = 108°; T = 0; Z ≤ 45 mm (after venting the chamber
the stage is unlinked). When the HVHS cables are connected, confirmation dialog appears to move the stage to
the Installation position automatically. After confirmation, new coordination system is set (R becomes 0°).
4. Put the HS module onto the mounting adapter; the stage has the cutout which ensures the sample is centred
beneath the beam.
Note:
Water hoses must be oriented towards the chamber back always.

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5. Tighten the securing screw on the HS assembly side.

FIGURE 7-33 High vacuum heating stage: Mounting adapter / Securing screw

6. Connect the cable connectors to the corresponding inside feed-through plate connectors; also plug the water
hoses (see above).
Note
Be aware the stage starts to move (after the cable was connected) to the Installation position (if it is not already there).

Flow controller and Water chiller installation and operation

1. Check that the water dam is fitted into the HiVac port in the chamber bottom.
2. Put the Flow controller between the chiller and the feed-through plate. The larger hose should connect from the
Water chiller Outlet to the Flow controller input marked From Chiller. The water flow path should make a loop
between the chiller, through the water flow controller and stage, then back.
3. Plug the water flow controller power cable but leave the power switched off. (The other end of this cable goes to
the +24 V power supply inside the microscope console. This should have been connected by a service).
4. Turn on the Water chiller. Water does not flow at this point, since the valves in the Flow controller are closed
when it is off.
5. Turn on power to the Flow controller. An alarm sounds, indicating that there is no flow through the box.
6. Press and hold the Start Flow button down until all the air is out of the water lines (this can be seen as water
flows through them). Thereafter release the button.
7. Make sure that the Flow OK light on the Flow controller is on. This indicates that water flow is working; i.e. that
there are no leaks in the system. The light remains illuminated until there is a leak, or if the Stop Flow button is
pressed, which could be done at any time to close the valves and shut off the water flow, for whatever reason,
which is indicated by an alarm sound. The Start Flow button must be pressed and held again to re-establish flow
through the system.
Caution!
Never pump the specimen chamber without checking for water leaks first.

Sample exchange
Move the stage by 10 mm (in the X- or Y-axis direction) from the center position before pumping the chamber to
protect the sample to be blown away.

Caution!
Do not heat samples like powders and materials producing fume and/or vapour! This can damage detectors inside the
electron column.
1. Place the Si wafer on the HS under the sample.
If a sample is placed directly on the HS body, it can be welded on the surface!
2. Cover the wafer by two clips and fix it with the use of the screw tool.
Note
The silicon wafer should be exchanged after each release of clips (re-used Si wafers tend to have bad thermal contact).

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FIGURE 7-34 High vacuum heating stage: Clip securing screw / Alumina foil fixed by clips

Depending on the sample nature:

3. Fix it under the clips too (see figure above),
or
let it on the surface freely,
or
fix it by the fixer (3 pcs. with different opening diameter – see figure below).
4. Place the heat shield to cover the stage heated area and fix it by 2 screws (see figure below – red ovals).

FIGURE 7-35 High vacuum heating stage: Sample fixed by fixer & Heat shield securing screw / Fixers

5. Move the stage by 10 mm (in the X- or Y-axis direction) from the center position before pumping the chamber to
protect the sample to be blown away during venting the microscope chamber.

Software control
The HS is software controlled using the xT Microscope Control software / Temperature page (added when High
vacuum HS is installed) / Temperature Stage module. If the stage is installed and detected, the type is indicated at
the top of the module and controls are available.
Note
Specimen chamber venting is disabled at temperatures above 500°C (configurable by service).

Heat shield selection

When the High vacuum HS is installed, or after the microscope
chamber is vented click the Manual Control / Heat Shield button to
open the Heat Shield Selection dialog. Selecting the Heat shield sets
the highest accessible temperature.
After completing the button changes to On; to repeat the Heat
shield selection at any time, use the Advanced tab > Heat Shield
button (see below).

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CAUTION!
Newer select Heat shield different from the one installed! This can cause a damage to equipment inside the chamber.
The HS can be operated up to temperatures according to the heat
shield used:
• Top-down imaging heat shield: 1 100 °C
• EBSD heat shield: 900 °C
CAUTION!
Selecting the EBSD heat shield disables the Stage menu / Z-tilt Safety
Map; be careful especially when tilting the stage!
• No heat shield: 600 °C

Temperature tab
See the µHeater software control above.

Advanced tab
See the µHeater software control above.
• By ticking the Direct Output Control check box the heating power
starts to be controlled by the Output Power slider; a user can
apply desired power directly to the heater.
This functionality is useful when sample temperature should be
monitored precisely, for example during a phase transition like
quenching or melting.
Note
When using the DBS (ABS / CBS) or CLD detectors (in any vacuum
mode), or any final lens pole is used (see the PLA accessories dialog),
or the chamber is vented, or the cooling water is stopped, the highest
Actual temperature is limited to 200 °C. In this case the Output
Power control is limited.

Caution!
Apply just as many Watts as needed in order not to exceed 50 °C/min
ramp speed, otherwise your heater lifetime shortens. For advanced
users ONLY.
• Sample Bias slider is used for the manual sample bias setting.
• Shield Bias slider is used for the manual heat shield bias setting.

Graph tab
See the µHeater software control above.

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Model difference
• Sample Resistance value can be recorded with period set.

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High Vacuum Heating Stage Limits Setup

Follow the Instructions.
• Maximum Ramp Speed [°C/min] could be set up to 300 K/min
(default value is 50 °C/min).

Caution!
Ramp speeds higher than 50 K/min strongly decreases the heater
lifetime and leads to regulation instability. When operating in higher
temperature ranges, high Ramp Speeds wear the heater much more
out.

High Vacuum Heating Stage Calibration

The HS assembly is factory calibrated by melting the gold sample
(1 064 °C). The calibration sample (Au wire) is a part of accessory.
Other samples with a verified theoretical melting temperature can
also be used.
Each calibration is valid for particular shield used.
Note
Gold already melted does not melt again.
Checking calibration
The assembly calibration typically does not change over the heater
lifetime. However, if greater precision is required in the actual
temperature read-out follow the procedure:
1. Put five small pieces of the gold wire onto the Si wafer (see
Sample exchange above).
2. Pump down the chamber. Obtain the sample image onscreen.
3. Start the High Vacuum Heating Stage Calibration alignment.
Follow the instruction within the individual steps.

By finishing the procedure, the temperature readout is corrected to

match the theoretical value.

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Remote Imaging

The Remote Imaging enables connection to the Microscope PC via a network using the VNC Connect application and
remotely controlling the microscope operation. This application is pre-installed and configured on the Microscope
PC and optionally on the Support PC.
For information how to install this functionality, see Installation Instructions available on the installation CD. For
more details on the remote connection and its possibilities, see VNC documentation available on the installation CD.

Connection to Microscope PC
Follow the steps below to connect to a Microscope PC using DNS or IP address. It is assumed, the VNC Viewer
application is downloaded and installed on the remote PC (see the producer’s web pages).
1. Click the VNC Viewer icon on the desktop to start the application.
2. Clear the Send anonymous usage data to help improve VNC Viewer check box.

3. Type the appropriate Support PC / Microscope PC name or IP address followed by port number:
– :5905 for configuration without optional Support PC
– :5910 for configuration with optional Support PC

4. Press Enter button.

5. Click the Continue button in the Identity check dialog.
6. In the following Authentication dialog, fill in your microscope Username (i.e. Factory, User) and the corresponding
Password and click the OK button.

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The Microscope PC desktop opens in the VNC viewer window. The set connection is stored within the VNC Viewer
as a corresponding icon for a next time selection.

To close the remote connection to the Microscope PC, just close the VNC Viewer window.
Note
If the VNC viewer reports an error message instead of opening the remote Desktop, check that the VNC Server is running
on the Microscope PC, and the SharedData folder is accessible from the Microscope PC.

Microscope PC’s desktop sharing

Several users can connect to the Microscope PC at the same time and thus share its desktop on the remote PC's.
This can be used e.g. for educational purposes. The typical scenario is that a dedicated user controls the
microscope (locally or remotely): the other connected users can only view the Microscope PC's screen over the
network.
1. Open the VNC Viewer application on the remote PC of the person who is to control the microscope and connect
remotely to the Microscope PC as a user.
2. Other users will then open the VNC Viewer application on their remote PC's and connect remotely as 'view-only'
users.
Note
Desktop sharing must be enabled in the VNC Server application on the Microscope PC. For instructions on how to do so, see
the VNC Server documentation available on the installation CD.

Controlling microscope remotely

When connecting remotely, be aware of the fact that there might be another person operating the microscope
locally, i.e. working directly with the Microscope PC.
After connecting remotely to the Microscope PC, you can do all the tasks as if you were working directly with that
computer. It is possible to control microscope operation, run the supportive applications, backup or restore user
data, view log files, etc.
In general, expect slower response to your commands and actions. This limitation comes from the amount of data
that has to be transmitted and from the network bandwidth, especially for network speeds below 10 Mbps.
In case the Microscope Control user interface stops responding or the Server Busy dialog appears, the Microscope
PC is probably overloaded and may have problems with the actual conditions being operated remotely. If such a
problem occurs, wait until the Microscope PC recovers, or restart it, if necessary.
Here are some recommendations for remote control operation:
• To obtain better remote performance, try to use the View menu / Remote Mode item (see Chapter 3).
• Be very careful when navigating the stage. Always keep in mind that because of delays in imaging data transmission,
what you see in the optical display is not the exact position of the stage.
• You can improve the performance / response time by setting the more convenient scanning conditions: the
quad image instead of the single image mode, single live display instead of more live displays; lower resolution
and slower scan (i.e. higher dwell time).
• Benefit from the automatic functions that are not affected by the delayed response problem (Auto Contrast
Brightness, Auto Focus, Auto Stigmator). In case you prefer to focus or correct astigmatism manually, it is better
to do so in a reduced area.

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Quick Loader

The Quick Loader was designed for:

• Easy Sample transfer
• Faster sample through-put
• Contamination free chamber environment
• Materials applications
Caution!
Minimize Quick Loader usage with the CryoCleaner (see further)
filled with LN2!
We strongly recommend venting the specimen chamber and
replacing the Nitrogen Vessel with a clean one after completing
about 20 subsequent Load cycles with the cool CryoCleaner!
This is because each Load cycle adds a small layer of gas and ice
onto the Nitrogen Vessel surface, decreasing the CryoCleaner’s
efficiency and increasing the amount of gas released into the
specimen chamber in case the LN2 dries out.

Description
The loader module can manually load and unload small samples into the SDB / SEM. The loader module is
connected to the specimen chamber of the SDB / SEM and it has its own pumping system.

The loader consists of a loading rod with set slide and parking positions and a loader chamber for loading and
unloading the sample carrier (with sample) onto a bayonet fitting located at the end of the rod. A gate valve seals
the vacuum of the SDB / SEM specimen chamber and can only be opened when the vacuum of the loader chamber
is correct. This is indicated by the OK labeled LED, which is prompted by an electrical and mechanical interlock.
The sample carrier can be entered into the main SDB / SEM specimen chamber by way of the rod and released by
the rotating motion of the rod at a predetermined position on the stage adapter.

Loading Rod
The loading rod has a pre-machined slot to move in to load or
unload a sample. At each end there is a side slot. There are 2 side
slots at the further end from the vacuum chamber. One is for
loading and unloading the sample carrier in the loader chamber;
the other is a parking position (prevents the rod from being sucked
in by the vacuum).
Caution!
Do not unload the sample carrier with the gate valve opened! The sample carrier can drop down from the rod.
At the end of the rod closest to the loader chamber is a large slot for coupling and de-coupling the bayonet into or
out of the sample carrier when positioned on the carrier adapter.
The bayonet is designed to make a positive and secure connection to the sample carrier so that it remains
horizontal and in a straight line to connect with the carrier adapter within the specimen chamber.

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Gate Valve
The Gate Valve has positions that are defined by the following statuses:
• rotated position of the Gate Valve Lever – LOCK / UNLOCK
The position has to be turned from LOCK to UNLOCK to be able to move the loading rod IN and OUT
• colored strips on the side of the exposed barrel axis – one / two when IN / OUT

• Position 1 - IN and LOCK

• Position 2 - IN and UNLOCK
• Position 3 - OUT and UNLOCK
• Position 4 - OUT and LOCK (prevents vacuum closing valve).
The Gate Valve has two safety movements.
• it can be placed over the entry hole on the slide
• it can be locked in place by a turn of the connecting knob (securing the closure of the valve)
A system interlock takes care of correct conditions (system vacuum, accelerating voltage) for loading and unloading
cycles (movement of the gate valve).

Controls
There are 2 buttons (illuminated while in operation) and 1 indicator lamp:
• P (pump) labeled button – press it to pump the loader chamber to the required vacuum; the stage moves to a
loading position at the same time. If the system reaches the appropriate vacuum level, the lever interlock is
released and the gate valve can be opened. The pump cycle is automatically terminated when the required
vacuum is reached.
• V (vent) labeled button – press it once to vent the loader chamber. The vent cycle continues untill the P button is
pressed or it is terminated by a time-out.
• OK labeled indicator lamp – lights up when vacuum is reached after pumping. When it goes out, this means the
wait time has been exceeded and the appropriate vacuum for a transfer has been lost. Pressing the P button
again will bring the system to vacuum OK status.
The control buttons do not shine when the system is recovering from vacuum status transition (e.g. immediately
after the load/unload sample, during venting the chamber…). After finishing the state transition, the control
buttons will again be in operation.

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Sample Carrier and Stage Adapter

A sample carrier (2 pcs.) is used to hold and transport the sample from the loader to the specimen stage of the
SDB / SEM. The carrier sits in the stage adapter with a dovetail joint. It is fixed to the loading rod via a bayonet
coupling. The loading rod is de-coupled at the bayonet coupling when the sample carrier is located in the adapter
and withdrawn, leaving the sample carrier ready for sample observation.
The Stage Adapter is connected to the rotation base of the stage by 3 hexagonal headed screws. The base of the
adapter has 3 high points for a firm 3-point contact to the rotation base to prevent vibration transmission.
The height of the stage adapter is distinct to the SDB /SEM system it is used with. The top of the adapter has a
dovetail slot for the acceptance of the sample carrier from the rod loading mechanism.

FIGURE 7-36: Sample Carrier / Stage Adapter

Sample Gauge
Before mounting the Stage Adapter, the stage must be homed with
the chamber door opened.
Only samples that fit the Sample Gauge can be loaded. One sample
stub with a diameter up to 32 mm (1 1/4") can be used, although
standard sizes of 25 mm and 12.5 mm can also be used. Height
can be no greater than 9 mm.
The shuttle clamps with a spring in the dovetail shaped slot of the
adapter. It is fixed to the loader arm via a bayonet coupling. The
maximum pin length of the stubs that can be used is 11 mm (most
common commercial type stubs have a pin length no greater than
8 mm).

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 System Options: Quick Loader

Installation
The Quick Loader is pre-installed in the factory. No special adjustment is needed only the loading rod is not
installed for transport.
1. Unpack the lead glass lid.
2. Remove four screws holding the cover of the loading rod feedthrough.
3. Use the same screws to attach the loading rod to the loader chamber.

Loading position
The load / unload position is factory preset. If calibration is needed, run the Quick Loader Alignments first.

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 System Options: Quick Loader

Operations

Loading a sample
1. Mount the sample with fast drying adhesive medium onto the stub. Allow to dry.
2. Check the sample satisfies the sample limits imposed by placing the top of the mounting tool over the base
mount.
Caution!
If the sample proves to be too large, this has to be addressed before the sample and carrier are allowed into the loader
chamber.
3. If the sample satisfies the limits, the sample-loaded carrier can be loaded into the loader chamber. A user can
either remove from or place a mounted carrier in the loader chamber by using tweezers for stubs that will fit around
the stub rim.
Note
Loading samples this way is easier and safer than trying to mount the sample directly into the sample carrier while it is in
the loader chamber.

Rod Loading Sequence

1. While holding the sample carrier on the loading table in the
loader chamber, move the rod out of the Parking position to
the far left, to the back of the slot, and forward to engage the
bayonet into the sample carrier. Place the rod back into the
Parking position after coupling to prevent the rod from slowly
creeping forwards.
2. Switch off the electron beam accelerating voltage. Retract the
GIS modules and STEM detector (if present) to a safe state
(cannot be used in combination with the loader).
3. Close the loader chamber lid. After the lid is properly closed
the P button starts to shine.
4. Press the P button. The button stops shining and the pumping
cycle starts. The stage moves to the loading position at the
same time. When the vacuum in the loader chamber is correct,
the pump light starts to shine and the OK button lights up,
indicating operation can continue. The gate valve lever interlock
is released.
5. Turn the Gate Valve knob lever from LOCK to UNLOCK position.
Then carefully pull the knob bar fully out from the first mark on
the knob drum to the second mark. Turn the knob bar
counterclockwise to the LOCK position.
6. Move the loading rod from the Parking position into the chamber
while still holding the rod bar. The Sample Carrier will engage
with the Stage Adapter at the end of the rod travel.
7. Turn the rod bar to the left (counterclockwise) to the base of
the slot. Pull back on the rod bar so it travels along the base of
the slot, then turn it to the right (clockwise) so that the rod bar
is vertical, and withdraw it back to the PARK slot at the far end
of the rod guide.
8. Close the Gate Valve by turning the knob bar to the UNLOCK
position and press the knob in to engage the valve over the
opening. This can be seen through the lead glass lid. Then turn the knob bar to the LOCK position to secure the
valve. Good practice is to leave the loader chamber under vacuum.

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 System Options: UMB Stub Holder Kit

Unloading a sample
1. If there is a sample carrier in the loader chamber attached to the bayonet, remove it (the chamber needs to be
vented and the carrier removed).
2. Switch off the electron beam accelerating voltage. Retract the GIS modules or STEM detector (if present) to a
safe state (cannot be used in combination with the loader).
3. Close the loader chamber lid. After the lid is properly closed, the P button starts to shine.
4. Press the P button. The button stops shining and the pumping cycle starts. The stage moves to the loading
position at the same time. When the vacuum in the loader chamber is correct, the pump light starts to shine and
the OK button lights up, indicating operation can continue. The gate valve lever interlock is released.
5. Turn the Gate Valve knob lever from the LOCK to the UNLOCK position. Then carefully pull the knob bar fully out
from the first mark on the knob drum to the second mark. Turn the knob bar counterclockwise to the LOCK position.
6. Move the unloading rod from the Parking position into the chamber while still holding the rod bar. When
resistance is found, turn the rod bar to the left (counterclockwise) to enter the bayonet. Push forward and turn
the rod to the right (clockwise. The bayonet will engage with the Sample Carrier on the Stage Adapter close to
the end of the rod travel.
7. Withdraw the rod back to the far end of the rod guide and place it in the Parking position. The rod, bayonet and
sample carrier are now out of the specimen chamber and sit in the Loader chamber.
8. Close the Gate Valve by turning the knob bar to the UNLOCK position. Press the knob in to engage the valve over
the opening. This can be seen through the lead glass lid. Then turn the knob bar to the LOCK position to secure
the valve.
9. Press the V button once. The loader chamber will be vented and the lid can be opened. The sample carrier can
be released by turning the rod bar to the far left and pulled back, then returned to the parking position. Remove
the sample carrier.
10. Close the loader chamber lid.
11. Press the P button to evacuate the loader chamber.
Note
In case the sample carrier falls from the loading rod, vent the specimen / loader chamber with gate valve opened, put the
carrier back to its correct position, and close the gate valve. Proceed from step 1.

UMB Stub Holder Kit

This option contains the following items:

• Universal mounting base (UMB)
• Storage box
• 2 stub modules each holding 3× 1/2” stubs or 2× 1” stubs
• 2 clamp bars
• User guide
• System calibration sample
The stub holder is mounted on the stage interface plate.

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 System Options: CryoCleanerEC

CryoCleanerEC

This equipment allows decreased contamination levels in the

system. The CryoCleanerEC can be efficient to approximately 24
hours (CryoCleaner – older version – has silver plated Dewar
vessel and can be efficient to about 10 hours).
WA R N I N G !
This option uses liquid Nitrogen (LN2), which may cause serious cold
burns.

Parts and Accessories

The CryoCleanerEC consists of a Nitrogen vessel that is
surrounded by an outer container, the Vacuum vessel, which is
connected to one of the specimen chamber ports by a vacuum
seal. The space between is then pumped by the microscope
vacuum system.
When the specimen chamber (together with the CryoCleaner) is
pumped, liquid Nitrogen is introduced into the Nitrogen vessel.
Its outside cold surface adsorbs contaminating products from the
specimen chamber. The vacuum in the specimen chamber improves over a short period, and contamination is now
reduced.
The Vacuum vessel has a special flange enabling mounting it to different chamber ports with the use of an interlink
with the desired shape (depending on the port to be used and its vicinity).
The interlink flanges can be mounted by means of the 3 screw-hole fittings on the perimeter of the vacuum flange.
Care must be taken that the 'O' ring held in the end of the flange is secure, free of dirt and is not crimped when
mounting.

FIGURE 7-37: Vacuum Vessel and Nitrogen Vessel with accessories / Flanges

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 System Options: CryoCleanerEC

CryoCleaner Operation
Once mounted, the Nitrogen vessel can be placed in the Vacuum vessel. Secure the two components by fixing the
clips to the top of the Nitrogen vessel and locking the clips down. Take care that the 'O' ring seal on the Vacuum
vessel is secure when joining the two components together.

Dewar Vessel Refilling

WA R N I N G !
The handling of LN2 should be performed wearing face and hand protection in the form of a face visor and a pair of
thermal protective gloves.
Users must not touch the cold surfaces of the Dewar, as this can result in burns. Use the Safety pliers provided when
handling the Nitrogen Vessel.
1. Pump the specimen chamber. The Vacuum vessel is pumped along with it.
2. When the specimen chamber vacuum is ready (Pumped status), partially fill the Dewar, using the funnel (the
plastic cap upside down). Wait until boiling stops.
3. Then fill the Dewar and place the plastic cap at the top of the CryoCleaner. The volume of liquid Nitrogen
needed is approximately 500 ml.
Note
The LN2 stops boiling very quickly so that no vibration is seen from this device. If the CryoCleaner needs to be used for longer
periods, it can be refilled with LN2.
Before re-filling it, vessel baking is recommended.

FIGURE 7-38: Plastic Cap Filling Position / Plastic Cap Operation Position

Removing Nitrogen Vessel

WA R N I N G !
Use the Safety pliers provided when handling the Nitrogen vessel.
Removing the Nitrogen vessel depends on the level of contamination found in the specimen chamber. If the level is
unusually high, then the CryoCleaner can work continuously till improvement is seen. Otherwise, normally after
approximately 2 to 3 hours, the Nitrogen vessel can be removed.
Note
We recommend not leaving it inside the vacuum vessel after all the nitrogen has evaporated, because contamination evaporates
back into the chamber.
If the chamber is vented with the Nitrogen vessel filled with LN2 (or still significantly below the ambient temperature), it
should be removed and baked before it is re-used.
1. Vent the specimen chamber (the excess LN2 starts to boil).

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 System Options: CryoCleanerEC

2. Unclip the Nitrogen vessel from the Vacuum vessel. Lift the
Nitrogen vessel out of the Vacuum vessel by the Safety
pliers placed under the ring on the neck of the Dewar
cylinder.
3. Place the Lid over the Vacuum vessel to seal it from the
atmosphere (fix the clips). Pump the specimen chamber
again. The microscope vacuum remains cleaner than
before, and sample contamination is still reduced.
4. Remove the cap from the Nitrogen vessel and pour out
the excess LN2 into a suitable container.
WA R N I N G !
When the LN2 is removed from the nitrogen vessel, the bottle
still remains at a very low temperature!

Baking Vessel
1. Place the Nitrogen vessel onto the stand ready for baking.
2. Place the vessel stand on a suitable heat-resistant surface.
3. Place the vessel onto it and use an Infra-red lamp to bake the base of the bottle. Baking should take place for
approximately 2 hours.
Alternatively, the vessel can be baked in an oven at 90 °C for 2 hours.
4. Allow the vessel to cool down before handling!
Regenerating the Dewar by heat allows removal of condensed contamination and subsequent reuse of the vessel.
Note
The oven that is used must have a venting system to extract any harmful fumes. Alternatively, it should be baked in a fume
cupboard using an infra-red lamp.

Replacing Vessel
1. Allow the vessel to cool down before handling!
2. Vent the specimen chamber.
3. Unlock two clips holding the Vacuum vessel lid. Remove the lid from the Vacuum vessel.
4. The Nitrogen vessel can be placed in the Vacuum vessel, taking care that the 'O' ring seal on the Vacuum vessel
is secure when joining the two components together. Secure the two components by fixing the clips to the top of
the Nitrogen vessel and locking the clips down.
5. Pump the specimen chamber. The Vacuum vessel is pumped along with the specimen chamber.

Maintenance
• Keep the 'O' rings clean of dust and fiber particles by inspecting the Vacuum vessel main 'O' ring on a regular
basis. If the Vacuum vessel is removed frequently from the specimen chamber, inspect the specimen chamber
'O' ring seal each time.
• Keep the sealing surfaces of the Nitrogen vessel and the Vacuum vessel lid clean and free of dust and fiber
particles.
• Do not use any kind of vacuum grease on the 'O' rings.
• Wipe the outsides of the stainless steel parts to remove fingerprint stains with a lint-free cloth dampened with a
neutral pH soap solution.

Spare Vessel
It is possible to obtain a secondary nitrogen vessel kit, which contains:
• Nitrogen Vessel
• Vessel Stand
• Vessel Plug

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 System Options: Plasma Cleaner

Plasma Cleaner

The Tools menu / Sample Cleaning item starts the Sample Cleaning
procedure, which is an efficient process for removing very thin
contamination layers, that are typically formed by hydrocarbon
residues remaining on vacuum parts after conventional cleaning or that
could have been transferred into the microscope chamber by a sample.
The plasma cleaner generates free oxygen radicals, that react with
hydrocarbon molecules on the surfaces to form CO, CO2, and H2O
molecules that can be pumped away. It is operated at special vacuum
conditions (~50 Pa) similar to the Low Vacuum mode.

FIGURE 7-39: Plasma Cleaner

The Sample Cleaning procedure uses settings from the Plasma Cleaning
Alignment (see Chapter 4).
For avoiding typical “weak” contamination artifacts during high resolution
imaging (image darkening), 1-2 minutes of plasma cleaning in combination
with cryo cleaning should be sufficient. When bulky deposition is visible
(mostly on image corners), 5 minutes of plasma cleaning is recommended.
Note
Porous, biological or hydrocarbon based samples cannot typically be viewed
without the presence of contamination artifacts that are caused by presence
of contamination sources within the sample itself even after plasma cleaning.
Sometimes, poor image quality can also be caused by e-beam etching and
re-deposition of etched material.
Caution!
Using the Plasma Cleaner is not recommended when the VolumeScope
ultramicrotome is mounted inside the microscope chamber!
Remove the VS DBS detector from the chamber (parking position) when the Plasma Cleaner is going to be used!
WA R N I N G !
If the EDS / WDS / EBSD system is mounted, use a 1 mm collimator on the EDS detector and do not exceed 5 minutes
overall procedure duration once a day at most.
Always retract the EDS detector before plasma cleaning!
Avoid leaving sensitive carbon-containing samples (e.g. photo resist) inside the chamber during the Plasma Cleaning
procedure, as they may be etched by the cleaning process.
Any material that can create or release oxide easily (e.g. silver) should not be plasma cleaned.
Only the Au-C resolution tests samples can be left inside the chamber during the Sample Cleaning procedure, but not
very often!

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 System Options: Plasma Cleaner

Sample Cleaning Procedure

1. Move the stage to the lowest Z-axis position and tilt it to zero.
This is to avoid any possible shadowing effect by the column if the sample is at a short working distance.
2. Run the Tools menu / Sample Cleaning procedure.
It is also possible to enter the procedure from the vented state by using the Sample Exchange window. While the
procedure is in progress, stage moves are disabled temporarily.
When the procedure is finished or aborted by a user, the system remains pumped.
3. Move stage back to the observation position.
When starting the procedure, some conditions are not allowed. In these cases,
a dialog or tooltip appears onscreen.
When Plasma Cleaning is started from the LoVac mode, the chamber is partly
pumped to a lower pressure. The user is asked to confirm this action before
Plasma Cleaning is started.
Note
When one is going to observe in LoVac immediately after plasma cleaning with a different gaseous environment, we advise
running the Purging procedure (see Chapter 3). 4

Chamber Cleaning
To periodically clean the whole system (due to build-ups from samples, carriers, service events, etc.), use the
Chamber Cleaning procedure from the Plasma Cleaning Alignment. The clean chamber environment enables an
operator to use the system at a level of cleanliness suitable for high-resolution imaging and analysis.
Caution!
Never use Plasma Cleaner for Chamber Cleaning with CryoCleaner filled with LN2!
WA R N I N G !
Do not exceed 30 minutes of chamber cleaning once a week at most when the DBS detector is installed.

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