3d Doctor PDF
3d Doctor PDF
3D DOCTOR
M.Sandhya1, G.Venkata Prasad2, J.Deepthi3
1
Student, 2Assistant Professor, 3Head of the Department
Computer Science & Engineering, Sphoorthy Engineering College
I. INTRODUCTION Each window has its own set of commands to open and save
3D-DOCTOR is an advanced 3D modelling, image files, edit, and process data associated with the display
processing and measurement software for MRI, CT, PET, window. You can click the left mouse button within a
microscopy, scientific, and industrial imaging applications. window to make it active.
3D-DOCTOR supports both greyscale and color images
stored in DICOM, TIFF, Interfile, GIF, JPEG, PNG, BMP, II. MINIMUM SYSTEM REQUIREMENTS
PGM, MRC, RAW or other image file formats. 3D- Operating Systems: Windows XP, Vista, 7 or newer version.
DOCTOR creates 3D surface models and volume rendering Other operating systems, including Macintosh and Unix, are
from 2D cross-section images in real time on your PC. You not currently supported.
can export the polygonal mesh models to STL (ASCII and CPU: Pentium, Pentium compatible or better
Binary), DXF, IGES, 3DS, OBJ, VRML, PLY, XYZ and RAM: A minimum of 128 MB is required, although 512 MB
other formats for surgical planning, simulation, quantitative or more is highly recommended to provide better
analysis, finite element analysis (FEA) and rapid prototyping performance for processing larger images.
applications. You can calculate 3D volume and make other HARD DISK: 50 MB are needed for the software and
3D measurements for quantitative analysis. 3D-DOCTOR's additional space is needed to store your 3D images.
vector-based tools support easy image data handling, DISPLAY: At least a 16-bit color or better display with
measurement, and analysis. 3D CT/MRI images can be re- OpenGL support. This normally requires setting up your
sliced easily along an arbitrary axis. Multi-modality images Display using the device driver provided by the video board
can be registered to create image fusions. Misaligned slices manufacturer. Use the Start/Settings/Control Panel option or
can be automatically or semi-automatically aligned using 3D- right mouse click on the PC screen and then use the
DOCTOR's image alignment functions. Other image Properties/Settings option to set up or change the display
processing functions include template-based film cropping, settings.
image re-slicing to correct slices of uneven thickness, volume
resizing, and image rotation. The 3DBasic scripting tool Terminology
makes it easy to create Basic-like sophisticated 3D imaging Many imaging terms have been used by 3D-DOCTOR.
programs. 3D-DOCTOR is cleared by FDA (US Food and Some are standard image processing terms and some are 3D-
Drug Administration 510K clearance) for medical imaging DOCTOR specific.
and 3D visualization applications. 3D-DOCTOR’s user
interface is similar to other Windows software programs. The best way to understand the terms and commands is to
You can use the menu items or toolbars to start the work with the software.
processing commands. You can use the keyboard to scroll an 2D Image/Image Slice/Image Plane: A single slice of an
image display window up, down, left, and right, and to rotate image is a 2D image. One slice of a volume image can be
a 3D display to different angles. You can use the mouse to called a 2D image. For example, when you scan a film and
draw a selection rectangle within an image window or save the scanned image to a TIFF or JPEG file, it’s a 2D
perform data editing functions. The right mouse button is image.
used to bring up a floating pop-up menu with available
editing options when in an editing mode. When you open a 2D image (single slice) in 3D-DOCTOR,
you only see the IMAGE PLANE WINDOW that displays
3D-DOCTOR has 5 main types of display windows: the single image and no MONTAGE
Single IMAGE PLANE VIEW to show a single
image slice at a time. WINDOW.
MONTAGE VIEW to display all slices from a 3D 3D Image/Volume Image: A 3D volume image includes a
image. The view can display the slices in a mosaic stack of 2D images. A 3D volume image can be stored in a
form, or a single slice as a side profile or top profile single image file or multiple files where each file contains
view. one image slice or plane. In 3D-DOCTOR, when a 3D image
VOLUME VIEW to display volume rendered is opened, you will see two display windows. The IMAGE
images. PLANE WINDOW shows a single slice with full details, and
SURFACE VIEW to display 3D surface models. the MONTAGE WINDOW shows all of the image slices
PLOT WINDOW to display histograms and within the 3D image. You can simply open the image to see
measurements. if it is properly organized as a 3D image or still a single 2D
slice. In 3D-DOCTOR, the File/New Stack command is used
to put single image slices together to form a 3D image for Region of Interest (ROI): User defined regions of interest
processing and analysis. Calibration: For a 3D image, the (ROI) are used to limit the image areas to be processed by
Voxel size (image resolution) must be provided to 3D- the image segmentation functions. After an image is open,
DOCTOR. This ensures that the 3D rendered image will have ROIs are defined using the Edit/Regions of Interest
the correct scale in all 3-dimensions and result in calibrated command before segmentation is done for an object. ROIs
computation for all the reporting functions. Calibration can be in several shapes or combinations of shapes, such as
parameters for voxel resolution include the size of a pixel in a polygons, circles, and rectangles. ROIs defined using
slice, for example, 1 mm, and the slice thickness. The slice Edit/Regions of Interest apply to all image slices and new
thickness is the sum of the image slice thickness plus the gap ROIs may need to be defined when segmenting other slices.
distance between two neighbour slices. For DICOM images, If you already have a boundary for an object and would like
these parameters are normally provided in the header, but to use the boundary as a temporary ROI for segmenting a
you may need to adjust the slice thickness if not all the slices new object within it, then use the Edit/Regions of
are used. Calibration parameters for voxel values can also be Interest/ROI by Boundaries command to create an ROI from
entered and used by reporting and quantitative analysis the existing object boundaries. The existing object must be
functions when available. Object: In 3D-DOCTOR, an object set as “Current” before you do this.
contains the boundaries and the image pixel data within the Segmentation: Segmentation is an automated image
boundaries. When a boundary is drawn, it always belongs to processing function to extract or generate object boundaries.
the current object. For example, a 3D image of a head can be 3D-DOCTOR has several image segmentation functions. For
separated into multiple objects, including the outline of the example, the 3D Rendering/Interactive Segment function
head, the skull, and the brain. Once boundaries are generated uses the image’s greyscale range to create boundaries. The
for every single object, the boundaries can be used for 3D 3D Rendering/Segment Object function uses a defined
rendering. You can set objects together to create different 3D training area to help detect similar image regions. The
displays by turning them on or off. For example, if half of a segmentation function can process all slices automatically.
head and the brain are selected as objects, an image of an Surface Rendering: Surface rendering creates polygon-based
exposed brain will appear with the half of the head that was 3D surface models from defined object boundaries. It
selected. Objects are defined and updated using the displays the surface model and allows you to change the
Edit/Object Setting command. Boundary/Contour: color and transparency properties of the rendered objects. 3D
Boundaries are contours that define the area of a 3D object in volume and surface area can be accurately calculated from
each slice within a 3D image. Because boundaries are used to these surface models. You can save surface models to 3D
tell which part of the volume image is included in 3D formats such as AutoCAD DXF and IGES. Saving a surface
rendering and quantitative analysis, they are required before model in VRML format allows for use over the Internet by
3D rendering can be done. On each image plane, one object web browsers with the necessary plug-ins. In addition, 3DS
can have any number of boundaries that are not self- format can be used for 3D Studio and STL format can be
intersected or intersected to each other. One boundary can be used for rapid prototyping applications. The WAVE FRONT
contained by another boundary of the same object to form a OBJ and raw surface triangles allow the transfer of data to
hole or island (See Figure on the next page). The polarity rule other software packages.
applies in boundary topology to indicate which part is Volume Rendering: Volume rendering creates a 3D display
included and which part is excluded. For example, when a using both the 3D image and the boundaries. Voxels are ray-
voxel is first contained by a boundary, it is included. The traced to show the image in a 3D space. Volume rendering
second time it is contained by a boundary of the same object, supports several rendering modes, including transparency,
it is outside the object or excluded. The third time it is where voxels are treated as transparent, direct object, where
contained by a boundary of the same object, it is included only surface voxels are displayed, and maximum density,
again. Boundaries can be generated automatically using the where only the brightest voxel is displayed along each ray.
Auto Segment, 3D Rendering/Interactive Segment or the 3D Because volume rendering creates each view by ray-tracing
Rendering/Segment Object command. You can manually the entire volume, it may take a longer amount of time to
define or update boundaries using the Edit/Boundary Editor rotate when you have a larger image. For 3D volume
command. Boundary data can also be imported from other rendering, you can save the data to a XYZ file, where each
digitizing devices and ASCII files. voxel location is recorded as a point.
3DS for 3D Studio, and WAVE FRONT OBJ and raw generated easily using the Boundary Report function for
triangle objects to transfer 3D surface model to other quantitative analysis.
programs. 3D volume rendering data can be saved as volume, Editors for Image, Point Markers, and Annotation : The
or as 3D XYZ format. The 3D XYZ format is compatible Image Editor allows pixel value editing, displaying, and
with many commercial 3D quantitative analysis and mapping to other values. Point markers are used to mark
simulation programs. locations in a 3D image and are controlled using the Point
Process Most Image Types: 3D-DOCTOR can process 8-bit Editor. Annotations are easily created using the Annotation
and 16-bit gray scale images, 8-bit and 24-bit color images, Editor.
and 1-bit black and white images. Image type conversion Image Measurements: Area, surface area, volume, distance,
functions are provided to change image types. For example, profile, and an image region histogram can all be calculated
converting a 24-bit RGB color image to greyscale, or in 3D-DOCTOR. With the Measuring Tool, you can quickly
converting a 16-bit greyscale image to an 8-bit gray scale measure the length, area of a region, image density in a
image reduces the size of the image. region, and view the pixel histogram.
Template Based Film Cropping: If your CT or MRI images 3D Image Re slicing: With a single command, you can re
come on film, then you can scan them using a film scanner or slice a 3D image along the X-axis, Y-axis, or an arbitrary
a regular image scanner with a transparency kit for 3D axis defined by a 3D angle. Re-sliced images allow you to
processing. 3D-DOCTOR’s template based Image/Crop make more accurate measurement or examination of certain
Image/Crop Film command can be used to crop image slices, objects that have different orientations.
and save them to image files automatically. 3D Image Registration, Auto Alignment, and Fusion: Easily
Powerful Display Functions: A 3D image is displayed in both register two images that are related by specifying 4 or more
an IMAGE PLANE WINDOW to show full details of a control points in 3D-DOCTOR. Once a pair of images are
single image plane/slice and a MONTAGE WINDOW where registered, you can create an image fusion by combining the
all image planes are displayed as thumbnail size panes to two images in any of the methods supported, including add
allow easy navigation between slices. The 3D volume (+), subtract (-), And, OR, transparent, Max, Min, etc. If you
rendering and 3D surface rendering allows you to see the have two images from a single source, for example, a CT
image in 3D.By using move creation function, all display image and an MRI image for the same patient, using the
windows can be animated and saved to an AVI move file. registration and fusion functions, you can create a brand new
You can switch the image plane display to another slice by image with information you could never visualize before.
double clicking on a pane in the MONTAGE WINDOW. 3D Volume Image Reconstruction: Create parallel cross-
With the palette control functions, you can change the palette section, volume images using x-ray images taken at angles
to pseudo color, red, green or blue. You can adjust the image around the object. This allows you to turn your x-ray
contrast to enhance the image display, or apply log scale or machine into a full CT (Computed Tomography) system
square root scale functions to the image histogram to give using 3D-DOCTOR.
stronger contrast to a certain range of pixel values. In 3D Image Restoration by Deconvolution: 3D-DOCTOR
addition, you can display images with or without pixel provides two highly efficient deconvolution methods for 3D
interpolation. image restoration and reconstruction, a fast nearest
3D Image Segmentation to Generate Object Boundaries: neighbour algorithm and an iterative maximum entropy
Before you create a surface or volume rendering for a 3D algorithm. If you have a 3D image acquired from a device
image, use one of the segmentation commands to extract where the point spread function (PSF) is known, then you
object boundaries. Multiple objects are supported so you can can easily get a restored image with much higher quality
visualize single objects or a combination of many objects in using 3D-DOCTOR's restoration functions.
3D. 3DBasic: Scripting support makes it easy to combine 3D-
3D Surface Rendering to Create 3D Surface Models: From DOCTOR functions for complicated batch mode processing
boundary data, 3D surface models are created using the and software customization. 3DBasic is easy to learn because
surface rendering functions. The display settings such as it uses standard Basic-like syntax and provides full support
color and transparency can be adjusted interactively within for flow control and different types of variables.
the 3D SURFACE WINDOW using the View/Object
command. You can export the models to formats such as User Interface
DXF, IGES, STL, VRML, and 3DS. 3D volume and surface 3D-DOCTOR software has a similar user interface as other
area can be calculated from the surface rendered models. Windows programs. It includes several types of windows to
3D Volume Rendering: The ray-tracing based volume display a 2D image plane (IMAGE PLANE WINDOW), 2D
rendering provides several display modes: opaque or image panes organized as a montage (MONTAGE
transparent voxels in color or greyscale. WINDOW), 3D volume images (VOLUME VIEW
Boundary Data Editing and Processing: You can define or WINDOW), 3D surface images (3D SURFACE WINDOW),
update object boundaries using the Boundary Editor. and 1D curves in a PLOT WINDOW. 3D-DOCTOR uses
Boundaries can be processed using functions under the menu bars, tool buttons, floating pop-up menus, a mouse,
Edit/Boundary Process sub menu, such as smooth, split and keyboard commands to interact between the user and the
object, delete by length, delete by image planes, and other software. The on-line help provides information on
functions. A detailed report for boundary data can be commands and options implemented in 3D-DOCTOR. The
menu options can be selected with either a mouse or with All functions under the View menu can be used to control
keyboard shortcuts. the display of the IMAGE PLANE WINDOW, including
zoom in, zoom out, pseudo color palette selection, image
IV. IMAGE PLANE WINDOW AND MONTAGE contrast adjustment, interpolation mode, and histogram
WINDOW enhancement.
A 3D image consists of a number of 2D image planes or When the IMAGE PLANE WINDOW is in the zooming
slices. When a 3D image is opened by 3D-DOCTOR, two mode (scroll bars will be displayed), the ARROW KEYS,
display windows are created: the IMAGE PLANE WINDOW PAGE UP and PAGE DOWN, HOME, and END keys can
and the MONTAGE WINDOW. If the image is initially be used to scroll the image. To zoom into a specific image
displayed only in the IMAGE PLANE WINDOW, it region, you can hold down the left mouse button and drag it
indicates the image has only a single slice and you may need to draw a select rectangle and then press the F2 key to zoom
to use the File/New Stack command to put multiple slices in. The F3 key zooms out.
together into a 3D image for processing. After the stack list is
created, you can use it directly to open the 3D image. Once V. VOLUME VIEW WINDOW
you have boundaries and other data, you can save all data to a 3D volume renderings are displayed in a VOLUME VIEW
project file. A project file contains all processed data, such as WINDOW. The 3D rendered image is created using ray-
objects, boundaries, point markers, annotations, and the file tracing algorithms and displayed at different user selected
path to the image file. Image data itself is not saved in the angles. The display can be animated along a certain viewing
project file. When you move your project file to a new angle using the View/Animate command. The screen image
location, make sure the image file is moved as well. The can be saved to an image file in TIFF format using the
IMAGE PLANE WINDOW displays one image plane at a File/Save Image As command.
time with the plane ID displayed at the top left corner of the
window. The IMAGE PLANE WINDOW is the main display
and analysis window for a 3D image, where all image
processing functions, editing functions, measurement tools,
and segmentation functions are used. Function keys F5 and
F6 move the display to the previous slice or next slice,
respectively.
The MONTAGE WINDOW displays all image planes that If no object boundary has been defined, you can draw a
are organized sequentially in one window. Each image plane selection rectangle in the IMAGE PLANE WINDOW and
is displayed as a pane with a plane ID in a MONTAGE use the 3D Rendering/Cube Boundary command to define
WINDOW. Double clicking in an image pane within the boundaries for a cube volume and then perform Volume
MONTAGE WINDOW will display the selected image plane Rendering. When boundaries are defined, volume rendering
in the IMAGE PLANE WINDOW. The MONTAGE can be used directly. You can use 3D Rendering/Split Object
WINDOW provides a navigation tool among the 3D image to slice object boundaries into 2 parts and then use the split
planes and an overview of the 3D image structure. object for volume rendering. The 3D volume can be saved to
XYZ, or 3D-DOCTOR’s own VOL file formats.
Note in 3D-DOCTOR, we count image planes starting from
0. If a 3D image has 256 planes or slices, the first plane is The VOLUME VIEW WINDOW has a set of display control
plane 0 and the last plane is plane 255. functions in the View menu to zoom in, zoom out, use
pseudo color palette, and adjust contrast and other display
3D-DOCTOR generated data, such as boundary lines, point controls.
markers, annotations, and control points are displayed in the
IMAGE PLANE WINDOW and are edited here as well. VI. 3D SURFACE WINDOW
Some data items may be displayed in both the IMAGE 3D surface models created by surface rendering functions are
PLANE WINDOW and MONTAGE WINDOW, but editing displayed in the 3D SURFACE WINDOW. The 3D surface
always takes place in the IMAGE PLANE models are in 3D polygon mesh form, represented by surface
WINDOW. triangles and polygons. The models can be viewed from any
selected angle and can be animated along a certain viewing The 3D image profile generated from the Edit/Measuring
path. The data created by surface rendering methods can be Tool/3D Profile command is
saved to a vector-based 3D graphics file format, such as DXF
format, to be used by other 3D modelling or graphics Displayed in a 3D PROFILE WINDOW (See Figure). The
software packages. The data can also be saved in STL format plot can be printed to a printer or saved to a text file.
for rapid prototyping applications, or in VRML format for
display through the Internet. Menu Bar
To select an option using the floating pop-up menu while in Turning on the specific editing mode can activate the
an editing mode, first use the right mouse button to bring up toolbars.
the pop-up menu and then use the left mouse button to select
the option.
The Mouse
Boundary Editor toolbars
A two-button mouse lets you position the cursor and select Measuring Tool toolbars
items on the screen.
The left mouse button is normally used to select menu
options, edit screen objects, and draw a selection rectangle
for zooming in and out.
Region of Interest (ROI) Tool toolbars
Click the right mouse button to display a floating pop-up
menu that provides the most frequently used commands,
depending on the processing status and the current data type.
Zooming and Rotating toolbars
The Keyboard
The keyboard can be used to start commands and enter text,
such as file names and annotations.
Object List and Object Setting toolbar. The drop down list
The keyboard is also used with some editing tools, for allows you to quickly select one object and set it as
example, the Boundary Editor and Measuring Tool. When “current”.
drawing a boundary polygon for an object boundary or region
of interest, hit the SPACE BAR to close the boundary and VIII. 3D-DOCTOR WORK FLOW
finish the current polygon. 3D-DOCTOR is developed using object-oriented
technologies that make the software highly efficient to
Some short cut keys are also enabled for specific functions, process and manipulate 3D images and other associated data
for example, F1 for help, F2 for zoom in, and F3 for zoom items in an integrated environment.
out. When in the Zoom In mode, use the ARROW keys, Open Image File: Use the File/New Stack command
PAGE UP, and PAGE DOWN keys to scroll in the IMAGE to put multiple slice image files into a 3D stack or
PLANE WINDOW. the File/Open command if multiple slices are stored
in a single image file. Your image can also be
When a 3D image is displayed, you can use F5 to go to the processed using the commands under the Image
previous image plane and F6 to go to the next image plane. menu.
Define Object and Object Boundaries: Use the
For the 3D SURFACE WINDOW and the VOLUME VIEW Edit/Object Settings to add objects to your project.
WINDOW, use the ARROW keys to rotate the 3D display. Use the 3D Rendering/Auto Segment to
automatically detect object boundaries. You can
Toolbars also use the Interactive Segment or Segment Object
commands to generate object boundaries for the
defined objects. You can use Edit/Boundary Editor
to trace object boundaries manually.
3D Surface Rendering and Volume Rendering: You
can export the 3D surface models using the
File/Export Model command to many commonly
At the top of the IMAGE PLANE WINDOW, toolbars used formats and create advanced animation using
provide access to the more frequently used functions, such as the View/Animation Control command.
view controls, editing tools, and other functions. If your
cursor stops on a tool button for a few seconds, a simple tool Register Image command (Image Menu)
tip will appear to show you the command. This command is used to interactively register the current
image against a target image by adjusting the orientation,
location and scale. The current image and the target image
should have multiple slices. the left mouse button and move to rotate the object. The
mouse wheel is used to zoom in and out. Hold down the right
mouse button to move the object within the display window.
If you want to adjust the orientation and scale of your current Use this command to turn the current 3D object up.
image, you can use it as the target image and repeat the above
steps. For example, you can re slice the image using this Turn Down…command (Viewing Angle sub menu)
command.
Use this command to turn the current 3D object down.
Surface Info…command
Turn CW…command (Viewing Angle sub menu)
This command shows the number of face triangles and nodes
for all currently rendered objects. When the Tools/Surface Use this command to rotate the current 3D object clockwise.
Info command is selected, a 3D-DOCTOR dialog box
appears with the surface information (See Figure) Turn CCW…command (Viewing Angle sub menu)
The number of triangles and nodes can be reduced using the Use this command to rotate the current 3D object counter
Tools/Smooth Surface command. clockwise.
G.VENKATA PRASAD
ASSISTANT PROFESSOR
COMPUTER SCIENCE & ENGINEERING
SPHOORTHY ENGINEERING COLLEGE
M.SANDHYA
STUDENT
COMPUTER SCIENCE & ENGINEERING
SPHOORTHY ENGINEERING COLLEGE
J.DEEPTHI
HEAD OF THE DEPARTMENT
COMPUTER SCIENCE & ENGINEERING
SPHOORTHY ENGINEERING COLLEGE