3D-DOCTOR Frequently Asked Questions

3D-DOCTOR is an advanced, 3D imaging software developed by Able Software Corp. It does 3D image segmentation, 3D surface modeling, rendering, volume rendering, 3D image processing, deconvolution, registration, automatic alignment, measurements, and many other functions.

What are the differences between 3D-DOCTOR and other products?

3D-DOCTOR uses its unique vector-based technologies to create 3D models from volumetric images such as CT, MRI and microscopy images. The following lists some of the main features of 3D-DOCTOR and the differences between 3D-DOCTOR and other packages:

3D-DOCTOR has the US FDA 510K clearance for medical imaging and modeling applications.
Unique vector-based technologies for faster 3D model creation and easy editing.
Surface model has less triangles while maintaining all details for high quality rapid prototyping applications.
Smart memory management with no limit for the number of slices to be used. It has been used to process images with over 2000 slices.
Volume calculation, 3D measurement for quantitative analysis applications.
Handles DICOM and other image formats, such as TIFF, JPEG, PNG, GIF, BMP, Interfile and RAW (vendor proprietary formats).
Works with both grayscale and color images (color classification and separation)
Supports CT, MRI, PET, microscopy, industrial CT, scanned film images, boundary slices, slice data and XYZ points.
Advanced 3D Image Processing Functions: image registration for multi-modality application, image fusion, image resizing, image reslicing, image slice alignment, etc.
Write your own programs with 3DBasic script to automated frequently used steps.
3D Output Formats: STL (ASCII and Binary), VRML, DXF, 3D Studio, IGES, Wavefront OBJ, PLY and more. Reasonably priced. All functions are tightly integrated in a single easy-to-use package. No need to buy any additional expensive modules.

Can you show me how 3D-DOCTOR works?

We have created several video clips to show you how 3D-DOCTOR works.

Click here to go to the video tutorial page.

What's are the main steps to create 3D rendering from 2D image slices?

The following lists the main 3D-DOCTOR functions and steps you
can use to create 3D rendering from your 2D image slices:

1. File/New Stack to add the slices to the stack list and open it.
Or the File/Open command if the slices are already in a list or
a single image file.

2. Function Keys F2 and F3 to zoom in and out. F5 and F6 to switch
to the previous and next image slice. Click on the animation tool bar to
fly through the slices. View/Image Contrast to adjust display contrast, etc.

3. Edit/Calibrations to enter image spatial/spectral resolution.

4. Edit/Object Settings to add new object groups for holding the boundary
data.

5. Use 3D Rendering/Auto Segment and define the number of objects
to be segmented for fast automatic segmentation. You can also use the 3D Rendering/Interactive Segment or Edit/Boundary Editor to trace object boundaries automatically or manually. The boundary data will be used by the following steps.

6. Use the 3D Rendering/Surface Rendering commands to create 3D
surface models. When the 3D surface models are displayed, use
View/Object to change the transparency and color properties and functions
under Tools submenu for further analysis.

7. Use the 3D Rendering/Volume Rendering to create 3D volume rendering
for 3D visualization.

8. Use Edit/Object Report and Boundary Report to get quantitative analysis of
your image.

What image formats does 3D-DOCTOR support?

3D-DOCTOR supports a variety of image formats in both 2D and 3D. These formats include DICOM, TIFF, JPEG, BMP, Interfile, GIF, PNG and RAW. Other non-standard image formats are also supported, but only with known dimensions (number of columns, rows and planes), bit depth per pixel, little endian or big endian, and the size of file header.

What 3D formats does 3D-DOCTOR support for export?

3D surface models created using the surface rendering commands can be saved as AutoCAD DXF, IGES, STL (ASCII and Binary), 3D Studio 3DS, VRML, Wavefront OBJ, PLY, raw triangles, and 3D-DOCTOR's own binary format.

3D models created by 3D-DOCTOR are polygonal models, not NURB (non-uniform rational B-splines) models. The models are saved in the form of surface polygons and triangles when exported to the above formats, including IGES. Many NURB based CAD software supports polygonal model and have functions to import them as surface body, solid body or graphics model. There are also software tools available to convert a polygonal model to a NURB model.

Object boundary contours can be saved as AutoCAD DXF, IBL (for Pro/Scan), ASCII boundary (BND), and XYZ formats.

Download sample files created by 3D-DOCTOR from the pelvis CT image in DXF, STL, VRML, OBJ, PLY, 3DS and IGES format to check the compatibility with other programs you use. The files are zipped for faster downloading. Click the right mouse button and use Save Target As to get the file:

DXF Format (AutoCAD DXF)
IGES Format
VRML Format
STL Format
3DS Format (3D Studio)
OBJ Format (Wavefront OBJ)
3D-DCOTOR's 3D .SUF Format
3D volume rendering can be saved as VOL and XYZ formats.

What types of images can be used in 3D-DOCTOR?

3D-DOCTOR can process a wide variety of images, including CT (computed tomography), MRI (magnetic resonance imaging), microscopy, industrial CT, seismic wave data, scientific volume data, 3D contours, and 3D cloud points. Images can be obtained from medical imaging devices or scanned from films or other image sources. 3D-DOCTOR supports TWAIN-compatible imaging devices and functions for cropping medical film images.

3D-DOCTOR supports grayscale images in 4, 8, 12 and 16 bits, 1-bit black/white images, and 8 and 24 bit color images.

Is there any limit on image size?

3D-DOCTOR can handle very large 3D volume images thanks to the efficient memory management implementation. 3D-DOCTOR does not load an entire 3D volume into memory for processing, instead it only keeps what's needed in memory to get the best performance. 3D-DOCTOR is designed to handle image sizes way above what today's scanners can produce.

It is always recommended to add more memory (RAM) to reduce disk swapping and improve performance. 512MB RAM should be a reasonable starting point for most 3D medical images.

How to convert DICOM image files to TIFF or JPEG?

Since most DICOM images are 16-bit and most image viewers for TIFF or JPEG files can only support 8-bit pixel, you'll need to convert DICOM images to 8-bit first and then save them to TIFF or JPEG format. The following lists the steps:
1. Use the "New Stack" command to put the DICOM image slices into a stack. Open the image stack.
2. Use the "Image/Conversion/Convert to 8-bit Grayscale" to create a new 8-bit image file with all image slices. Use a TIFF file as the out.
3. Open the converted 8-bit image. Use the "File/Save/Save Image As" to save the stack to TIFF or JPEG files. Check the box "Separate Image Slices to Separate Files".

How do I bring my images into 3D-DOCTOR? What can be done if the images are on film?

Images are brought into 3D-DOCTOR by file. You can read an image file directly from a server where the image is stored when direct network access is available. If direct access is not available, you can copy the image file to a removable storage media (ZIP disk, CD, or tape) and then move the data file to the system where 3D-DOCTOR is installed. Read the image file into 3D-DOCTOR and start from there.

If your image is on multiple films where each film has a matrix of slices, then simply scan the films using a regular image scanner with a transparency kit or a film scanner. Bring the scanned images into 3D-DOCTOR and then use the template based Crop Film command to separate the slices for 3D visualization with just a few simple mouse clicks.

Can I process color images using 3D-DOCTOR?

Yes, 3D-DOCTOR supports both 24-bit and 8-bit color images. The 3D Rendering/Segment Object function lets you segment both color and grayscale images to get object boundaries. You can also use the Image/Processing/Color Classification function to group the colors and then extract boundaries using the segmentation function. Color images can also be used in 3D Volume Rendering.

You can convert color images to grayscale using the Image/Conversion function.

How do I import the raw image files from the Visible Human Project?

3D-DOCTOR can import the raw images files from the Visible Human Project for 3D rendering and modeling. Many 3D-DOCTOR users have successfully used the datasets to create anatomical model for research, education, product design, finite element analysis and other applications.

The Visible Human Project^® is the creation of complete, anatomically detailed, three-dimensional representations of the normal male and female human bodies. Acquisition of transverse CT, MR and cross sectional images of representative male and female cadavers has been completed. The male was sectioned at one millimeter intervals, the female at one-third of a millimeter intervals.

To import the files, use the "File/Raw Image File Import/Multiple Files" command. Add the raw data files to the list and enter the image size information (described in the README.TXT file in the image file folder).

For example, if you are importing the color raw image files, the parameters will be entered like this:

Number of Columns: 2048

Number of Rows: 1216

Bits Per Pixel: 8

Number of Bytes to Skip: 0

Photometric Display: RGB Color

Little Endian: checked

For the Calibration: X, Y are 0.33mm, Z = 1 mm

Here is a screen shot of the color image imported into 3D-DOCTOR and models created (Image courtesy of H. Gall, CIRS):

What is 3D surface rendering?

3D-DOCTOR's, 3D surface rendering commands create 3D surface models from object boundary lines or contours. The 3D surface model consists of triangle faces. Multiple objects can be combined together using 3D surface rendering.

There are 2 surface rendering commands in 3D-DOCTOR: Simple Surface Rendering and Complex Surface Rendering. They both create 3D surface model but use different algorithms and are suitable for different objects.

The simple surface rendering uses a proprietary algorithm to create smooth and simpler surface models. This method is fast and the models are better suited for rapid prototyping and volume calculation applications.

The complex surface rendering uses a triangulation algorithm. This method is slow but robust, and is better for rendering objects with complicated branches and topologies.

With 3D-DOCTOR, you can select the proper rendering method for an object and mix multiple objects created using different rendering methods for 3D display.

How do I adjust the scale (X, Y, Z) of my 3D rendering?

When you create a 3D rendering with only a few slices, the 3D rendering may appear as a very thin object because, by default, 3D-DOCTOR assumes the slice thickness (or distance between slices) is the same as the pixel size in the XY plane (column and row).

This can be adjusted easily by using the Edit/Calibrations command. At the dialog box, enter the values for X, Y, and Z. The X and Y are the size of a pixel within a slice. The Z value is the slice thickness plus the distance or gap between slices. If you need to increase the slice thickness, enter a larger value for Z so its scale will be adjusted automatically in the 3D rendering.

If you know the size in all dimensions and the physical unit, you can enter them in the Image Calibration Parameters dialog box, and the correct scaling will be applied when making measurements and calculating 3D volume and surface area.

How do I create a 3D surface model from my images?

The following steps explain the process of creating a 3D surface model from images. More details can be found in the 3D-DOCTOR tutorial:

Step 1. Open the 3D image using the File/Open Image command.

Step 2. Segment the image using one of the segmentation commands to generate boundaries for an object.

Step 3. Edit the boundary lines using the Edit/Boundary Editor, if necessary. Use the File/Boundary/Export Boundary command to save the boundary data to a file. If you need to render only part of an object, you can use the 3D Rendering/Split Object command to split the object along an arbitrary axis.

Step 4. Now you can create a 3D surface rendering using the 3D Rendering/Surface Rendering commands. You can also create a volume rendering using the 3D Rendering/Volume Rendering command.

How do I create a smoother model from a low resolution scan (wide spacing between slices)?

As a basic guideline, higher resolution scans (small spacing between image slices, small voxel size) will generally allow you to create higher quality models. However, sometimes you may have to work with images that have wide spacing (or large slice thickness, very few slices).

The following lists some tools you can use to improve the image quality and create smoother image:

Reslice the image to create a new image with thinner slice thickness by using the "Image/Reslice" command. Simply enter a new slice thickness that's smaller than its current slice thickness, a new image file name to create a reslices image. The reslicing command uses image interpolation algorithms to add additional slices.
Segment the resliced image to get object boundaries. Select the "View/Overlay/Neighbor Boundaries" option to show boundaries on neighboring slices. Use the "Edit/Boundary Editor" to edit the boundaries to ensure smoother transition between slices.
Create a surface model using the Surface Rendering command. If you have used the "Complex Surface" command, you can use the "Tools/Smooth Surface" to smooth the model. You can repeat the smoothing process. If you have used the "Simple Surface" command, you can then use the "Tools/Refine Models" command to refine the surface model by adding additional surface triangles.
Besides 3D-DOCTOR, if you have other software tools available, you can export the object boundaries to a file, such as IGES or DXF, then use the boundaries to create a NURB model.

How do I create a 3D surface model using contour data from other programs?

The following steps explain the process of creating a 3D surface model from object boundary or contour data. More details can be found in the 3D-DOCTOR tutorial:

Step 1. Use File/New Workspace to open a blank window.

Step 2. Use File/Boundary/Import Boundary to open the boundary data file for display in the blank window. The boundary data must be stored in a format supported by 3D-DOCTOR. The boundary file format (*.BND) is an ASCII file. A very simple example is shown below:

Z1
X11,Y11
X12,Y12
...
X1N,Y1N
X11,Y11
END
Z2
X21,X21
X22,Y22
...
X2M,Y2M
X21,Y21
END
...
ZK
XK1,YK1
XK2,YK2
...
XKO,YKO
XK1, YK1
END
END

The Z value is the slice number for a contour. It must be an integer and its neighbor contour should be either Z-1 or Z+1 in order to create proper 3D rendering.

Step 3. If you need to adjust the size of the workspace, use the Edit/Resize Workspace command. Changing the workspace size will not affect the size of boundary lines, only the relative location in the window.

Step 4. If you need to edit your boundary data, use the Edit/Boundary Editor On command.

Step 5. Use the 3D Rendering/Surface Rendering command to create a 3D surface model.

How do I create a movie or animation using 3D-DOCTOR?

You can use 3D-DOCTOR to create a movie for your 3D rendering. Click here to see an example.

Once you have your 3D rendering (either surface or volume rendering) created and displayed in 3D-DOCTOR, you can start the View/Animate/Create Movie command. Define the AVI file where you want to save the movie. Press Start Recording and then go back to 3D-DOCTOR to get actions you want to put in the movie file. When you are done, click Stop to finish. The movie is saved in the AVI file. Make sure you have enough hard disk space as the movie file can get quite big.

You can also use a screen capture program to record 3D-DOCTOR screen actions into an AVI file.

Or you can use the File/Save/Save Window command to save each rotation to a .BMP file and then use an animation program to put the frames together for a movie.

What is 3D volume rendering?

While surface rendering creates 3D models with surface polygons and triangles, 3D volume rendering creates a 3D display from the voxels directly. Object boundaries are used to include or exclude image volume in the rendering process. The volume rendering displays voxel intensity in 3D space. With the 3D Rendering/Split Object command, you can cut object into smaller pieces and then use volume rendering to show the volume. The process of creating volume rendering is similar to surface rendering.

How do I define an ROI (region of interest) for segmentation?

A properly defined ROI can normally enhance the performance of the segmentation functions.

The following steps describe how to define one or more ROI:

Step 1. Select Edit/Region Of Interest/ROI Tool On/Off to toggle the drawing tool on. The default drawing option is polygon, however, you can select the rectangle or circle method using the right mouse button.

Step 2. Click the left mouse button within the image window to draw polygons. Press the spacebar key to close and finish the polygon.

Step 3. Repeat Step 2 to draw more ROIs.

Step 4. When you are finished, press the right mouse button to bring up the pop-up menu options and select "Done" to leave the ROI editing mode.

Once the ROIs are defined, you are now ready to start the segmentation process.

How do I get images created by 3D-DOCTOR into my presentation program, for example, PowerPoint?

Use 3D-DOCTOR's File/Save/Save Window command, which saves the current display window to a Windows bitmap (BMP) file. You can then open the bitmap file from your presentation program.

You can also use the "Edit/Copy" command to copy the display window and then "Paste" into your document editing program.

The Save Window command saves only the bitmap displayed in the window, use other file formats to save the data, for example, the project (*.prj).

You should set your display to 16-bit or 24-bit color if you plan to use the File/Save/Save Window command.

What display settings should I use to run 3D-DOCTOR?

Set your display to either 16-bit or 24-bit color. 3D-DOCTOR is optimized for these settings.

Can I use the demo version for my work?

Yes, you can use 3D-DOCTOR's demo version to create 3D rendering and publish your results and images. In return, we ask you to mention 3D-DOCTOR wherever appropriate and give us some feedback and comments about the software and your work. We'd love to hear from you..

Please keep in mind that the demo version is not a full version, and many high end image processing and export functions are not available in the demo.

How do I split or cut objects for 3D rendering?

With 3D-DOCTOR, an object defined by object boundaries can be cut or split into smaller objects.

The following are the steps required for cutting or splitting objects:

Step 1. Activate the image plane window where the object boundary is displayed. Select the 3D Rendering/Split Object command. The cursor will change to a cross. Move the cursor to the starting location of the cutting line and click the left mouse button. Now you'll see a rubber band line which connects the cursor to the starting location. Move the cursor to the ending location and click the left mouse to define the line. A dialog box appears to let you select the range of image slices to be cut. Select the option "Only keep object on the right" to keep the split object on the right side of the cutting line or uncheck it to keep objects on both side.

Step 2. Once the new object boundaries are cut, use Edit/Object Settings to turn off objects that are not to be used for 3D rendering. Now select a 3D rendering (surface or volume) command to create the 3D rendering of the split objects.

What types of measurements can be done by 3D-DOCTOR?

3D-DOCTOR can make a variety of image measurements, including distance, area, surface area, volume, profile, and image region histogram.

3D-DOCTOR lets you measure angles using the Angle Measurement tool.

3D volumes of 3D surface models can be calculated easily. When the surface model window is displayed, use the Process/Calculate Volumes command.

Can I calculate the 3D volume of my 3D surface model?

Yes, the volume of a 3D surface model can be calculated easily using the Process/Calculate Volume command within the surface model window. This command computes both volume and surface area. To adjust the scale and unit for volume calculation, the scaling parameters should be entered using the Edit/Calibration command before rendering is done.

If you have your 3D model saved in a format supported by 3D-DOCTOR, such as DXF, STL, PLY, raw triangle, etc., you can use File/Open Model to read the 3D model into 3D-DOCTOR and then calculate the volume.

How do I calculate the surface area of a 3D surface model?

The surface area of a 3D surface model can be calculated easily using the Process/Calculate Volume command within the surface model window. This command computes both volume and surface area. To adjust the scale and unit for volume calculation, the scaling parameters should be entered using the Edit/Calibration command before rendering is done.

How do I combine and compare multiple 3D models?

Multiple 3D surface models can be combined and displayed together using 3D-DOCTOR for 3D simulation and analysis. The following explains how it can be done:

Step 1. Use the File/Open Model command to display the base model or skip this step if you already have a surface window.

Step 2. Use the File/Add/Merge Model command to add another model into the current display window. Repeat this step to add more models.

Step 3. Use the View/Object command to adjust the display (the Material button) and shape properties (the Shape button). You can rotate, move and resize an object in 3D space to align with other objects.

How do I display image slices together with 3D models?

3D-DOCTOR can easily displays the image slices together with your 3D models. If you have a surface model display window open, use the View/Image Planes command to turn on the image plane display. You can use the View/Image Settings command to change the transparent and opaque properties and individual plane display status.

This is an example of knee bone model displayed together with the original MRI image:

How do I control the animation of objects separately?

The View/Animation Control command allows you to define and control the animation sequence and movement for each object.

The View/Object Control command allows you to hide, or show objects with certain display settings during the animation process.

To define the movement of an object in the animation, first select the object from the Object List and then enter the following parameters:

Rotate (in degrees): The X, Y, and Z are the increments in degree that changes the three angles that control the rotation of the object at each frame. The X is for the angle that rotates counterclockwise around the X-axis while Y and Z are similar for the Y and Z-axis respectively.
Move By: The increments for location shifting along the X, Y and Z-axis at each frame.
Scale: The increments for the scaling factors along the X, Y and Z-axis at each frame .
Steps: This defines the number of steps to be used in a loop for the above movement parameters. For example, if Rotate has 10 steps and the X increment is 5, then the object will be rotated 10 times, each time the angle is the current angle plus 5 degrees. The next parameter controls how the loop continues to the next loop .
Loop Control: Two options can be used: “Return to Starting Point” and “Reverse Direction”. When the “Return to Starting Point” is used, the object will jump back to its initial position and shape when each loop ends. When “Reverse Direction” is used, the increment will become decrement at the end of each loop and the object will move back in reversed direction .

The viewing angle controls the change of the three angles by using the three increments. The viewing angle controls the global display.

You can use the “Test” button to preview the animation. Click here to see an example. (The animation is courtesy of G. Martins, Confocal Microscope and 3-D Imaging Facility, SUNY at Buffalo.)

How do I create a video of flying through an object?

With 3D-DOCTOR, you can create a fly through video (AVI file) for 3D objects.

You first create or load some 3D objects in to 3D-DOCTOR, start the "Animation/CreateMovie" process, then use the mouse to fly through the object while recording the AVI file.

The left mouse rotates the object, the middle mouse wheel moves into or out the object, and the right mouse moves the view port.

What platforms (Operating Systems) does 3D-DOCTOR run on?

3D-DOCTOR runs on PC running Windows, including Windows 7/8/10, or newer versions of Windows.

3D-DOCTOR has native Windows 64-bit version that runs on XP 64-bit, Vista and Windows 7 64-bit. The 64-bit version uses more than 4GB of system memory and is capable of processing very large size images.

What are the licensing options? USB Dongle, Software key, etc.

The following table shows the licensing options available for 3D-DOCTOR:

License Type	Installation Method	Validation	Multiple PCs
USB Key (Dongle), delivered by mail.	Plug into a USB port	Not needed	Runs on one PC at a time but can move easily between PCs
Software-Key, delivered by email.	license key file by email	Yes, validation is required to receive the license key file	Only on a single PC. Requires revalidation when transferring license to a different PC.
Network Floating License (USB Net Key), delivered by mail	Plug into a USB port on a server	Not needed	Runs on multiple PCs at the same time based on the number of licenses purchased

Does 3D-DOCTOR run on a Unix system?

Not directly. However, it could work on a Unix machine if a Windows binary emulator is installed.

Does 3D-DOCTOR run on a Linux system?

The current version does not run directly on a Linux system. There are Windows binary emulators available but we have not tested them for compatibility. We are looking into the possibility of creating a Linux version for a future release.

Does 3D-DOCTOR run on a Macintosh system?

No native MAC version yet. Some users have used 3D-DOCTOR on a MAC through a Windows emulator.

3D-DOCTOR Basics

Applications

3D Formats, File Handling, and Reslicing

3D Image Segmentation & Editing Tools

3D Surface Modeling, Rendering & Animation

3D Volume Rendering

Measurement, Report, Quantitative Analysis, and Presentation

3D Image Registration, Fusion and Comparison

Image Slice Alignment & Reslicing

3DBasic Scripting Tool

How do I create a smoother model from a low resolution scan (wide spacing between slices)?

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