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3D-Doctor를 어떻게 사용하는지 쉽게 이해
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Tutorial 2 (단계별 따라 해보기)
- The Basics
- Put Image Slices into a Stack List
- Reading a 3D Image Stored in Raw or Non-Standard Format into
3D-DOCTOR
- Defining Voxel Size and Slice Thickness for Calibration
- Creating 3D Models from your Image
- Creating a 3D Volume Rendering Using Cube Boundaries
- Registering Two 3D Volume Images and Creating a Fusion
Image
- Reslicing a 3D Image Along an Arbitrary Axis
- 3-D Image Segmentation Using a Training Area
- Creating Object Boundaries Using the Boundary Editor
- Creating a 3D Rendering From 3D Contours Without Using an
Image
- 3D Volume Rendering for 3D Scientific Data
- Automatic Alignment of Image Slices
- One Step 3D Image Deconvolution
- Cutting Objects in 3D Rendering
- Use 3DBasic to Write Programs Using 3D-DOCTOR's
Advanced Imaging Functions
3D-DOCTOR was developed using object-oriented technology and provides
efficient tools to process and analyze 3D images, object boundaries, 3D models
and other associated data items in an easy-to-use environment.
The main steps to create 3D models and volume rendering from a 2D slice
images (CT, MRI, microscopy): 1) Open the 3D image, which is displayed by a
single plane window and a montage window with all slices. 2) Define objects and
create object boundaries for each object. 3) 3D surface rendering and volume
rendering.
The following explains each step and commands used:
Step 1. Open a 3D image. If your 3D image is stored in a series of
DICOM files or in a format that's directly supported (DICOM, TIFF, BMP, PNG,
JPG, raw image data with a header *.HDR), you can use the File/New Stack
command to put the files into a stack list and open it.
This Figure shows an opened CT pelvis image: 
If the image format is not directly supported, use the File/Raw Image File
Import command to add a header or multiple header files and then open the
image data files.
If your image is on a film, for example, one film has 12 slices, you can scan
the film using a scanner and then use the Image/Crop Image/Crop Region
command to crop each slice and save a separate file using the File/Save/Save
Image As command. Once you have the image files, then use the File/New
Stack command to create the 3D stack list. All slices must be cropped to the
same size so they can be put together as a 3D image for further processing.
Step 2. Define objects and create boundary lines for each object. Use
the 3D Rendering/Auto Segment for fully automatic object boundary
detection or the Interactive Segment command to trace object boundaries
interactively. 
This Figure shows the image segmented using the Auto Segment command with the
number of objects defined as 2.
Boundary lines can be edited using the Boundary Editor under the
Edit menu or processed using the boundary line processing functions under
the Edit/Boundary Process menu. Boundary lines are organized by object
groups for more effective management and more flexible use by the rendering
functions.
You can use the Object Report to get detailed quantitative analysis of the
objects.
Step 3. When boundary lines are generated, use 3D surface rendering to
create 3D surface models or 3D volume rendering. The 3D models can be exported
to many 3D formats for simulation, animation, rapid prototyping, finite element
analysis and other applications.
This Figure shows the model created for the bone structure.
Very often, a 3D image is very large in size
and the image planes or slices are stored in separate files. They may be stored
in a format supported by 3D-DOCTOR, such as DICOM, TIFF, JPEG, or BMP or stored
in a format that can be imported into 3D-DOCTOR.
The following lists the steps needed to
create a stack list for 3D image processing and 3D rendering.
Step
1.
Select File/New Stack. The Create 3D Image Stack dialog box will
appear.
Step 2. If a “DICOMDIR” file exists, you can use the
“DICOMDIR” button to open it.
If there is no DICOMDIR file, use the "Add
Files" button to add image slices files to the stack list.
A Select Image Files dialog box is
used to browse and select files. The Select Image Files dialog box
supports multiple file name selections so you can add several files in one
group. Make sure the order of the files added correspond to the order the image
planes are acquired. To select multiple files, hold down the SHIFT KEY and click
the left mouse button to select a group files. You can also hold down the CTRL
KEY and click the left mouse button on individual files to select. If
all files displayed in the list are to be added, use the “Select All” button and
then “Open” to add them to the list.
The "Delete" button allows you to delete a
file from the current list. Select a file from the list first and then press the
"Delete" button. The deleted files can
be added before or after a selected file using the “Add Before” or the “Add
After” buttons.
If you need to take a look at an image file
added in the list, select the file name in the list and then press the "Preview"
button. The image will be displayed in the preview window.
Note: If
the image can not be previewed, then you may have a problem with the file or the
file format used. You may have to use 3D-DOCTOR's File/Raw Image File
Import function to configure the file first.
Step 3. Once the files are added to the list, save the list
to a stack list file. In the future, you can also open the stack list directly
for processing.
Step 4. Sorting Options: for most DICOM images, use the “Sort
By Image Position” option. If the image slices do not appear to be sorted
correctly, you can use the “Image/Reslice/Sort By Image Number” command to
resort the slices after the stack is open.
For other image formats, you should add them
in the correct order or use the “Sort By Name” button to sort them.
Step 5. Click the "Open" button to open the 3D image stack
you just created. In the future, you can use the File/Open command to
open the list file directly. All files stored in the list will be treated as an
image plane within the 3D image.
About the “Stack List” File:
The stack list file is a simple ASCII text file that looks
like this
STACK LIST FILE
C:\images3d\HeadCTHalf\17283179
C:\images3d\HeadCTHalf\17283197
C:\images3d\HeadCTHalf\17283215
C:\images3d\HeadCTHalf\17283233
C:\images3d\HeadCTHalf\17283251
C:\images3d\HeadCTHalf\17283269
C:\images3d\HeadCTHalf\17283287
The first line indicates the file type. After that, each line
is a file path to an image slice. You can edit the stack list file using Windows
NotePad or any text file editor.
To delete an image slice file from the stack, find the line
and delete it.
To add an image slice to the stack manually, you need enter the file path at
the correct location.
File
order can be also re-arranged by changing the order of the files in the Stack
List.
3D-DOCTOR supports various image file formats directly,
including DICOM, TIFF, JPEG, Interfile and BMP. For other non-standard image file
formats, such as a raw binary file or a vendor proprietary image file format ,
3D-DOCTOR’s raw image import function will create an image header file for the
raw image data file when its configuration or file structure is known.
If an image is 256 by 256, uncompressed, and 12-16 bits deep (and hence
usually stored as two bytes per pixel), then the file is going to contain
256*256*2=131072 bytes of pixel data at the end of the file. If the file is
145408 bytes long, as all GE Signa 3X/4X files are for example, then you need to
skip 145408-131072 = 14336 bytes of header before you get to the data. If you
are sure the pixel data is stored at the end of the file, then you can enter ?1
and let 3D-DOCTOR calculate it automatically for you.
Because images can be stored either by row or by column, the imported image
orientation may be different or incorrect. In this case, the Image/Flip or Transpose commands can be used to adjust the
orientation.
3D-DOCTOR has two functions under the File menu for importing raw image files, File/Raw Image File Import/Single File and File/Raw Image Import/Multiple Files. The
first command is used to create a header file for a single image data file,
either stored as a 3D volume or as a 2D plane. The second command is used to
create headers for a group of image data files belonging to a 3D volume image.
When creating headers for multiple files, an image stack list file (*.lst) can be created as well, which will be used by
3D-DOCTOR to open the volume image.
Once the header file is created correctly, you can then use
the header file (*.HDR) instead of the image data file to open the image and
read the data into 3D-DOCTOR. The file will be treated the same as a directly
supported file format, like DICOM or TIFF.
The following are the steps needed to create a header file
for a single non-standard image file or a list file for an image volume stored
in multiple files:
Step 1. Select File/Raw Image Import/Single File if dealing
with only one raw image data file or the File/Raw Image Import/Multiple Files command
if working with multiple files for an image volume. Both commands
create a header or configuration file for each image data file, which allows
3D-DOCTOR to read a non-standard or proprietary image data file directly. The command for multiple files can also
generate a list file for the volume image. This provides a universal
image reader capable of handling most uncompressed image file formats so you can
bring your data directly into 3D-DOCTOR for processing and rendering.
Step 2. All
parameters listed in the dialog box must be correctly entered in order for the
software to read the image data correctly. If you do not know the parameters,
you should contact the vendor or source where you received the file to obtain
these parameters. The figure below shows how the parameters correspond to data
stored in an image file.
Enter the following parameters:
1. Non-Standard Image Data
Files (Multiple Files): Use the “Add Files” button to add the data files to be
imported to the list. Make sure the files are added in the same order as they
exist in the volume image. When the file open dialog box appears, you can select
multiple files by holding down the shift key and the left mouse
button. The file open dialog box has a limit on the number of files to be
selected, so don’t select too many files each time. Header files will be created
when the “OK” button is pressed for all the data files. Each data file will have
a corresponding header file. If the configuration is different from data file to
data file, then you should use the command for Single File to create header
files for each individually.
2. List File Name (Multiple Files): Use this button to define an image stack
list file name to save the list of the files to be imported. If the list file name is not defined, then
only header files are created.
3. Header file name (Single File): Use this field to enter a header file
name to save the configuration parameters. This will be used again later in
3D-DOCTOR to read your image. If you want to copy or edit all the information
from an existing header file, use the browse button to open the existing header
file. All parameters will be read in for you to modify.
4. Image data file name
(Single File): Use the “Browse” button or enter directly the file name where the
image data is stored. Enter the file name exactly the way it appears as it is
used by 3D-DOCTOR to find the image data.
5. Number of columns: This is the number of pixels in the X or column
direction in one image plane or slice.
6. Number of rows: This is the number of rows or pixels in the Y direction
in one image plane or slice.
7. Number of image planes or slices: This is the number of image planes or
slices in the file.
8. Number of bits per pixel: This tells the size of each image pixel, if the
number of bits is 8, then each pixel is one byte in size and can store up to 256
levels. If the number of bits is 16, then each pixel has 2 bytes of data and can
store up to 65536 levels.
9. Number of bytes to skip before the image data array: Some image files
have a fixed length header for storing vendor specific information. The length
or the size of the header must be provided so the software knows to skip it in
order to read the image data correctly.
Enter -1 if you want the software to estimate it.
10. Little endian or big endian:
This parameter only matters when the number of bits per pixel is greater
than 8, for example, when an image is in 16-bit. For most images created on a
PC, the file is stored as little endian (default). If your image is created on a
Macintosh or a Unix workstation, it is possible the pixel is stored as big
endian. You can tell right away if the image does not display correctly, for
example, discontinuous gray levels. In this case, uncheck the little endian box
to set it as big endian.
Step 3. Select
“OK” to save all the information to the header file. You are now able to work
with your image data by using File/Open
using header file type (*.HDR). If a
list file is saved for an image volume, it will be automatically opened.
For a 3D image, the voxel size (image resolution) must be
provided so 3D rendering will have the correct scale in all 3-dimensions and can
be used by the reporting and measurement functions. If your image is stored in
DICOM format, the parameters may already exist in the file header and will be
used automatically by 3D-DOCTOR. However, you may need to adjust the slice
thickness if some slices are not used when you create the 3D stack.
The following explains the parameters and how they are
defined. Your image must be open before you start the following steps.
Step 1. Select the Edit/Calibrations command. The dialog box
shown below appears.
Step 2. If your image already has calibration
parameters, for example, DICOM image files, the provided values will be
displayed in the fields. Otherwise, default values are used. The X and Y values
for voxel resolution is the size of one pixel in a slice. For example, a CT
image has a pixel size of 1.5mm. You can enter 1.5 for both X and Y fields and
the unit as mm. The slice thickness is the physical thickness of one slice plus
the gap distance between 2 neighbor slices in the same measurement unit as the
XY sizes. You can also think of slice thickness as the distance between the
centers of 2 neighbor slices in the 3D space.
If your image is scanned from a film or from other sources,
the XYZ parameters can be estimated from the physical size of the imaged volume
and the image size. For example, a 3D image covers a 3D volume with the physical
width of 200mm, a height of 400mm and a depth of 100mm. The Image/Information command shows that the
number of columns for the image is 1000, the number of rows is 2000 and the
number of slices is 50. The calibration parameters can then be calculated by
dividing the physical size by the image size.
For this image,
X = 200mm/1000 (cols) = 0.2mm
Y = 400mm/2000 (rows) = 0.2mm
And the slice thickness Z = 100mm/50 = 2mm
You can then enter 0.2, 0.2 and 2 for the X, Y and Z
fields, respectively.
Step 3. The parameters for the Pixel Rescale
portion of the dialog box are used to calibrate pixel values to their physical
units, for example, the Houndsfield unit used by a CT image. Two parameters,
slope and intercept, are used to define a linear transformation between the
pixel value and the calibrated pixel value:
NewValue = PixelValue * Slope + Intercept If
you do not have the parameters, they can be calculated from the calibration step
wedge, in an image where pairs of pixel values and calibrated values are
available. Click the “Calculate” button to do this.
3D-DOCTOR allows you to 3D surface models quickly from your
cross-section image. To create 3D models, you first need to generate boundary
(or contour) lines for objects in the image and then use the surface rendering
command to create the model. The boundary lines define image regions to be used
by both volume rendering and surface model creation.
For each 3D image, you can define multiple objects and change
their display status using the Edit/Object
Setting command. After the objects are defined, you can set one as “Current”
and generate boundaries for it using one of the segmentation commands or the
boundary editor. Boundary data can also be imported from other sources or
exported to other programs.
The following explains the process of generating boundary
lines using image segmentation for 3D rendering:
Step 1. Open
the 3D image using the File/Open command.
If the image has multiple slices, you should see two windows, one window
displays a single slice and another window displays a montage of all the slices.
If you don’t see the montage window and the image plane number is not displayed
in the single slice window, then you’ll need to use File/New Stack to put the 2D image files into
a 3D stack first.
Step 2. If you want 3D-DOCTOR to detect object
boundaries automatically, simply select the 3D Rendering/Auto Segment command
and enter the number which indicates how many possible objects you'd like to
detect. Click OK and wait for the boundaries to be detected. If you are happy
with the boundaries, then go to Step 7.
If you'd like to segment the image planes interactively,
then follow Step 3 to Step 6.
Step 3. Use Edit/Object Settings to add new object names
for this image. When the dialog appears, enter a new object name in the edit box
at the bottom and click the “Add” button to add to the object name list.
Highlight one object from the list and click the “Current” button to set it as
current to receive boundaries from the segmentation process in Step 5. Click the “OK” button to finish this
step.
Step 4. The Regions of Interest (ROIs) can be defined
using Edit/Region of Interest to limit the
image areas for the segmentation. If ROIs are defined, only pixels within the
ROIs are processed for boundary extraction. This is especially useful when
segmenting objects with complex boundary lines across the image planes. Once the
ROI editing is ON, you can click the left mouse button within the image to draw
polygons. Press the spacebar to close a polygon.
ROIs are displayed as thick blue lines.
Step 5. Select
the 3D Rendering/Interactive Segment
command. Answer “Yes” when asked if you want to keep the current object for
segmentation. The interactive segmentation dialog box appears and the display of
the single image plane window is changed.
The red color is used to show pixels that fall within the threshold range
specified by the Min and Max values. Use the slider bar to adjust the Min and
Max values. The display of the current image slice is updated in real-time
according to the current threshold selection. When pixels that belong to the
intended object are displayed in red color, you can click the “Segment Plane”
button to extract the boundaries for the current image plane. Use the “Next
Plane” or “Prev Plane” button to go through other planes to segment them
individually. If the threshold values are applicable to all slices, you can
click on the “Segment All” button to extract boundaries for all image slices.
Click “Finish” to leave the interactive segmentation function.
Step 6. Now,
you can repeat Steps 3 to 5 to segment boundaries for other objects.
Step 7. The boundary lines can be edited using the
tools provided by the Edit/Boundary
Editor. If you need to split the object into two sub objects, then use the
3D Rendering/Split Object command to do
it. Use the File/Save/Save Project command to save the
boundaries and other data to a project file.
Step 8. Once
the boundaries are defined, you are ready to create 3D surface models. This can be accomplished using the 3D Rendering/Simple Surface Rendering or the
3D Rendering/Complex Surface
commands. You can also create 3D volume
rendering using the 3D Rendering/Volume Rendering command.
Step 9. When
the 3D rendering display window appears, use commands under View to change the viewing angles and other
controls.
If quick visualizing a cubic type volume of a 3D image is the
goal, then the 3D Rendering/Cube
Boundaries command can be used to create boundaries that define the volume
for 3D rendering.
The following explains the process of using the Cube Boundaries command for 3D volume
rendering:
Step 1. Open
the 3D image using the File/Open command.
If the image has multiple slices, you should see two windows, one window
displays a single slice and a second window displays a montage of all the
slices. If you don’t see the montage window and the image plane number is not
displayed in the single slice window, then you’ll need to use File/New Stack to put the 2D image files into
a 3D stack first.
Step 2. If you don’t need to use multiple objects, you
can simply go to the next step by using the current Default object. If
you need to use more than one object and keep the cube boundaries in a separate
object, then use Edit/Object Settings to
add new object names for this image. When the dialog box appears, enter a new
object name in the edit box at the bottom and click the “Add” button to add to
the object name list. Highlight one object from the list and click the “Current”
button to set it as current for getting boundaries. Click the “OK” button to
finish this step.
Step 3. Within the single plane image window, hold
down the left mouse button and drag to draw a selection rectangle to indicate
the image region for the cube volume in the current image slice. Select the 3D Rendering/Cube Boundaries command. In the
dialog box, select the range of image slices to be included for the cube
boundaries. Click “OK” to generate the boundaries. The boundaries are displayed
in both the single image plane window and the montage window. You can repeat
this step to create cube boundaries for different image areas.
Step 4. Use 3D Rendering/Volume Rendering to create 3D
volume rendering using the cube boundaries. Once the 3D rendering window is
displayed, all the view control and settings can be adjusted using commands
under the View menu.
3D-DOCTOR provides an easy method to geometrically
transform, register, or correct a 3D image to a coordinate system of another 3D
image using user supplied control points.
When you have two images from the same source but acquired
using different devices, for example, a CT and MRI image of a head, registering
the two images to the same coordinate system will allow you to compare them more
accurately. In addition, a fusion image will display more information about the
source studied.
When an image is acquired with some geometric distortion,
for example, an ultrasonic image of a curving object, it can be geometrically
corrected to its original shape.
The following steps are used to register a 3D image and
create a fusion image from two registered images:
Step 1. If
available, open the base 3D image that is going to be used as the target to
register the source image. Then open the source 3D image that is going to be
registered. Now move the windows so the two images are displayed side by side.
Step 2. Select
the Edit/Control Points On command for the
source image. Define 4 or more control points. The cursor will be changed to a
cross cursor.
Step 3. Move
the mouse to a position in the source image that is identical to a position in
the target or base image. Use the montage image window to switch to the right
image plane. Click the left mouse button in the source image to add a control
point at this location. The control point definition dialog box appears. On the
left (From) side, the values of column, row, and plane are obtained from the
source image. The values on the right side (To) are defined using the
coordinates of the identical point in the base or target image. Image
coordinates of the current cursor position are normally displayed at the bottom
of the window.
Step 4. Repeat
Step 3 until you have 4 or more control points defined for the source
image. Make sure the control points are
spread out within the volume. They should not all be in a single image
slice.
Step 5. Select
the Image/Registration command. Enter the
parameters required: the output file name and the dimension of the output image
(use the same as the base image if fusion is going to be done). Click on the
“OK” button to start the process. When the process is done, a new registered
image is created and saved to the name as specified. Step
6.
If image fusion or color fusion needs to be done, select the Image/Fusion or Image/Color Fusion command. Enter the file
names and select the required image combination option and then click on “OK” to
start.
3D-DOCTOR provides functions to reslice a 3D image along a
user-defined axis, or simply the X or the Y-axis of the current image coordinate
system. With these functions, you can easily overcome the limitations of an
imaging device and create image slices along another axis. By reslicing a 3D
image, certain features that may be difficult to see in the original form can
become more visible in the new image. The resliced image is saved in a new image
file.
For simple reslicing along the X-axis to create a side view
of the image, use the Image/Reslice X Axis
command. For reslicing along the Y-axis to create a top view of the image, use
the Image/Reslice Y Axis command.
If you need to reslice the image along an arbitrary axis that
is defined by a 3D angle, then use the Image/Reslice Volume command.
The dialog box appears for entering the 3D angle for the
axis, namely X (up/down angle), Y (left/right angle) and Z (clockwise
angle):
Click here to see an example of the
reslicing function.
If you do not know the desired angle, you can use the
following steps to estimate it:
Step 1. Use the 3D
Rendering/Volume Rendering command with Transparent mode selected.
Step 2.
Once the volume rendering is displayed, use the array keys or the viewing angle
control tool buttons
(
) to adjust volume orientation to the position you want to see in the new image
after reslicing.
Step 3. Use the View/Viewing Angle/Angle Setting command to
show the current viewing angle. Write down the 3 values (X, Y, Z).
Step 4. Now start the Image/Reslice Volume command and enter the 3
values from Step 3 and provide a new image file name. Click “OK” to reslice and
save the new image to file. Use File/Open
to open the new image file for processing.
The following steps are used to segment an object in a 3D
volume image based on a user defined training area:
Step 1. It is
highly recommended to define a ROI (region of interest) before this segmentation
method is used. A carefully defined region of interest will keep the region
growing process staying in the proper image area and from jumping to other areas
when image noise is present. An ROI is defined using Edit/Region of Interest and updated by using
the ROI drawing tool later.
Step 2. To
start the process, select the 3D
Rendering/Segment Object/Draw Training Area command to get into the drawing
mode. The right mouse button will bring up the options you can use. The training
area is used to create a set of features for the 3D segmentation so it should be
big enough to cover most of the typical features of the object.
Step 3. To draw
a training area, move the cursor to a location and click to define the first
point. Move the cursor to the next location and click the left mouse button
again to define the line segment. Repeat this process until you are close to the
starting location. Hit the spacebar to close the polygon and the current
image plane is segmented automatically. The object boundary in the current image
plane is displayed in the image window.
Step 4. If you
want to continue the segmentation process to another plane, use the View/Previous Plane or View/Next Plane option from the main menu or
from the floating pop-up menu. Hit the spacebar or select Segment Current to segment with the same
training area, or draw a new training area by clicking the left mouse button in
the image. The existing training area will automatically be removed when a new
training area is defined.
Step 5. If the
defined ROI and the training area are general enough for the entire volume
image, you can select Segment All from the
right mouse button menu or from the main menu. This command will apply the
signatures generated from the training area to segment all image planes that
have not been segmented. If
you want to remove the boundary lines from the current plane and restart the
process, use the Remove Plane
command.
Although 3D-DOCTOR provides several ways of automatic or semi-automatic image
segmentation functions, sometimes when an object is complex and does not have a
distinguishable edge, it is necessary to create the boundaries manually using
the Edit/Boundary Editor menu. Manual boundary editing may seem to take a
longer time, but once you are familiar with the editing functions, it is easy to
do and faster than you would think.
The following steps are suggested to draw boundaries for an object:
Step 1. If multiple objects are going to be used for 3-D rendering,
you should define your new object before the boundaries are drawn. Use the
Edit/Object Settings command to add a new object and set it as the
"Current" object.
Step 2. Select the Edit/Boundary Editor On/Off command to start
the editor. The default editing mode is the Piecewise Boundary option.
This editing mode allows you to draw a closed polygon for the object in the
current image plane. You can click the right mouse button to bring up the
floating pop-up menu for additional editing options.
Step 3. To switch to a specific image plane, you can double click your
left mouse button on a image pane in the montage view window. You can also use
the function key F5 or F6 to move to the previous or
next image plane.
Step 4. Move
the cursor to a place on the edge of the object. For Free Hand Boundaries you must hold
down the left mouse button while you draw the entire boundary. For drawing Piecewise Boundaries,
click and release the left mouse button to start the drawing. Once the first
point is drawn, move the cursor to the next point along the boundary. Click the
left mouse button again to confirm the point. Repeat this step to draw more
points along the boundary. If a point is not correctly defined, use the Backspace (←) key to undo the
point. With the Backspace key you can undo
multiple steps. When you are close to the starting point, hit any key on the
keyboard to close the boundary. You now have a finished boundary for the object
in this image plane.
Although you can use the same process in this step to draw a new boundary for
another image plane, we have found it is easier to copy the current boundary to
the next plane and modify the new boundary instead. In this tutorial, we'll use
the copy to next plane approach.
Step 5. Click the right mouse button to show the editing options.
Select the Copy to Next Plane option and then click on the boundary to
copy it to the next image plane. You will not see the boundary for the next
plane unless you have selected the View/Overlay/Neighbor Boundaries
option. However, the copied boundary will be displayed in the montage window if
one is present.
Step 6. Click the F6 key to move to the next image
plane. To modify the boundary so that it fits the object in the current plane,
use the Add Node, Move Node, or Delete Node options within the Boundary
Editor. If you need to move some points, first click the right mouse button
to bring up the editing menu, then select the Move Node option. If you want to see the
exact location of the points, select the View/Overlay/Boundary Nodes command. Move the
cursor to a node, hold down the left mouse button and drag it to a new location.
Release the left mouse button to confirm the new location.
Step 7. Repeat Step 5 and Step 6 to continue working on a plane by
plane basis. Once all boundary lines are created, you can save the boundary
lines to a boundary file, and then create surface or volume rendering.
When you have only object boundaries or 3D contours created from other programs or 3D measurement
devices, you can use 3D-DOCTOR to edit and analyze the boundaries and create a
3D surface rendering for visualization.
The following are the steps for creating a 3D
rendering from contours with or without an image:
Step 1. Use File/New Workspace to open a blank window.
Step 2. Use the File/Boundary/Import Boundary command 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 native boundary data format
(*.BND) used by 3D-DOCTOR is an ASCII file. For each closed boundary, the first
number is the Z value, followed by point pairs of X and Y values (X,Y) along the
boundary. The last point is the same as the first point to indicate that it is a
closed boundary. The word "END" follows the last point of the boundary. The next
boundary starts the same way. After the "END" of the last boundary, the word
"END" is used one more time to indicate the end of the file. The following
example shows what the syntax looks like: 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
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 their 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/Simple or Complex Surface
Rendering command to create a 3D display of your data.
For 3D scientific data that do not have distinguishable object boundaries,
3D-DOCTOR provides an easy way to create 3D volume rendering for visualization
and analysis.
Click here to see an example.
The following are the steps for creating 3D Volume Rendering for Scientific
Data:
Step 1. Open the 3D image. If each image slice or plane is stored in a
separate file, use File/New Stack to create a 3D stack list.
Step 2. Use the 3D Rendering/Cube Boundary command to create a
cubic boundary for the 3D volume. If you want to visualize part of the 3D
volume, use the 3D Rendering/Split Object command of right mouse click on
the Split Object command to cut the cube.
Step 3. If the three dimensions have different scaling factor, for
example, the spacing between slices or pixels is not even, use
Edit/Calibrations to enter the scaling factor so the scales can be used
to correct the display of the 3D rendering.
Step 4. Use the 3D Rendering/Volume Rendering command to do the
3D rendering. Use the options under the View menu while in the Volume
View window display to select the desired rendering mode and adjust the display.
When
objects move during the imaging process or you are working with images taken at
different times, image slices may not be aligned properly and this can affect
the accuracy of image analysis. 3D-DOCTOR's Auto Alignment command uses maximum
likelihood algorithm to align slices automatically and accurately across the
stack.
Click here to see an example.
The following are the steps for auto alignment:
Step 1. Open
the 3D image. If each image slice or plane is stored in a separate file, use File/New Stack to create a 3D stack list.
Step 2. Define
an image region using the left mouse button. An image region is an area with
strong contrast, visible patterns, and variations.
Step 3. Select
the Image/Auto Alignment command. Adjust the matching parameters if needed and
define an output file name. Select "OK" to start the process. A properly aligned
image is created and saved as a new image file.
Step 4. Use File/Open to display the new image file.
Image deconvolution is used to remove or reduce degradations caused during
the imaging process. These include the blurring introduced by optical systems
and by image motion, as well as noise due to electronic and photometric sources.
3D-DOCTOR provides two types of deconvolution to restore degraded 3D images, one
is a Fast Nearest Neighbor deconvolution and the other is an iterative Maximum
Entropy deconvolution method.
Click here to see a deconvolution
example.
Although the deconvolution process is quite complex,
3D-DOCTOR provides a very simplified user interface to make it easy to use. To
do a deconvolution, you simply select the Image/Deconvolution/Maximum Entropy command
to start.
The following explains the parameters in the dialog box
that appears (See Figure) and how to define them:
The feedback factor is in the scale of 1 to 100. The larger
the feedback factor, the stronger the deconvolution will be applied during
iteration. However, if the original image is noisy, a smaller feedback factor
should be used to reduce the noise.
The “number of iterations” controls how many iterations the
process will take. If both the image and the point spread function (PSF) are in
good quality and do not have much noise, a smaller number of iterations may be
sufficient.
With 3D-DOCTOR, an object defined by object boundaries can be cut or split
into smaller objects. To get the most accurate 3D rendering, cutting an object
is done in 2 steps:
Step 1. Activate the image plane view window where the object boundary
is displayed. Select the Edit/Boundary Process/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 to confirm. 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, the Object management
dialog box appears. In this dialog box you can 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.
Movieclip test |
