Biomedical User Group Documents
This document is to teach you how to write a simple 3D Image Reconstructor which reconstructs 3D models from 2D medical images by using Biomedical Toolkit VIs.
If you have installed Biomedical Toolkit LabVIEW 2012(32-bit) Support version, it is very easy to load 2D slices from BMP/JPEG/PNG/DICOM images and do 3D visualization in LabVIEW 2012.
There are 4 main steps to write the 3D Image Reconstructor VI as the following block diagram shown:
Use Read Image Express VI to read images from files
Read Image Express VI is to load images from different file types, such as BMP, JPEG, PNG and DICOM.
VI Location
You could find Read Image Express VI on the palette of Biomedical Toolkit to load images from different file types, such as BMP, JPEG, PNG and DICOM:
Configure Read Image
- In the Read Action section, select Read multiple files when you want to load an image series.
- In the File Type section, select the image type you want to load.
- In the File Path Configuration section, do the following steps. Firstly, click Browse button next to the Folder path to select a folder path that the image files locate. Secondly, configure the name of image series in the Image Name Format subsection and Image Index subsection. For example, if the name of image series is CThead_000, CThead_001, … , CThead_112, then String prefix is CThead_, Number suffix width is 3, Start is 0 and End is 112. You can preview the file path through the File path preview.
- Once you configure the file path correctly, you can preview the images in the Preview Image section. Drag the Image index slider to preview one of the images from Start to End.
- (Optional) If the size of your input image series is too larger, you can downsample them by selecting Scale factor.
(Option) Advanced Configure Read Image
Check the Show folder path terminals?, then you can change the folder path programmatically instead of opening the Configure Read Image dialog to change the Folder path. But then you must decide the Output data type. If the image data type is U16 but you select U8, then the image data will be lost the high 8 bits.
Use 2D Viewer Control to display the 2D slices
Displays the X-Y, X-Z and Y-Z plane that intersect the coordinates of 3D volume data. You can mouse down and drag on the 2D Viewer to see the three planes under different positions.
Control Location
Set Properties
On the block diagram, right-click 2D Viewer and select “Create->Property (Invoke) Node”. Then you can set or get properties by using 2D Viewer Property nodes or invoke nodes. As the following snapshot shows, we can set the window center/length value and X/Y/Z coordinate by through their corresponding property nodes.
Short-cut Menu
Right-click 2D Viewer, you will find the Show Cursor, Show Color Ramp, Color Style and Display Default Window menu.
Show Cursor (Up/Low)
Displays the up or low cursor on the 2D Viewer. You also can use Up/Low Cursor Visible property to display the up or low cursor on the 2D Viewer programmatically.
Show Color Ramp
Displays the color ramp on the 2D Viewer. You also can use Ramp Visible property to display the ramp on the 2D Viewer programmatically.
Color Style
Color style of the 2D Viewer. You can select the predefined color map including Shaded, Color Spectrum and Gray Scale.
You also can customize color map. Select the High color and Low color.
Display Default Window
Display the images with the following window center/length value:
window center = (Max + Min)/2;
window length = Max-Min, Max specifies the maximum intensity value of the input 3D volume data while Min specified the minimum intensity value of the input 3D volume data.
You can also use Window Center/Length property to set the window center/length value programmatically.
Use the Isosurface Extractor VI to extract isosurface and isonormal from 2D slice.
VI Location
How to Use
After getting the 3D volume data by using Read Image Express VI, connect the 3D array output to the volume input terminal of Isosurface Extractor VI, which extracts the isosurface and isonormal from a 3D volume data set. Each page or slice of volume stores the volume data on a particular z-coordinate. On one page or one slice of volume, each row or column stores the volume data on a particular y- or x-coordinate. Spacing input terminal specifies the spacing between adjacent pixels or slices in x-, y- and z-axis, correspondingly. When you input DICOM image series and they have spacing properties, you can get the spacing attributes from Read Image Express VI and connect to the spacing input terminal of Isosurface Extractor VI.
Iso value specifies the volume level at which this VI generates the isosurface and isonormal. You should determine a suitable isovalue to generate the isosurface and isonormal.
Use the Draw Isosurface VI to draw the isosurface and isonormal to the 3D picture control
VI Location
This VI is not located on the palette. You find it under the folder …\National Instruments\LabVIEW 2012\vi.lib\addons\Biomedical\Medical Image.
How to Use
Connect the isosurface and isonormal output terminals of Isosurface Extractor VI to isosurface and isonormal input terminals of Draw Isosurface VI. Finally, connect the isosurface refnum to the 3D Picture Control.
You can operate the 3D Picture Control as follows:
- Shift + left-click: Zoom in or zoom out
- Ctrl + left-click: Move
- Alt + left-click: Rotate
The following is the front panel of the example VI described in this document. If you have installed Biomedical Toolkit LabVIEW 2012(32-bit) Support version, you can find this example under the folder …\National Instruments\LabVIEW 2012\examples\Biomedical\Medical Image. And you can find the sample data used in this example under …\National Instruments\LabVIEW 2012\examples\Biomedical\Data\image\CThead.
Feel free to let us know your questions in using these VIs and Controls.
