Vessel branch segmentation
Updated 5 Apr 2012
Segment the blood vessels from a dynamic image of fluorescent microscopy.
== Install ======
- Add all attached files to matlab path
- Download "Better Skeletonization" from following URL and add to matlab path
== Instruction =========
1. Save time lapse images by tiff format in a directory.
The alphabetical order of file name must correspond to the order of time frame.
2. Read Tiff format files in a directory and save it in a matlab file.
>> imgData = VBSreadTiff('directory name');
Here, "imgData" is a structure of x,y,t image and the header of tiff.
3. Lounch VesselBranchSegmentation
4. In Menu, Select "File > New", then select a saved matfile.
5. In Menu, Select "Estimation > Vessel Mask", then vessel region is extracted from vessels.(*)
6. In Menu, Select "Estimation > Vessel Class", then vessel region is classified into artery and vein.(*)
This process takes a bit long time (~ 1 hour).
7. In Menu, Select "Estimation > Segmentation to Branches".
New window appears and skeleton of artery mask is calculated. (**)
Then press "To branch" button for segmentation to vessel branches.
After closing the skeleton-shown window, repeat the same process for vein region.
(*) The extracted mask can be modified by the edit tool.
Turn "Editable checkbox" on to use the edit tool.
See the document of impoly function for details.
(**) The undesired skeleton will be calculated for low SNR images because of the ambiguous edge of vessel.
The skeleton can be manually modified by the edit tool in the window.
Hiroshi Kawaguchi (2023). Vessel branch segmentation (https://www.mathworks.com/matlabcentral/fileexchange/36031-vessel-branch-segmentation), MATLAB Central File Exchange. Retrieved .
MATLAB Release Compatibility
Platform CompatibilityWindows macOS Linux
- Sciences > Biological and Health Sciences > Biomedical Imaging >
- Sciences > Physics > Biological Physics >
Inspired by: Better Skeletonization
Community Treasure Hunt
Find the treasures in MATLAB Central and discover how the community can help you!Start Hunting!
Discover Live Editor
Create scripts with code, output, and formatted text in a single executable document.