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Vessel branch segmentation

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Segment the vessel branches from dynamic image of fluorescent microscopy

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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
http://www.mathworks.com/matlabcentral/fileexchange/11123-better-skeletonization

== 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
>> 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.

Comments and Ratings (5)

Sarina Lalla

The input of the read tiff function makes no sense.

Maziyar

I have same problem as lakshmi.
Appreciate if you could provide a sample input for the code you generated.

can any one please tell me how to Read Tiff format files in a directory and save it in a matlab file and in this code its asking for channel in the function data=VBSreadtiff(directoryName,channel)i tried giving 'r' and 'g' but its showing error....please help me as soon as possible

Joy King

Could you list a few references that we can read on this method, or any literature for the implementation please? Thank you!
There is also another problem. When I run the VesselBranchSegmentation.m, the GUI interface shows at the top of the screen without the title bar. I really don't don't know why. Could you help me?

Joy King

There is also another problem. When I run the VesselBranchSegmentation.m, the GUI interface shows at the top of the screen without the title bar. I really don't don't know why. Could you help me?

MATLAB Release
MATLAB 7.12 (R2011a)
Acknowledgements

Inspired by: Better Skeletonization

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