Vessel branch segmentation

Segment the vessel branches from dynamic image of fluorescent microscopy

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.