This code here is designed to trace the vasculature in serial-two-photon-tomography (STPT). The code take normalized stitched TIF files, binarize them with two (local and global) threshold, skeletonize them, remove artifacts from skeletonization, and finally group/document the data with a .mat file.
Copy this folder to the data folder and execute the the following four files with Matlab. If you are using a slurm HPC system, you can try the slurm batch file.
-
- binarization
-
- skeletonization
-
- radii from skeleton
-
- tracking
- The code is currently only support the 1x1x5 um (5 um optical sectioning) resolution
- The file structure is fixed. All background TIF files are in folder ch1 and all foreground TIF files are in folder ch2. The TIF files need to neamed as Z###_ch##.tif.
Matlab 2019a
Free academic use.