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STPT Vasculature Tracer

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.

How to use

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.

    1. binarization
    1. skeletonization
    1. radii from skeleton
    1. tracking

Limitations

  • 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.

Environment

Matlab 2019a

Liscense

Free academic use.