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lightmicroscope_neuron_skeletonization

Automated processing of light microscope image stacks (.tif) using ImageJ, 3D skeletonization of processed stack, and efficient GUIs for neuron branching analysis. Saves results as excel file.

Alterations to pipeline:

  • 'processing_from_csvs.py' = lets user run GUIs and branching analysis from a csv file describing the x,y,z positions of every point in a point cloud of the neuron
  • 'run_branching_swc.py' = UNFINISHED. ideally, will let the user save their neuron branching structure as a swc file that can then be analyzed using other software

GUI Features:

pre-branching

  • removing noise clutter
  • connecting broken branches
  • setting root,start,and end nodes of neuron
  • setting threshold for branch length and number of nodes
  • setting scale of x,y,z pixels

post-branching

  • removing branches
  • naming branches
  • measuring euclidean distance between points
  • measuring angle between points
  • measuring branch lengths by fitting

Instructions for use

  1. Install dependencies
pip install -r requirements.txt
  1. Edit Main.py to point to correct file directory with .tif image stacks
root_folderpath = 'example\folder\path'

  1. Edit thresholding, nuclei removal, and slice removal settings in Main.py as desired

  2. Run Main.py

python Main.py