seg_track_shape_2d

Python code to analyze cell shape changes over time in 2d

• segments cells using stardist
• tracks cells using trackpy
• visualises tracks and plots shape features

Installation

• install python using anaconda (or miniconda https://docs.conda.io/en/latest/miniconda.html)
• open terminal and navigate to a suitable folder on a disk with enough space (cd ...)
• git clone https://github.com/m-albert/seg_track_shape_2d.git
• cd seg_track_shape_2d
• on MAC:
  • check if gcc-9 is installed, if not run 'brew install gcc'
  • export CC=gcc-9
  • export CXX=g++-9
• conda env create --file seg_track_shape.yml

Usage

• open terminal and navigate to folder /seg_track_shape_2d
• conda activate seg_track_shape
• jupyter notebook (a browser window should open)
• in the browser, open the notebook segment_track_analyse.ipynb