EpiStats: collection of morphological cell statistics from segmented 3D images of epithelial tissues

This repository contains tools for computing and analysing morphological statistics of cells in 3D images of epithelial tissues. It also provides methods to transform the segmented cells into mesh files and to fix these meshes in case they present any issues.

INSTALLATION:

Install venv if not already done

pip3 install virtualenv

Create a virtual environment

python3 -m venv EpiStatsVenv

Activate the virtual env

source ./EpiStatsVenv/bin/activate

Install the required packages

pip3 install -r requirements.txt

USAGE:

• Scripts for morphological statistics computation, data post-processing, and plotting is in

  src/statistics_collection/
  

• Scripts for mesh refinement and preparation is in

  src/mesh_fixing/