This repository contains a python pipeline to plot the spatial distribution of proliferative cells and total cells in the caudal fin of the developing zebrafish embryo, for the paper :”Tissue depolarization xxx” The jupyter notebook loads a series of .csv files containing XY positions of each cell, identified with the spot detection function in Imaris.
This notebook is compatible with Python 3 and has been tested with v. 3.11.6.
To use the code, please clone this repo. If in doubt how to do so, check this guide: https://github.com/git-guides/git-clone
Assuming you have cloned it into the folder proliferation_analysis, then you can use the following commands to install the required dependencies:
$ cd proliferation_analysis/
$ python3 -m venv proliferation-analysis/
$ python3 -m pip install -r requirements.txt
Then run the jupyter notebook proliferation_distribution.ipynb.
This automatically creates a folder where the plots are saved in .pdf format.