This repository is a backup code posting in a slightly more accesible format than is also available on Dryad at: https://doi.org/10.5061/dryad.k0p2ngfg2. This codebase is a collection of the Jupyter notebooks used in running simulations (Julia) and analyzing/graphing data (Python).
Basic code for assembling a dataset from microscopy data is provided under Datasets Tools folder. Most is written in python for use as a script launched from the terminal (step1,3,4), and step 2 is a Jupyter notebook. Also included in the step2 part of the Datatoolsets part is the custom trained Stardist model used in the labeling of nuclei. All environments used for this work were done with Anaconda and the yml file for the environment is included under Coding Envs folder. Figure generation and analysis was done via Jupyter notebooks and python under the Figure Analysis Examples folder. Folder structure matches the figures of the linked publication. Also included are the Julia env file (Coding Envs) and the Julia code used to run the mathematical simulations for the work.
Feel free to ask questions or post comments to this Github which I will monitor!