Repo for analysing hydra reaggregation data.

Cell tracking, calcium signal processing, and analysis of regeneration of ensembles.

Installation

To install this into a new mamba env:

First clone the github repo and navigate into it

$ cd <directory_where_repo_will_be_cloned> # i.e. desktop or github, wherever you want the code to be
$ git clone <repo_url> # clone repo
$ cd <repo>

Create a new mamba environment and install python

$ mamba create -n rebirth python, ipykernel # env will be called rebirth. Add ipykernel if using jupyter notebooks
$ mamba activate rebirth

Install the package and requirements

$ pip install -e . # Install in editable mode for now
$ pip install -r requirements.txt

Usage

• Notebooks for loading multiple tiff stacks and creating a memmap file from them
• Notebooks for loading these memmap files and visualising the data
• Notebooks for tracking the tdTomato labelled cells
• Notebooks for using the tracked tdTomato