This repository contains the data and analysis scripts for the paper Human pluripotent stem cell-derived microglia shape neuronal morphology and enhance network activity in vitro.

Data is available upon request.

Setup

All scripts were run using Python 3.11.

To clone and access this repo, run:

git clone https://github.com/koenhelwegen/hpsc-microglia-neuron-co-culture
cd hpsc-microglia-neuron-co-culture

Option 1: use a virtual environment (recommended)

To install & run within a virtual environment, run:

python3 -m virtualenv venv
source ./venv/bin/activate
python3 -m pip install -r requirements.txt

You may need to install virtualenv first:

python3 -m pip install virtualenv

Option 2: install requirements in main python environment

To install the requirements in your main python environment (WARNING: this may change the versions of previously installed packages), run:

python3 -m pip install -r requirements.txt

Analysis

To perform the analysis, run:

python3 analysis.py