cellPACK analysis pipeline

Warning

This repository is a work in progress and is not yet ready for public use.

This repository contains tools that analyze cellPACK generated synthetic data and compare it to experimental data.

Installation

This project requires Python 3.11. The installation is managed using uv.

Dependencies are listed in the pyproject.toml file and locked in the uv.lock file.

1. Navigate to where you want to clone this repository

cd /path/to/directory/

2. Clone the repo from GitHub

git clone git@github.com:mesoscope/cellpack-analysis.git
cd cellpack-analysis

3. Install the dependencies using uv

uv sync

4. Activate the virtual environment

Activate the virtual environment in the terminal:

For Windows:

\path\to\venv\Scripts\activate

For Linux/Mac:

source /path/to/venv/bin/activate

You can deactivate the virtual environment using:

deactivate

Alternative installation using pip

This project also includes a requirements.txt generated from the uv.lock file, which can be used to install requirements using pip.

Note

This installation method will only install core dependencies. We recommend using uv to handle more complex installations of development and optional dependencies.

After cloning the repository, follow these steps:

1. Create and activate a new virtual environment

python -m venv .venv
source .venv/bin/activate

2. Install the dependencies using pip

pip install -r requirements.txt

3. Install the package

pip install -e .

Example usage

Analyze the radial bias for peroxisomes in cells from the hiPSC single cell image dataset.

1. Download images

python cellpack_analysis/preprocessing/get_structure_images.py --structure-id SLC25A17

2. Get meshes from images

python cellpack_analysis/preprocessing/get_meshes_from_images.py --structure-id SLC25A17

3. Run simulations with radial bias rules

python cellpack_analysis/packing/run_packing_workflow.py -c cellpack_analysis/packing/configs/examples/peroxisome_example.json

4. Extract structure coordinates from segmented images

python cellpack_analysis/preprocessing/get_structure_coordinates.py --structure-id SLC25A17

5. (WIP) Calculate grid distances from membrane and nucleus

python cellpack_analysis/preprocessing/calculate_available_space.py --structure-id SLC25A17

6. (WIP) Run distance analysis workflow

python cellpack_analysis/workflows/run_analysis_workflow.py -c cellpack_analysis/workflows/configs/distance_analysis_config_peroxisome.json