photon-mosaic 0.2.0

Automating calcium imaging analysis

photon-mosaic

photon-mosaic is a Snakemake-based pipeline for the automated and reproducible analysis of multiphoton calcium imaging datasets. It currently integrates Suite2p for image registration and signal extraction, with plans to support additional analysis modules in the future.

 

Overview

photon-mosaic can leverage SLURM job scheduling, allows standardized and reproducible workflows configurable via a simple YAML config file and produces standardized output folder structures following the NeuroBlueprint specification.

This tool is especially suited for labs that store their data on servers directly connected to an HPC cluster and want to batch-process multiple imaging sessions in parallel.

The current structure sets the stage for future modular integration of preprocessing, neuropil decontamination and deconvolution of choice, and more.

Installation

Photon-mosaic requires Python 3.11 or 3.12.

conda create -n photon-mosaic python=3.12
conda activate photon-mosaic
pip install photon-mosaic

To install developer tools (e.g., testing and linting):

pip install 'photon-mosaic[dev]'

Contributing

We welcome issues, feature suggestions, and pull requests. Please refer to our contribution guidelines in the documentation for more information.

References & Links

• Snakemake Docs
• Suite2p Docs
• SLURM Executor Plugin
• NeuroBlueprint Standard