slarson / minian

miniscope analysis pipeline with interactive visualizations

MiniAn

MiniAn is an analysis pipeline and visualization tool inspired by both CaImAn and MIN1PIPE package specifically for Miniscope data.

Quick Start Guide

1. Create a new conda env: conda create -y --name minian
2. Activate the environment: conda activate minian
3. Install MiniAn: conda install -y -c conda-forge minian
4. Install the pipeline notebooks: minian-install --notebooks
5. Optional install the demo movies: minian-install --demo
6. Fire up jupyter: jupyter notebook and open the notebook "pipeline.ipynb"

Documentation

MiniAn documentation is hosted on ReadtheDocs at:

https://minian.readthedocs.io/

Contributing to MiniAn

We would love feedback and contribution from the community! See the contribution page for more detail!

License

This project is licensed under GNU GPLv3.