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. Activate conda env: conda activate minian
5. Fix Panel installation:
   • On Windows: Copy panel files from .conda/envs/minian/site-packages/ to .conda/envs/minian/Lib/site-packages/
   • On Linux: Install panel with pip in minian conda environment: pip install panel=0.8.0
6. Install pywiz libraries with conda: conda install -n minian -c pyviz pyviz_comms=2.2.1
7. Install shot-scraper CLI tool in minian conda environment: pip install shot-scraper. If this is the first time you will have to install additional dependencies via shot-scraper install and/or playwright install. Follow the directions on the command line.
8. Install the pipeline notebooks: minian-install --notebooks
9. Optional install the demo movies: minian-install --demo
10. 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.