minian 1.3.0

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

MiniAn

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

Prerequisites

• FFmpeg (ffmpeg and ffprobe on PATH for video I/O)

Quick Start Guide

1. (Recommended) Create and activate a fresh environment, e.g. python -m venv minian-env && source minian-env/bin/activate or conda create -y -n minian && conda activate minian
2. Install MiniAn, either:
   • with pip: pip install minian (install FFmpeg separately, see Prerequisites), or
   • from conda-forge: conda install -y -c conda-forge minian (includes FFmpeg)
3. Install the pipeline notebooks: minian-install --notebooks
4. Optional install the demo movies: minian-install --demo
5. 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.