minian 2.0.0

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. Copy the pipeline notebook into your working directory: minian notebooks copy pipeline
4. Fire up jupyter and open it: jupyter notebook minian-notebooks/pipeline/pipeline.ipynb

The notebook downloads its demo recording automatically on first run (cached and checksum-verified). Browse and manage the bundled notebooks with minian notebooks list and the demo datasets with minian data list. See the command line interface reference for all commands and options.

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.