MiniAn
MiniAn is an analysis pipeline and visualization tool inspired by both CaImAn and MIN1PIPE package specifically for Miniscope data.
Prerequisites
- FFmpeg (
ffmpegandffprobeonPATHfor video I/O)
Quick Start Guide
- (Recommended) Create and activate a fresh environment, e.g.
python -m venv minian-env && source minian-env/bin/activateorconda create -y -n minian && conda activate minian - 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)
- with pip:
- Copy the pipeline notebook into your working directory:
minian notebooks copy pipeline - 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.
2 maintainers
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