Metadata-Version: 2.4
Name: minian
Version: 1.3.0
Summary: MiniAn is an analysis pipeline and visualization tool inspired by both CaImAn and MIN1PIPE package specifically for Miniscope data.
Keywords: calcium-imaging,miniscope,neuroscience,cnmf,image-processing
Author-Email: MiniAn Developers <denisecailab@gmail.com>
License-Expression: GPL-3.0-or-later
License-File: LICENSE
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Project-URL: Homepage, https://github.com/miniscope/minian
Project-URL: Documentation, https://minian.readthedocs.io/
Project-URL: Repository, https://github.com/miniscope/minian
Project-URL: Issues, https://github.com/miniscope/minian/issues
Project-URL: Changelog, https://github.com/miniscope/minian/blob/master/CHANGELOG.md
Requires-Python: >=3.10
Requires-Dist: bokeh>=1.4.0
Requires-Dist: cvxpy>=1.1.11
Requires-Dist: dask>=2025.1.0
Requires-Dist: datashader>=0.12.1
Requires-Dist: distributed>=2025.1.0
Requires-Dist: ecos>=2.0.7
Requires-Dist: ffmpeg-python>=0.2.0
Requires-Dist: holoviews>=1.12.7
Requires-Dist: jinja2>=2.11.3
Requires-Dist: jupyter
Requires-Dist: matplotlib
Requires-Dist: medpy>=0.4.0
Requires-Dist: natsort
Requires-Dist: netcdf4
Requires-Dist: networkx>=2.4
Requires-Dist: numpy>=1.20.2
Requires-Dist: opencv-python>=4.2.0.34
Requires-Dist: pandas>=1.2.3
Requires-Dist: panel>=0.8.0
Requires-Dist: pyfftw>=0.12.0
Requires-Dist: rechunker>=0.3.3
Requires-Dist: scikit-image>=0.18.1
Requires-Dist: scikit-learn>=0.22.1
Requires-Dist: scipy>=1.4.1
Requires-Dist: scs
Requires-Dist: simpleitk>=2.0.2
Requires-Dist: sk-video
Requires-Dist: sparse>=0.11.2
Requires-Dist: statsmodels>=0.11.1
Requires-Dist: tifffile
Requires-Dist: xarray>=0.17.0
Requires-Dist: zarr
Provides-Extra: numba
Requires-Dist: numba>=0.52.0; extra == "numba"
Provides-Extra: test
Requires-Dist: minian[numba]; extra == "test"
Requires-Dist: pytest>=8.4.1; extra == "test"
Requires-Dist: pytest-cov>=7.1.0; extra == "test"
Requires-Dist: ruff>=0.15.14; extra == "test"
Requires-Dist: psutil>=7.2.2; extra == "test"
Description-Content-Type: text/markdown

<p align="center">

![minian logo](img/minian_logo.png)

</p>


[![pytest status](https://github.com/miniscope/minian/workflows/pytest/badge.svg?branch=master)](https://github.com/miniscope/minian/actions?query=workflow%3Apytest)
[![codecov](https://codecov.io/gh/miniscope/minian/branch/master/graph/badge.svg)](https://codecov.io/gh/miniscope/minian)
[![conda version](https://img.shields.io/conda/vn/conda-forge/minian.svg)](https://anaconda.org/conda-forge/minian)
[![documentation status](https://readthedocs.org/projects/minian/badge/?version=latest)](https://minian.readthedocs.io/en/latest/?badge=latest)

[![license](https://img.shields.io/github/license/miniscope/minian)](https://www.gnu.org/licenses/gpl-3.0)
[![code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
[![commit style](https://img.shields.io/badge/commit_style-conventional-orange)](https://conventionalcommits.org)


# MiniAn

MiniAn is an analysis pipeline and visualization tool inspired by both [CaImAn](https://github.com/flatironinstitute/CaImAn) and [MIN1PIPE](https://github.com/JinghaoLu/MIN1PIPE) package specifically for [Miniscope](http://miniscope.org/index.php/Main_Page) data.

# Prerequisites

- [FFmpeg](https://ffmpeg.org/download.html) (`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`
1. 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)
1. Install the pipeline notebooks: `minian-install --notebooks`
1. Optional install the demo movies: `minian-install --demo`
1. 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](https://minian.readthedocs.io/en/latest/start_guide/contribute.html) for more detail!

# License

This project is licensed under GNU GPLv3.
