Installation

You need FFmpeg on PATH for video I/O (ffmpeg and ffprobe). Install it with your OS package manager or follow the FFmpeg download page.

Install with pip

MiniAn is available on PyPI:

# regular installation (most platform compatible)
python -m pip install minian
# installation with optimized numba routines
python -m pip install 'minian[numba]'

We recommend installing into a fresh virtual environment. A pip install does not include FFmpeg, so make sure it is on your PATH (see above).

Note

Windows: if the install fails while unpacking deeply nested files (such as JupyterLab widget extensions), enable long path support and reinstall. Windows’ default 260-character path limit (MAX_PATH) truncates these paths. Set the registry value HKLM\SYSTEM\CurrentControlSet\Control\FileSystem\LongPathsEnabled to 1 (requires admin), or run as administrator in PowerShell:

Set-ItemProperty -Path 'HKLM:\SYSTEM\CurrentControlSet\Control\FileSystem' -Name 'LongPathsEnabled' -Value 1

Install with conda

MiniAn is also on conda-forge. Installing this way pulls in FFmpeg automatically, so it is convenient if you do not already have it:

conda create -y -n minian
conda activate minian
conda install -y -c conda-forge minian

You can use mamba as a faster drop-in replacement for conda when solving dependencies:

mamba install -y -c conda-forge minian

Install from source

Install from the GitHub repo to track the latest development or to contribute to MiniAn:

git clone https://github.com/miniscope/minian.git
cd minian/
python -m pip install -e .

This gives you an editable copy of MiniAn, so any change you make to the source is reflected in your pipeline. Maintainers can use pdm install to set up the locked development environment.

Getting notebooks and demos

The main features of MiniAn are exposed through the pipeline.ipynb and cross-registration.ipynb notebooks, backed by demo datasets hosted on Zenodo. Both are managed through the single minian command line tool, which has two command groups: minian notebooks for the bundled notebooks and minian data for the demo datasets. See Command line interface for the full command reference.

Notebooks

The notebooks ship inside the installed package. Copy one (notebook plus its figures) into your current folder with:

minian notebooks list              # show the available notebooks
minian notebooks copy pipeline     # -> ./minian-notebooks/pipeline/

Use -o/--output DIR to copy somewhere other than ./minian-notebooks/, or --all to copy every notebook.

Data

Each notebook fetches its demo recording automatically on first run (downloaded once, then cached and checksum-verified). You can also manage the demo datasets directly:

minian data list                      # show datasets + sizes
minian data download pipeline-demo    # download and cache the dataset
minian data path pipeline-demo        # print the local cached path

The demo datasets are hosted on Zenodo, each with its own citable DOI; see minian.data for details.

If you choose to Install from source you already have a local copy of everything and can check out different versions using git.

Start the pipeline

And that’s it! Once you have installed MiniAn and copied out a notebook (see above), start the jupyter interface on it with:

jupyter notebook minian-notebooks/pipeline/pipeline.ipynb

(Remember to activate the environment if your computer complains about command not found.)

You can then either run the notebook, or refer to Pipeline and Cross-registration for some ideas about expected outcomes when running with demo data.