About MiniAn

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

Quick Start Guide

1. Download and install conda.
2. Make sure your conda is up to date: conda update -n base -c default conda
3. Download the MiniAn package: git clone https://github.com/phildong/minian.git
4. Go into MiniAn folder you just cloned: cd minian/
5. Create an conda environment: conda env create -n minian -f environment.yml
6. Activate the conda enviornment you created during CaImAn installation: source activate minian
7. Fire up jupyter: jupyter notebook and open the notebook "pipeline_noted.ipynb"

Additional steps for Windows:

The package cvxpy in conda-forge channel is out-dated and you would need to install with pip. Here are the steps:

1. Download and install Visual C++ Build Tools
2. Within the minian environment, do: pip install --upgrade cvxpy