About MiniAn

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

Quick Start Guide

Option #1: conda

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/DeniseCaiLab/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 minian installation: source activate minian
7. Fire up jupyter: jupyter notebook and open the notebook "pipeline_noted.ipynb"

Option #2: docker

1. Download and install docker.
2. Read the notes below first then run: docker run -p 8888:8888 -v MY_DATA_PATH:/media denisecailab/minian:latest
3. Once you read the following, open a browser and navigate to localhost:8888:

The Jupyter Notebook is running at:
http://blahblah:8888
Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

Note: this approach runs everything in a more isolated docker container, which makes customizing/extending the code harder and may affect performance. It is recommended to use this approach only when you encounter errors during installation or running demo data with the first conda option, in which case it is highly recommended to submit an issue first as well.

As a result of isolation, you have to explicitly expose resources from within the container to your machine. In our case we want to expose two things: the network port that jupyter is listening to and a file system shared across your machine and the container. The -p 8888:8888 argument in the docker command expose port 8888 from within the container to port 8888 on your machine. If you prefer another port, for example in case another jupyter application is already running and occupies port 8888, change the number after the colon. The -v MY_DATA_PATH:/media argument creates a bind mount from MY_DATA_PATH on your machine to /media within the container, so that files under this two paths are synced and act as one, and you can refer to anything under MY_DATA_PATH by substituting that with /media from the notebook within the container. See here for more details and change the path to suit your needs.

As a final note, everything within the container does not persist across sessions except those in the bind mount, which means all the modifications you made to the default notebook under /minian will be reset to the state in the original image. Thus it is advised to keep a working copy of minian on your local machine and mount them in the container if you are using this in production mode.

License

This project is licensed under GNU GPLv3.