Pipeline

pipeline.ipynb is the main MiniAn analysis pipeline: load videos, pre-processing, motion correction, seed initialization, then CNMF spatial and temporal updates, and visualization.

Running this notebook

Copy the notebook out of the installed package and open it with Jupyter:

minian notebooks copy pipeline
jupyter notebook minian-notebooks/pipeline/pipeline.ipynb

See Installation for installation and Command line interface for the full command reference.

The notebook fetches its demo movie automatically via minian.data.fetch() (cached and checksum-verified, no manual download step). The demo is a mouse CA1 recording acquired on a Miniscope V3, 5x temporally downsampled (10 msCam .avi files, 2000 frames at 480x752).

Using your own data

To run the pipeline on your own recording, edit the dpath cell near the top of the notebook to point at your data directory.