a pipeline for calcium imaging data built out of modular components

This is a small package for performing common steps in processing calcium imaging data. There's actually very little code here, because all the analyses are implemented in separate packages. This just wraps them with common arguments into something that can be run from the command line.

If this doesn't match your needs, you can build your own version from the same components!

For now, just clone this repository and run by calling

bin/imaging-pipeline

Once it's more fleshed out it will be installable using pip.

Perform image registration.

Options

• -i input data
• -o output location
• -a algorithm

Perform source extraction.

Options

• -i input data
• -o output location
• -a algorithm

Generate a movie to visualize raw data with optional filtering and downsampling.

Options

• -i input data
• -o output location
• -ft temporal filtering
• -fs spatial filtering
• -dt temporal downsampling
• -ds spatial downsampling

Perform pixel-wise linear regression.

Options

• -i input data
• -o output location
• -x covariates

Summarize a data set using summary statistics (mean, variance, max, local correlation).

Options

• -i input data
• -o output location