CalSciPy 0.3.0

A collection

CalSciPy

This python packages contains a variety of useful methods for handling, processing, and visualizing calcium imaging data. It's intended to be a collection of useful, well-documented functions often used in boilerplate code alongside software packages such as Caiman, SIMA, and Suite2P.

Highlights

• Assign unique colormaps to subsets of ROIs to generate rich, informative videos
• Perona-Malik diffusion for edge-preserving denoising
• Methods for handling Bruker's PrairieView data
• Interactive visualization

Installation

pip install CalSciPy

Subpackages

• Bruker - MAIN
• Coloring - TODO
• Event Processing - DEV
• Input/Output (I/O) - MAIN
• Image Processing - DEV
• Interactive Visuals - TODO
• Reorganization - MAIN
• Signal Processing - DEV
• Static Visuals - TODO

Documentation

Hosted at ReadtheDocs. Available locally as HTML, LATEX and PDF.

Roadmap

TODO - UNDOCUMENTED / OFFLINE
DEV - UNTESTED / IN DEV BRANCH
MAIN - COMPLETE / IN MAIN BRANCH

Generally completing each module before the next.
Exceptions done last:

• Bruker's Prairiview XML
• Bruker's Prairieview ENV parsing
• Trace Processing's Diffusion
• Event Processing's Covariance
• Interactive's ROI methods