CalSciPy 0.3.5

A collection

CalSciPy

This python packages contains a variety of useful tools for handling, processing, visualizing, & designing calcium imaging experiments. I noticed I was constantly re-writing boilerplate, "one-liners", and copy/pasting code between environments. I wrote this so I don't have to you don't have to. 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, as well as a collection of more bespoke software designed for use with Bruker's PrairieView Imaging Software and MeadowLark Spatial Light Modulators. Essentially, it's a collection of code written for my imaging experiments that might be considered useful to others.

Active Development

• The current implementation is unstable and should be considered an open beta.

Highlights

• Assign unique colormaps to subsets of ROIs to generate rich, informative videos
• Perona-Malik diffusion for edge-preserving denoising
• Fast, convenient functions for handling, aligning, and compiling data collected in Bruker's PrairieView software
• Functions for generating protocols for use in Bruker's Prairieview.
• Interactive visualization of data

Installation

pip install CalSciPy

Documentation

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