CalSciPy 0.7.5

A toolbox for analyzing, designing, and visualizing multiphoton imaging & optogenetics experiments.

CalSciPy

CalSciPy is a utility toolbox for calcium imaging experiments. It contains a variety of useful features, from interactive visualization of data to computer-generated holography for "read/write" experiments, and everything in-between. Essentially, it's a collection of code written for my imaging experiments that might be considered useful to others. Its inspiration is to solve the following issues:

Motivation: I was inspired to upload my own code to solve some of these issues--or at least create a neat package my friends and I could use to easily analyze data across various environments and computers.

1. 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. Examples of such tasks include compiling imaging stacks, normalizing signals to baselines, reorganizing data, and common data visualizations. No more wasting time writing 6 lines to simply preview your tiff stack, extract a particular channel, or bin some spikes. No more vague tracebacks or incomplete documentation when re-using a hastily-made function from 2 months ago.

2. Most scientific software these days have GUIs. But if you want to visualize your data after performing some arbitrary transformation? Womp womp. Maybe you use different tools to extract the same sorts of data, and just want one darn gui to look at them both? Womp womp Well, I want generic, interactive visualization tools. I want to assess the quality of spike inference from recently published spike-finder number #12, I want to sort through ROIs, and I want to explore population activity. I want to do so directly from the relevant data--independent of the software used to collect or analyze it. I want to have my delicious cake and eat it too. So I made some interactive visualization tools that require only the exact information that ought to be required to plot them.

3. I needed tools for holographic optogenetics, "read/write" experimentation, and general optics in python for my own experiments. Since I was already doing it, why not make them abstracted enough for all neuroscientists to use...not for only the optical or imaging experts. I want them to be tested, documented, and easy-to-use.

4. I needed some more bespoke software for use with Bruker's PrairieView imaging software for tasks such as parsing metadata, generating protocols programmatically, and aligning collected data.

5. Finally, I wanted a flexible & extensible system for neatly organizing & timestamping data.

Active Development

The current implementation is unstable, partially untested, partially finished, and should be considered an open alpha/beta. Please be patient, refactoring my code for public use is a pet-project. I have to graduate at some point.

Stable Modules

Until things are more stable, I'll explicitly note which modules' are stable, have >90% test coverage, and are ready-to-use.

• io_tools as of version 0.4.0

Installation

Eventually I will break things up into sub-packages so you don't have to install everything together...
pip install CalSciPy

Contributions

Save me from myself

Documentation

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