I plan on breaking up this repo because its many of its contents are way too decoupled (e.g., bruker prairieview tricks / helpers vs experiment organization). All code related to computer-generated holography and holographic optogenetics will be migrated to my forthcoming neurobeam package (Neuroscience Experiments Using Real-time Optogenetics, BEhavior, and Microscopy). All prairieview specific code will become a submodule. Experiment organization will become a submodule and contain functionality to convert to and from the NWB format. It will be some time before this is updated; neurobeam is my primary focus.
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. I was inspired to upload my own code to solve some of the issues outlined in the motivation section of the docs or at least create a neat package my friends and I could use to easily analyze data across various environments and computers.
As of version 0.9.8, 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 and I have a newborn.
Until things are more stable, I'll explicitly note which subpackages are stable, have >90% test coverage, and are ready-to-use.
- The main module is ready to use as of 0.7.5. New features will be demarcated by a label indicating the version added in the docs.
- The organization module is untested but incorporated into the distributed pypi version
- The bruker module is untested but incorporated into the distributed pypi version
- The optogenetics module is untested but incorporated into the distributed pypi version
- The interactive module is unstable but partially incorporated into the distributed pypi version
- The optics module is unstable and not incorporated into the distributed pypi version
Eventually I will break things up into sub-packages so you don't have to install everything together...
pip install CalSciPy
Save me from myself, contributions welcome :)
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