Python tools for extracellular electrophysiology at the Wisconsin Institute for Sleep and Consciousness.
Updated 11/19/2024.
I reccomend Python 3.12. Currently, the bottleneck is numba (required by spikeinterface, and used in unit module code). It should support 3.13 by the end of the year.
You need to use the CSC-UW fork of spikeinterface. The specific branch you need depends on your intent. For running spike sorting, use wisc/sorting. For everything else, use wisc/dev.
If you are spike sorting, you probably also want pytorch for spikeinterface's drift correction.
Unfortuantely, this package cannot be published to PyPI so long as its dependencies include git URLs (e.g. our spikeinterface fork)
The parts of ecephys that are tied to our fork because of reliance on the old API need to be factored out into their own package. Then, hopefully updated and brought back in. Otherwise, they will block the package from being able to use the latest spikeinterface indefinitely.
Also, we desparately need to update from pandas 1.x to 2.x and/or polars (WIP).