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MouseLand/Kilosort: Kilosort v4.0.33

Authors: Jake Pennington; Marius Pachitariu; Cyrille Rossant; Nick Steinmetz; carsen-stringer; Shashwat Sridhar; Jennifer Colonell; +23 Authors

MouseLand/Kilosort: Kilosort v4.0.33

Abstract

This release includes three main changes: Added matplotlib versions of the GUI plots to the API. These will be generated during sorting and stored in the results directory in the same manner. This also adds matplotlib to the list of required dependencies for non-GUI installations. Updated kilosort.bench.py to work with the current version of Kilosort4, and added a tutorial to readthedocs demonstrating how to run the benchmarks: https://kilosort.readthedocs.io/en/latest/tutorials/benchmark.html The API and GUI will now allow a list of paths to be specified for the filename argument/setting instead of requiring a single path, so that data stored as many files can be sorted without needing to concatenate it. Note that this only applies to binary files (.bin, .raw, etc). The data conversion tool skill expects a single file. If you want similar behavior for another file format, you can accomplish that with the API using RecordingExtractorAsArray and BinaryFileGroup from kilosort.io. Note for developers: making these changes required some re-organization of run_kilosort. I don't think this will be a problem since the overall argument/return structure is unchanged, but you may run into some differences. For example, filename is stored as a list instead of a Path even if only one path is specified, and that carries through the pipeline to be saved in params.py for Phy. Full Changelog: https://github.com/MouseLand/Kilosort/compare/v4.0.31...v4.0.33

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