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Published July 18, 2025 | Version v4.1.0
Software Open

MouseLand/Kilosort: Kilosort v4.1.0

Authors/Creators

  • 1. Janelia
  • 2. Group Leader
  • 3. @int-brain-lab @cortex-lab
  • 4. HHMI Janelia Research Campus
  • 5. Princeton Neuroscience Institute
  • 6. 1998
  • 7. Austrian Academy of Sciences - OEAW
  • 8. Humboldt-Universität zu Berlin
  • 9. Univ. of Texas Austin
  • 10. Stanford University
  • 11. Nara Medical University
  • 12. Luniondata
  • 13. Hausser Lab
  • 14. University of Colorado Denver
  • 15. Kyoto University
  • 16. Charité & Aix-Marseille Université
  • 17. Max Planck Institute for Plasma Physics

Description

This release includes includes a change to the default behavior of the clustering step. For each section of a probe, all spikes will be used in clustering up to a maximum of 25,000 spikes, which is a change from the old default of using every 20th spike (cluster_downsampling parameter) with no maximum spike count (max_cluster_subset parameter). The new settings are better-aligned with the methods published in the Kilosort paper.

The new default dramatically reduces sorting time for long recordings. For two ~13 hour Neuropixels datasets, sorting time was reduced by 65% with no qualitative change to sorting results. The change also did not impact Kilosort4's performance on the published benchmarks. Additionally, we expect better clustering of probe sections with low spike counts since they will be more densely sampled than before.

Full Changelog: https://github.com/MouseLand/Kilosort/compare/4.0.37...v4.1.0

Files

MouseLand/Kilosort-v4.1.0.zip

Files (831.7 kB)

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Additional details

Related works

Is supplement to
Software: https://github.com/MouseLand/Kilosort/tree/v4.1.0 (URL)

Software

Repository URL
https://github.com/MouseLand/Kilosort