Shared Code and Datasets

  • Datasets recorded with Neuropixels probes.
  • Kilosort, a tool for faster and more accurate spike sorting, designed for very large datasets. Developed primarily by Marius Pachitariu.
  • Phy, a graphical user interface for manual-stage spike sorting, also designed for very large datasets. Developed primarily by Cyrille Rossant.
  • Spikes, code for performing many basic analyses of spike trains in Matlab.
  • sortingQuality, code for assessing the quality of spike-sorted neurons.
  • Widefield, code and GUIs for analyzing widefield calcium imaging data in Matlab.
  • allenCCF, code and GUIs for browsing and working with the Allen Institute's Common Coordinate Framework atlas in Matlab.
  • Alyx, a database framework for management of experimental subjects and associated datasets, in PostgreSQL. Developed with Cyrille Rossant, Max Hunter, and Kenneth Harris. Associated code for working with the database from Matlab.
  • Wiki and user forum for practical details of using Neuropixels probes. See also our training course on the use of Neuropixels probes.
  • Wheel task: hardware designs and software for deploying this task.