Shared Resources


Neuropixels resources


  • Pinpoint software for probe insertion planning in the mouse brain. Developed by postdoc Dan Birman with undergraduates Kenneth Yang and Kai Nylund.
  • "Kilosort2", 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.

Hardware designs

  • Wheel task: hardware designs and software for deploying a behavioral task that we use. This resource was developed by the Carandini/Harris lab.