Shared Resources

Datasets

• Recordings of detailed neuronal waveforms made with Neuropixels Ultra: Download data here, explore data here.
• Electrophysiology and two-photon imaging data from an olfactory Pavlovian conditioning task from Ottenheimer, Hjort, Bowen et al. 2023.
• Neuropixels 2.0 recordings with imposed probe-brain motion from Steinmetz et al 2021.
• Neuropixels recordings during visual discrimination from Steinmetz et al 2019. Also accessible in Neurodata Without Borders (NWB) format here and via the Open Neurophysiology Environment (ONE) interface here.
• Recordings with eight Neuropixels simultaneously during spontaneous behavior from Stringer, Pachitariu, et al 2019.
• An example dataset recorded with a Neuropixels probe, with original raw data available.
• An example dataset recorded with two Neuropixels probes, from Jun, Steinmetz, Siegle, Denman, Bauza, Barbarits, Lee, et al 2017.

Neuropixels resources

• Wiki and user forum for practical details of using Neuropixels probes.
• Training course on the use of Neuropixels probes (see wiki for others).

Software

• 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.