2023 Neuropixels course

A free online course on Neuropixels, 17-18 October 2023

Neuropixels probes are transforming neurophysiology, and are now adopted by hundreds of laboratories worldwide. This free online course trained scientists to use these probes in their experiments, and to process their output. The course is supported by the Wellcome Trust. Click on the titles of the lectures to see them in our YouTube channel.  

The 2023 course is divided in two days. Day 1 (17 October 2023) covered the basic knowledge needed to start working with Neuropixels probes. Day 2 (18 October 2023) did a deep dive into 4 hot topics: the latest release of Neuropixels 2.0, Kilosort, chronic recordings implants and unit-tracking software.  

Organizers

• Célian Bimbard (UCL)
• Enny van Beest (UCL)

Advisory Board

• Matteo Carandini (UCL)
• Nick Steinmetz (UW)

Day 1 - Introduction to Neuropixels

Day 1 covers the basics with many short talks. These provide a quick summary of the basics with lots of pointers to resources with in-depth info and recent updates. People who are already expert users or who took previous courses may want to skip this day.

• 1.1. Introduction to Neuropixels (PDF) - Matteo Carandini (UCL) 
• 1.2. Neuropixels technology (PDF) - Carolina Mora Lopez (imec)
• 1.3.1 Neuropixels trajectory explorer - Andrew Peters (Oxford)
• 1.3.2 Trajectory planning with HERBS - Pearl Saldanha (NTNU)
• 1.3.3 Trajectory planning with Pinpoint (PDF) - Dan Birman (UW and IBL)
• 1.4. Recording hardware (PDF) - Julie Fabre (UCL)
• 1.5.1 Recording software: SpikeGLX (PDF) - Bill Karsh (HHMI and JHU) 
• 1.5.2 Recording software: OpenEphys (PDF) - Josh Siegle (Allen Institute)
• 1.6.1 Acute recordings with Neuropixels (PDF) - Enny van Beest (UCL) 
• 1.6.2 Surgical techniques for brainwide recordings - Anna Lakunina (Allen Institute)
• 1.7 Spike sorting and SpikeInterface (PDF) - Alessio Buccino (Allen Institute)
• 1.8.1 Quality control for Neuropixels data (PDF) - Julie Fabre (UCL) 
• 1.8.2 Spike sorting quality metrics (PDF) - Noam Roth (UW and IBL)
• 1.9.1 Aligning spikes to histology with BrainGlobe (Slides) - Adam Tyson (UCL)  
• 1.9.2 Aligning spikes to histology with HERBS - Pearl Saldanha (NTNU)
• 1.9.3 Aligning spikes to histology with the IBL GUI (PDF) - Mayo Faulkner (IBL) 
• 1.10. Reproducible Neuropixels recordings and the IBL map (PDF) - Chris Langdon (Princeton and IBL)

Day 2 - News of the (Neuropixels) world

Day 2 has in-depth talks about recent Neuropixels developments: Neuropixels 2.0, Kilosort 4, chronic implants, and software to track neurons across days. These lectures require basic knowledge of Neuropixels (e.g. as provided by the lectures on Day 1).  

• 2.1. Kilosort (Slides) - Marius Pachitariu (Janelia)
• 2.2. Neuropixels 2.0 and Ultra (PDF) - Nick Steinmetz (UW)
• 2.3. Chronic Neuropixels implants (PDF) - Célian Bimbard (UCL)
• 2.4.1 Tracking neurons across days with Kilosort (PDF) - Anna Lebedeva (UCL)
• 2.4.2 Tracking neurons across days with EMD (PDF) - Augustine Yuan (JHU)
• 2.4.3 Tracking neurons across days with UnitMatch (PDF) - Enny van Beest (UCL)