A free online course on Neuropixels, 14-16 October 2024

Neuropixels probes are transforming neurophysiology, and are now adopted by hundreds of laboratories worldwide. This yearly online course trains scientists to use these probes in their experiments, and to process their output. The course is free and is supported by the Wellcome Trust. Lectures appear in our YouTube channel. Click on the titles below to see the videos. The exercises and other materials are in this GitHub page.
Days 1-2 (14-15 October 2024) had short talks that cover the basics so you can start working with Neuropixels probes, with lots of pointers to further resources and recent updates. People who are already expert users, or who took previous courses, may want to skip these days. Day 3 (16 October 2024), instead, did a deep dive into hot topics: developments of the Neuropixels probe; Neuropixels recordings across species; and the output of the International Brain Laboratory (IBL).
Organizers
- Célian Bimbard (UCL)
- Enny van Beest (UCL)
- Matteo Carandini (UCL)
Before the course
Install all software! Registered students will receive instructions for installing the IBL pipeline, IBLsort, phy, bombcell, UnitMatch, and more.
Day 1 - Introduction to Neuropixels - Part 1
- 1.1. Introduction: the past and future of Neuropixels - Matteo Carandini (UCL)
- 1.2. Planning your Neuropixels trajectory - Dan Birman (UW and IBL)
- 1.3. Recording hardware - Flora Takacs (UCL)
- 1.4.1 Recording software: SpikeGLX - Bill Karsh (HHMI and JHU)
- 1.4.2 Recording software: OpenEphys - Josh Siegle (Allen Institute)
- 1.5.1 Recording techniques: acute recordings - Karolina Socha (UCLA and IBL)
- 1.5.2 Recording techniques: chronic recordings - Célian Bimbard (UCL)
- 1.6 Inspecting raw data - Olivier Winter (IBL)
- 1.7.1 Spike sorting with SpikeInterface - Alessio Buccino (Allen Institute)
- 1.7.2 Spike sorting with IBLSort - Olivier Winter (IBL)
- 1.8 Exercises: inspecting and sorting raw data - Olivier Winter (IBL)
Day 2 - Introduction to Neuropixels - Part 2
- 2.1.1 Review of exercises: planning your Neuropixels trajectory - Dan Birman (UW and IBL)
- 2.1.2 Review of exercises: inspecting and sorting raw data - Olivier Winter (IBL)
- 2.2.1 Quality control with Phy and Bombcell - Julie Fabre (UCL)
- 2.2.2 Quality control with IBL metrics - Christopher Langfield (IBL)
- 2.3.1 Aligning spikes to brains with BrainGlobe - Alessandro Felder (UCL)
- 2.3.2 Aligning spikes to brains with the IBL GUI - Mayo Faulkner (IBL)
- 2.4 Tracking neurons across chronic recordings with UnitMatch - Enny van Beest (UCL)
- 2.5 IBL visualization - Matt Whiteway (Columbia University and IBL)
Day 3 - News of the Neuropixels world
- 3.1.1 Review of exercises: Bombcell - Julie Fabre (UCL)
- 3.1.2 Review of exercises: Align data to histology - Mayo Faulkner (IBL)
- 3.1.3 Review of exercises: IBL data visualization - Matt Whiteway (IBL)
- 3.2 Neuropixels Technology: an outlook - Carolina Mora Lopez (IMEC)
- 3.3.1 Neuropixels across species: NHPs - Eric Trautmann (Columbia)
- 3.3.2 Neuropixels across species: bats - Kevin Kaiwen Qi (UC Berkeley)
- 3.3.3 Neuropixels across species: octopus and squid - Kostas Tsaridis (OIST)
- 3.4.1 The IBL brainwide map: accessing the data - Mayo Faulkner, Miles Wells (IBL)
- 3.4.2 The IBL brainwide map: electrophysiological atlas - Yanliang Shi (IBL)
- 3.4.3 The IBL brainwide map: reproducibility - Marsa Taheri (IBL)
- 3.4.4 The IBL brainwide map: effect of age - Fenyin Zang (IBL)