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2024 Neuropixels course

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

A 4-shank Neuropixels 2.0 probe

Neuropixels probes are transforming neurophysiology, and are now adopted by hundreds of laboratories worldwide. This free online course trains scientists to use these probes in their experiments, and to process their output. The course is supported by the Wellcome Trust. Lectures from past years appear in our YouTube channel.  

The course is divided in two. Days 1-2 (14-15 October 2024) have many short talks that cover the basics to 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, does a deep dive into hot topics: developments of the Neuropixels probe; Neuropixels recordings across species; and the output of the International Brain Laboratory (IBL).   

To register, click here. Registration is free, but it must be completed by October 7. 

Organizers

Advisory Board

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

2-6 pm UK time

  • 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)
  • 1.8.1 Practical: plan a trajectory - Dan Birman (UW and IBL)
  • 1.8.2 Practical: spike-sort raw data - Gaelle Chapuis and Olivier Winter (IBL)
  • 1.8.3 Practical: inspect sorting results with viewEphys - Gaelle Chapuis and Olivier Winter (IBL)

Day 2 - Introduction to Neuropixels - Part 2

2-6 pm UK time

  • 2.1 Review of practicals from Day 1
  • 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 - Adam Tyson (UCL)
  • 2.3.2 Aligning spikes to brains with the IBL GUI - Mayo Faulkner (IBL) 
  • 2.4.1 Tracking neurons across chronic recordings with UnitMatch - Enny van Beest (UCL) 
  • 2.4.2 IBL visualization - Matt Whiteway (Columbia University and IBL)
  • 2.5.1 Practical: Quality control with Bombcell and IBL metrics - Julie Fabre (UCL)
  • 2.5.2 Practical: Align data to histology - Mayo Faulkner (IBL)
  • 2.5.3 Practical: Analyze neural activity on the IBL website - Matt Whiteway (IBL)
  • 2.5.4 Practical: Match neurons across days with UnitMatch - Enny van Beest (UCL) 

Day 3 - News of the Neuropixels world

2-5:30 pm UK time

  • 3.1 Review of practicals from Day 2
  • 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 - Miles Wells, Gaelle Chapuis, Mayo Faulkner (IBL)
  • 3.4.2 The IBL brainwide map: interpreting the data - Yanliang Shi, Marsa Taheri, Fenyin Zang (IBL)