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Welcome to the Neuropixels User Guide wiki

Neuropixels 1.0 now publicly available! Visit neuropixels.org for more.

This website is intended as a practical user's guide to the use of Neuropixels Phase3 electrode arrays and the analysis of data they produce.

The information in the IMEC-supplied user manual supersedes anything on this website, so please reference that document first. Please request that manual from Tim Harris if you have probes but haven't received it.

The information provided here comes from users of the Neuropixels testers consortium, and should be taken as-is, and at your own risk. No one involved in the creation of this resource is responsible for your experiments working or your probes remaining intact.

Have a question that isn't answered here? Post an issue here and someone in the community may respond, or consider joining the Neuropixels Slack channel. To join the slack channel, click this link.

Training Courses

• Upcoming: 2023 October - UCL Neuropixels Course 2023: more information and signup
• 2022 October - UCL Neuropixels Course 2022
• 2021 October - UCL Neuropixels Course 2021
• 2020 July - University of Strathclyde
• 2020 June - Neuropixels Workshop at the Allen Institute for Brain Science
• 2020 April - UCL Neuropixels Course 2020
• 2019 July - FENS Cajal "Interacting With Neural Circuits"
• 2019 June - Neuropixels Workshop at the Allen Institute for Brain Science
• 2019 May - Paris Neuro
• 2019 April - UCL Neuropixels Course 2019
• 2018 October - FENS Cajal "Linking Neural Circuits and Behavior"
• 2018 May - Paris Neuro
• 2018 April - UCL Neuropixels Course 2018
• 2017 July - FENS Cajal "Interacting With Neural Circuits"
• 2017 May - UCL Neuropixels Course 2017

Getting Started

• 1.0 (aka 'Phase 3B') vs Phase3A vs 2.0
• About Neuropixels - probe description, terminology
• Equipment List, example setup and aligning data tips
• Probe handling/mounting
• Chronic implants
• Probe sharpening
• Probe care

Acquiring data

• Acquisition software
• Referencing and Grounding
• Gain settings
• Filter settings
• Impedance testing
• Synchronization
• Multiple probes on one computer
• Light artifacts
• Troubleshooting

Processing data

• Recommended preprocessing
• Spike sorting
• [Automated curation: quality metrics]
• Other analysis methods, and tutorial for getting started with Neuropixels Phase3 data in matlab
• Identifying tracks in histology

Thanks to Josh Siegle, who contributed some graphics and text to this resource.