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Neuropixels and OpenScope Workshop

September 21, 2022 - September 23, 2022

Co-hosted by Allen Institute for Neural Dynamics, Allen Institute MIndScope Program, and University of Washington

In this workshop, you will gain in-depth exposure to the tools and techniques used by the Allen Institute to collect in vivo physiology data at scale. The Allen Institute was a key contributor to the development of Neuropixels probes (along with researchers and engineers at HHMI Janelia Research Campus, University College London, and Imec), which are quickly becoming the standard for extracellular electrophysiology recordings. The Institute has also pioneered rigs and protocols needed for high-throughput recordings from the mouse visual system, which are now accessible to the community via the BRAIN Initiative–funded OpenScope program.

In this workshop, participants from around the world will have the opportunity to tour our in vivo electrophysiology and imaging facilities and learn the details of these methods from Allen Institute and UW scientists and staff. Lectures and demonstrations will cover all aspects of generating high-quality physiology datasets, from surgery to behavior training to neural recordings. Participants will also learn how to access data from the Allen Brain Observatory and about the OpenScope program.

You can expect to come away from the workshop with a better understanding of proven techniques for improving the quality and throughput of recordings in your own lab.

Applications are due June 1, 2022. The workshop is geared towards graduate students, postdocs, staff scientists, and PIs with some experience with in vivo recordings.

Workshop tracks

The workshop will last 3 days. All participants will complete the Foundations of Neuropixels and introduction to the Allen Brain Observatory on September 21-22. A subset will continue to Advanced Neuropixels Techniques on September 23; space in the advanced training is more limited. The program includes in-lab demos and tours, presentations, and discussions. Topics are subject to change and additional topics may be added.

Foundations of Neuropixels and introduction to the Allen Brain Observatory – all participants (September 21-22):

  • Days 1 and 2 will be held at the Allen Institute.

  • Lectures and demonstrations on surgical techniques, mouse behavioral training, Neuropixels probe insertion and recording, Neuropixels data acquisition software.

  • Roundtable discussions with Allen Institute and UW scientists.

  • Introduction to the OpenScope program.

  • Afternoon of September 22, participants select one of two tracks:

    • Track A, Neuropixels software: Lectures and software demonstrations on spike sorting, probe trajectory planning, and anatomical registration.

    • Track B, 2-photon imaging: Lecture and lab tour on 2-photon imaging and data analysis.

Advanced Neuropixels Techniques – advanced track participants only (September 23):

  • Day 3 will be held at the Steinmetz Lab at the University of Washington.

  • Lecture on chronic Neuropixels recording.

  • Lab demonstrations on multi-shank probes and combining Neuropixels with imaging.

  • Further discussions with Allen Institute and UW scientists.


Allen Institute
615 Westlake Avenue N.
Seattle, WA 98109 United States
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