2022 Neuropixels and OpenScope Workshop

2022 Allen Institute Neuropixels and OpenScope Workshop Attendee Information

Workshop information

Thank you for joining us at the Allen Institute Neuropixels and OpenScope Workshop on September 21-23, 2022. All workshop information for attendees will be posted on this page as it becomes available. Please see below for important information on travel to the workshop, required pre-reading, and the workshop schedule.

Please note that your acceptance email indicates whether you have been accepted for the foundations course (September 21-22) or the advanced course (September 21-23). We have limited capacity in the advanced course due to space restrictions in the labs at UW.

If you have questions or technical difficulties, please contact events@alleninstitute.org.

Schedule     Pre-reading

Travel to the workshop

All participants: Plan to arrive at the Allen Institute by 8:30am on Wednesday, September 21.

Foundations participants: Plan to depart the Allen Institute at 5pm on Thursday, September 22.

Advanced Neuropixels Techniques participants: Plan to arrive at the University of Washington by 8:30am on Friday, September 23, and depart at 5pm.

Travel between SeaTac airport/Allen Institute:

  • Transit: Follow signs in the airport to the light rail. Ride to University Street station (not University of Washington or University District - the station between Pioneer Square and Westlake) and transfer to the Rapid Ride C line bus to the stop at Westlake and Mercer. The ride takes about an hour and costs $4.

  • Uber, Lyft, and other rideshare: Follow signs in the airport to the rideshare and taxi zone in the parking garage. The drive to or from the Allen Institute takes about 25 minutes during off-peak times and up to 50 minutes during rush hour. The fare is typically $40-50.

  • Taxi: Follow signs in the airport to the rideshare and taxi zone in the parking garage. The drive to or from the Allen Institute takes about 25 minutes during off-peak times and up to 50 minutes during rush hour. The fare is typically $40-50.

Advanced Neuropixels (Friday 9/23) participants only, travel between Allen Institute/UW:

  • The Advanced Neuropixels activities will be held in the UW Health Sciences Building. The building is locked at all times. Plan to meet at the front door of the Health Sciences Education Building by 8:45am. If you have trouble, contact Ljuvi at 650-271-1300.

  • Please see signage at the Allen Institute on Thursday for codes for free Lyft rides between South Lake Union and UW. There is a turnout for Lyft dropoffs at the Health Sciences Education Building.

  • For those wishing to leave directly from the University of Washington campus at the end of the workshop, the University of Washington light rail stop located at the football stadium is a flat ~10 minute walk from the Steinmetz lab.

We cannot host you at the Allen Institute after 5pm on Thursday, but we can provide recommendations of locations around the neighborhood to spend time before an evening flight if you have already checked out.

We will provide breakfast, lunch, and snacks on all days of the workshop for all participants.

Tentative Workshop Schedule

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. Your acceptance letter to the workshop indicates whether you have been accepted for the foundations course on September 21-22 or the advanced course that also includes September 23.

The schedule is subject to change.

Wednesday, September 21 - all participants

Speakers

Time

Arrive at Allen Institute

N/A

8:30-9:00am

Welcome and introductions

Josh Siegle and Jerome Lecoq

9:00-10:00am

Introduction to the Allen Brain Observatory

Pete Groblewski and operations team

10:00-11:00am

Pipeline standardization

MPE team

11:00am-12:00pm

Lunch

N/A

12:00-1:00pm

Rotate through lab demos (one hour each): Surgery (room 155), ISI (room 447), behavior (346), Neuropixels rigs (room 325)

TBA

1:00-5:00pm

 

Thursday, September 22 - all participants

Speakers

Time

Arrive at Allen Institute N/A 8:30-9:00am
Introduction to OpenScope Jerome Lecoq 9:00-10:00am
Neuropixels data acquisition software demo Josh Siegle 10:00-11:00am
Lunch and networking N/A

11:00am-1:00pm

 

Afternoon of Thursday, September 22 - split into two tracks. All participants have been assigned to the track requested at the time of application. If you cannot remember which track you requested, signs will be posted with your assignment.

Thursday, September 22 - Neuropixels track

Speakers

Time

Kilosort and Phy Nick Steinmetz 1:00-1:45pm
SpikeInterface Alessio Buccino 1:45-2:30pm
DataJoint for Neuropixels Kabilar Gunalan 2:30-3:00pm
Trajectory planning Dan Birman 3:00-3:30pm
Registering probe tracks to CCF Josh Siegle 3:30-4:00
Roundtable discussion of applying Allen Institute standardization and pipelines All participants (both tracks) 4:00-5:00pm

 

Thursday, September 22 - 2p track

Speakers

Time

Introduction to 2p technology Jerome Lecoq and Natalia Orlova 1:00-1:45pm
2p rig demo Sheilla Caldejon, Natalia Orlova, Sam Seid, Xana Waughman 1:45-2:30pm
Data QC Marina Garrett, Natalia Orlova, Sam Seid 2:30-3:15pm
DeepInterpolation in practice Jerome Lecoq 3:15-3:30pm
DataJoint for 2p Kabilar Gunalan 3:30-4:00pm
Roundtable discussion of applying Allen Institute standardization and pipelines All participants (both tracks) 4:00-5:00pm

 

Friday, September 23 - advanced course participants only

Speakers

Time

Arrive at UW - gather at Health Sciences Education Building by 8:45am N/A 8:30-9:00am
Chronic Neuropixels recordings Kasper Kondrakiewicz 9:00-10:00am
Recording with multishank Neuropixels 2.0 probes Nick Steinmetz 10:00-10:30am
Break   10:30-10:45am
Combining Neuropixels and imaging/optogenetics Zhiwen Ye 10:45-11:30am
Sorting quality metrics Noam Roth 11:30am-12:00pm
Lunch   12:00-1:00pm
Rotate between stations: Lab demo on Neuropixels 2.0 with widefield imaging; spike sorting and trajectory planning Anna Li, Zhiwen Ye, and Dan Birman 1:00-4:00pm
Networking N/A 4:00-5:00pm

Pre-reading

The workshop organizers have provided required and recommended pre-reading materials to help you prepare for the workshop.

Required pre-reading

Recommended pre-reading

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