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NWB Workshops and Hackathons

Remote hackathon

Welcome to the 9th NWB User Days Workshop!

Dates and Location

Overview

The workshop will focus primarily on user training, including lessons for complete beginners to NWB and training in more advanced usage of NWB. There will be breakout sessions where the developers of state-of-the-art data analysis, visualization, and management tools (e.g., CaImAn, SpikeInterface, DANDI, suite2p, DataJoint, and more) will demonstrate their tools and show how to use NWB with their tools. There will also be time for attendees to work on NWB-related projects, such as converting data to NWB, using NWB-compatible software tools, or going through the NWB online tutorials.

To accommodate researchers in Europe, the Middle East, and Africa, we are holding this workshop 9am-6pm Central European Time (UTC+2).

Registration

Registration is now closed. Please stay tuned for the next NWB User Days Workshop in 2021.

The workshop is open to the public. Please complete our registration form to attend the event.

Note: The workshop schedule is centered around 9am-6pm Central European Summer Time (UTC+2).

Logistics

We will be using the Zoom videoconferencing platform for the meeting. We will send an email in the days before the workshop with Zoom links.

It is possible to use Zoom from the browser, but we recommend you install the Zoom app on your computer or phone. See installation instructions here.

Organizing Committee

Program chairs: Ryan Ly, Benjamin Dichter, Andrew Tritt, Pam Baker, and Oliver Rübel

Additional organizational support is provided by the Kavli Foundation.

Resources

Recorded talks will be uploaded after the talks are given.

How to prepare?

Install the Python or MATLAB software for NWB:

Projects

During the workshop, there will be time to work on NWB-related projects to practice using the NWB software and ask questions to the NWB developers. Working on a project is optional but encouraged for you to get the most out of this workshop.

Here are suggestions for projects:

Please create a project page with a description of the goals of your project. See the instructions here to create a project page. We will use these pages to connect people who are working on similar projects (e.g. converting data from the same acquisition system) and follow your progress.

If you have questions about choosing a project or creating a project page, please attend the pre-workshop session on Thursday, September 17 at 4-4:30pm CEST (Zoom link will be sent by email) or email the organizers.

Project Pages

Objective

The Neurodata Without Borders: Neurophysiology project (NWB, https://www.nwb.org/) is an effort to standardize the description and storage of neurophysiology data and metadata. NWB enables data sharing and reuse and reduces the energy barrier to applying data analysis both within and across labs. Several laboratories, including the Allen Institute for Brain Science, have wholeheartedly adopted NWB. The community needs to join forces to achieve data standardization in neurophysiology.

The purpose of the NWB User Days training workshops is to bring the experimental neurophysiology community together to further the adoption and development of NWB, the NWB software libraries, and scientific workflows that rely on NWB. Members of the community will exchange ideas and best practices for using NWB, share NWB-based tools, surface common needs, resolve coding issues, make feature requests, brainstorm about future collaboration, and make progress on current blockages. The event will also enable NWB developers and users to interact with each other to facilitate communication, gather requirements, and train users.

Agenda

All times are in Central European Summer Time (CEST; UTC+2)

This calendar view shows the workshop agenda. We strongly encourage you to attend the first three hours of Day 1 for an introduction to NWB and NWB software tools. In the afternoons of all three days, there will be optional breakout sessions where you can learn more about community software tools that support NWB. And in the mornings of Days 2 and 3, there will be optional tutorials on how to use NWB for different types of data and situations, as well as a discussion about NWB and data standardization in neurophysiology on Day 3.

We recommend that you attend the sessions that would be useful to you. When you are not attending a session, we encourage you to work on your NWB-related projects (e.g., converting your data to NWB, doing NWB exercises, running the tutorials yourself). Developers will be available to answer questions on Slack throughout the workshop, as well as on Zoom during the virtual coffee breaks.

You can add this Google Calendar or iCal calendar to your personal calendar to see the workshop sessions in your time zone.

Agenda calendar graphic

Detailed agenda:

Day 1 Monday, September 21
8:45 - 9am (CEST) Call-in time, work out any technical issues
9 - 9:10am Welcome and introduction: How to get the most out of this workshop (Ryan Ly)
9:10 - 9:55am Overview of NWB: An ecosystem for neurophysiology data standardization (Oliver Ruebel)
Recording on YouTube
10 - 11:45am NWB tools showcase (5-7 min per tool),
- MIES
- calciumImagingAnalysis
- CaImAn
- suite2p
- SpikeInterface
- DataJoint
- NWB Explorer / Open Source Brain
- NWB Widgets
- DANDI
- NWB & DataJoint Integration in the Frank Lab, UCSF
12 - 1pm Break / Virtual coffee shop - Hack on projects, do NWB exercises, ask questions to NWB developers on Zoom
1 - 2pm Tutorial: Reading NWB data in Python and Matlab (Ben Dichter, Ryan Ly)
2 - 6pm In-depth tool breakout sessions, Day 1:
2 - 2:55pm NWB Explorer / Open Source Brain - Padraig Gleeson, Matteo Cantarelli
3 - 3:55pm CaImAn - Changjia Cai, Andrea Giovannucci
Recording on YouTube
4 - 4:55pm suite2p - Carsen Stringer
Recording on YouTube
5 - 5:55pm SpikeInterface - Alessio Buccino, Cole Hurwitz
Recording on YouTube
Day 2 Tuesday, September 22
9 - 9:55am Introduction to NWB for intracellular electrophysiology (Oliver Ruebel, Pam Baker)
10 - 10:55am Introduction to NWB for extracellular electrophysiology in Python (Ryan Ly)
11 - 11:55am Introduction to NWB for extracellular electrophysiology in MATLAB (Ben Dichter)
12pm - 12:55pm Introduction to NWB for optical physiology in Python (Ryan Ly)
1pm - 1:55pm Introduction to NWB for optical physiology in MATLAB (Ben Dichter)
2 - 3pm Break / Virtual coffee shop - Hack on projects, do NWB exercises, ask questions to NWB developers on Zoom
3 - 6pm In-depth tool breakout sessions, Day 2:
3 - 3:55pm DANDI - Yaroslav Halchenko, Satrajit Ghosh
4 - 4:55pm NWB Widgets - Ben Dichter
Recording on YouTube
5 - 5:55pm calciumImagingAnalysis - Biafra Ahanonu
Recording on YouTube
Day 3 Wednesday, September 23
9 - 9:45am NWB extensions: How to store and share non-standardized data types in NWB (Ryan Ly)
Recording on YouTube
9:50 - 10:20am Advanced write in PyNWB (compression, chunking, iterative write, and parallel access) (Andrew Tritt)
<a href=https://youtu.be/wduZHfNOaNg>Recording on YouTube</a>
10:20 - 10:40am Advanced write in MatNWB (compression, chunking, and iterative write) (Ben Dichter)
<a href=https://youtu.be/PIE_F4iVv98>Recording on YouTube</a>
10:40 - 10:55am Review of workshop projects
11 - 11:55am Discussion: The current state of NWB and data standardization in neurophysiology
  • What is the future of NWB?
  • What would you like to see in NWB that is not yet supported?
  • What hardware and software tools would you like to see integrated with NWB?
  • How can we make NWB easier for you to use?
12 - 3pm Break / Virtual coffee shop - Hack on projects, do NWB exercises, ask questions to NWB developers on Zoom
3 - 6pm In-depth tool breakout sessions, Day 3:
3 - 3:55pm MIES - Thomas Braun
Recording on YouTube
4 - 4:55pm DataJoint - Thinh Nguyen, Dimitri Yatsenko
Link to Jupyter notebooks
Recording on YouTube
5 - 5:55pm NWB & DataJoint Integration in the Frank Lab, UCSF - Loren Frank

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