2nd Get Your Brain Together Hackathon | Monday, May 22nd - Tuesday, May 23, 2023 | Hybrid in-person and online event



The Get Your Brain Together hackathons bring together neuroimage data generators, image registration researchers, and neurodata compute infrastructure providers for a hands-on, collaborative event. This community collaboration aims to create reproducible, open source resources that enable discovery of the structure and function of brains.

There are three components to the hackathon. First, the primary goal of each hackathon is the generation of a Reproducible Resource for registration and analysis of a specific brain imaging modality. Tutorial sessions share how to work with open source registration tools, open access datasets, or neurodata archives. Birds-of-a-Feather (BOF) Breakout sessions enable participants interested in collaborating to work on relevant topics.

This hackathon will focus on registration of mouse brain lightsheet volumes to the Common Coordinate Framework version 3.1 (CCFv3.1).

Example ways to participate:

  • Contribute a registration pipeline resource to register the challenge datasets.
  • Give a tutorial about your registration tools. A pre-recorded or live presentation, along with example code and recipes, can teach a data analyst how to run your tool and use the output on the challenge dataset and/or another open dataset.
  • Come and learn about registration from experts in the field.

How does it work?

Before the Hackathon

  • Register for the event.
  • Sign up for the mailing list.
  • Optionally prepare a tutorial or organize a Birds-of-a-Feather (BoF) Breakout.

During the Hackathon

The week will start 9 AM Pacific Time, 12 AM Eastern Time, Monday, May 22nd in an introductory all-hands videoconference.

Following the introduction, participate in the Reproducible Resource Challenge, join the tutorials, and take part in BoF breakouts. Please bring a laptop.

At the end of the day on Tuesday, participants will delegate one member to present their registration processing pipelines, results, and discuss lessons learned.

Who can attend?

Get Your Brain Together hackathons are open to all and publicly advertised. Email announcements are sent to the mailing list.



Click here for up-to-date agenda and links


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@muratmaga @pieper @lassoan

While all events are relevant to problematic we are having in our community, the following events may be particularly interesting in the context of the handling of large scale data in Slicer.


Birds-of-a-Feather (BoF) Breakout Sessions:

cc: @thewtex @tom.birdsong


Are registrations still open for this event? I’ve registered using the link, but haven’t received a confirmation email.

Would it be possible to provide zoom/webex links here to the NGFF sessions?

Thanks for the info @jcfr - it does look like an interesting event.

One timing issue: Matt’s (@thewtex) OME-Zarr NGFF tutorial is listed as 10:30 - 11:00 PDT in what you posted and on the page, but 11:00-11:30 in the calendar link. Do we know for sure which is correct?

Thanks for the follow-up, I reached directly to folks from the organizing committee and also posted question on the “Zulip” chat linked in the event description.

I will follow-up when I hear back.

This teams link should used for remotely joining the sessions.

Hi folks, would love to have your participation!

Copying a few of the questions (but it would be better to follow up on Zulip):

Re: 1.: Registrations made after Friday will not receive a summary mail, but here are the contents of that mail.
Not present on the website:
a) The link to the Microsoft Teams Meeting (to prevent Zoom Bombing).
b) An invitation to the Allen Institute Code Ocean Cloud computing platform.
If someone would like an invitation, please send a message on the chat with the desired email.

One timing issue: Matt’s (@thewtex) OME-Zarr NGFF tutorial is listed as 10:30 - 11:00 PDT in what you posted and on the page 2, but 11:00-11:30 in the calendar link. Do we know for sure which is correct?

There are two OME-Zarr items.

  1. A tutorial today
  2. A discussion on how to store orientation metadata tomorrow.
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One timing issue:

Times reported in the google calendar are the authoritative ones, I submitted a pull-request to fix the others

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