Get Your Brain Together Hackathons
Welcome to the 2nd Get Your Brain Together Hackathon !
What?
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.
When, where, how much?
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Dates: Monday, May 22nd - Tuesday, May 23, 2023
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Location: The second hackathon will be a hybrid in-person and online event, held:
- At the Allen Institute in Seattle, WA, USA
- On Microsoft Teams videoconferencing - link is sent via email to registered participants
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Image.sc Island Gather.Town virtual space (see this quick Intro to Gather Town, and
- Image.sc Zulip Chat.
If travelling to attend in-person,
- Courtyard by Marriott Seattle Downtown/Lake Union
- EVEN Hotel Seattle - South Lake Union, an IHG Hotel
- Astra Hotel Seattle
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Pan Pacific Seattle are among nearby hotels.
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Lead organizers / contacts: Matt McCormick (Kitware), Sharmishtaa Seshamani (Allen Institute for Neural Dynamics)
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Registration: Limited seats will be available for in-person attendance. Registration details will be announced in the mailing list below.
- Communication: to receive information about this and future events please join the Hackathon Mailing List.
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.
Agenda
How to add this calendar to your own?
Reproducible Resource Challenge
This aim of this hackathon is to generate reproducible pipelines to register whole-brain lightsheet microscopy image data to the CCFv3. Two datasets are provided, each with their unique quirks. You may work on either dataset during the hackathon.
In order to work with the neuroimage data generators, these pipelines will take a standardized input without assumptions of directory structures, filenames, etc and generate standardized outputs. Expected outputs include: resampled brain, spatial transformation, and a manifest of outputs. The processing pipelines should be designed to executed in independently in parallel. The output should be a resampled image with the same size, orientation, and origin as the provided CCFv3. The output should include an affine transformation file, and a deformation field transformation file to transform SWC and/or annotation files from the challenge dataset image space into the CCFv3 space.
Criteria for inclusion in a summary paper:
- Open source with an OSI-approved license
- The code can be executed in the future
- Researchers can understand what the code is doing
- Researchers can extend or fix as needed
- Works on open standard data formats used by data providers and consumers
- The provided input NIFTI or OME-NGFF images
- Deployable
- Can be executed across many environments
- Provided in a published singularity image
- Can be executed by an independent analyst
The primary goals for this hackathon is to ensure that everyone’s code can run on the dataset provided and can be replicated.
Tutorials
Tutorial sessions share how to work with open source registration tools, open access datasets, or neurodata
Monday 5/22
- About the AIND Lightsheet Challenge Dataset, 10 - 10:30 AM PT, (David Feng, Sharmishtaa Seshamani, Tom Birdsong)
- About the Translucence Challenge Dataset, 10:30 - 11 AM PT, (Damian Wheeler)
- Working with OME-Zarr NGFF, 11 AM - 11:30 AM PT, (Matt McCormick)
- Working in CodeOcean, 11:30 AM - 12 PM PT, (Jake Valsamis)
- D Tward Registration, 1 PM - 1:30 PM PT, (Daniel Tward)
Tuesday 5/23
- itk-elastix and MONAI, 8:30 - 9 AM PT, (Konstantinos Ntatsis, Niels Dekker)
- Large Scale Registration, 9 - 9:30 AM PT, (Matt McCormick)
- Registration Quality Metrics, 9:30 - 10 AM PT (Tom Birdsong)
- Visualization for Registration and Image Data, 10 AM - 10:30 AM PT (Briana Major, Paul Elliott)
- Image Varifold LDDMM for Spatial Transcriptomics - 11:00 AM - 11:30 AM PT, (Michael Miller)
Birds-of-a-Feather Breakouts
Birds-of-a-Feather (BoF) breakout sessions enable participants interested in collaborating to work on relevant topics.
To lead or join a Birds-of-a-Feather (BoF) breakout session, create or join a topic in this spreadsheet. During the BoF, find the leader by clicking on their name in the Image.sc Island Gather.Town and moving towards their avatar with the keyboard arrow keys. When you are close to their avatar in the virtual space, you will be able to see, hear, and talk to each other.
If notes are taken during the BoF, please add them to the BoF breakouts folder. We recommend HackMD for collaborative, well-formatted notetaking.
Code of Conduct
Participants and contributors are expected to adhere to the ITK Code of Conduct.
Participants
| Name | Organization |
|---|---|
| Christine Lin | Allen Institute |
| Nicholas Lusk | Allen Institute |
| Jack Waters | Allen Institute |
| Yun Wang | Allen Institute |
| Omid Zobeiri | Allen Institute |
| Di Wang | Allen Institute |
| Xiao-Ping Liu | Allen Institute |
| Tom Chartrand | Allen Institute |
| Scott Daniel | Allen Institute for Brain Science |
| Mike Taormina | Allen Institute for Brain Science |
| Staci Sorensen | Allen Institute for Brain Science |
| Raymond Sanchez | Allen Institute for Brain Science |
| Camilo Laiton | Allen Institute for Neural Dynamics |
| Sharmishtaa Seshamani | Allen Institute for Neural Dynamics |
| Gabor Kovacs | Allen Institute for Neural Dynamics |
| Chao Liu | Anhui University |
| Liyuanyuan | Anhui University |
| Yuxiao Zhang | AnHui University |
| Beatriz | Cajal Neuroscience |
| Christian Gaetano | Cajal Neuroscience |
| Nile Graddis | Cajal Neuroscience, Inc. |
| Yaroslav Halchenko | Dartmouth College, CON, DANDI |
| Koen van der Kuil | Erasmus MC dept. Of Neuroscience |
| Koen van der Kuil | Erasmus University Rotterdam |
| Johanna Perens | Gubra ApS |
| Casper Salinas | Gubra ApS |
| Jacob Skytte | Gubra ApS |
| THOMAS WHEATCROFT | HARVARD MEDICAL SCHOOL |
| Ruilong Wang | Hefei university of technology, Anhui, China |
| Brock Wester | JHU/APL |
| Matthew McCormick | Kitware |
| Tom Birdsong | Kitware |
| Brianna Major | Kitware |
| Paul Elliott | Kitware |
| Dženan Zukić | Kitware |
| Edward O’Donnell | Kleinfeld lab, UCSD |
| Konstantinos Ntatsis | Leiden University Medical Center |
| christov | Lorraine University, Nancy, France |
| Yael Balbastre | MGH |
| Omar Kana | Michigan State University |
| Vlad Grouza | Montreal Neurological Institute and Hospital |
| Ming Zhan | NIMH/NIH |
| Josh Moore | OME |
| Fae Kronman | Penn State |
| Deniz Parmaksiz | Penn State College of Medicine |
| Yongsoo Kim | Penn State University |
| Sanjeev Janarthanan | Princeton Neuroscience Institute |
| Andrei Kalinichenko | Skolkovo Institute of Science and Technology |
| Ekaterina | Skolkovo Institute of Science and Technology (Skoltech) |
| Ved Sharma | The Rockefeller University |
| Damian Wheeler | Translucence Biosystems |
| Gary Zhou | UCLA |
| Daniel Tward | UCLA |
| Daniel Tward | UCLA |
| Guolong Zuo | UCSF |
| Adam Tyson | University College London |
| Alessandro Felder | University College London |
| Ian Curtin | University of North Carolina at Chapel Hill |
| Rohit Jena | University of Pennsylvania |
| Philip Cook | University of Pennsylvania |
| Tianjia Zhu | University of Pennsylvania |
| Hyung Seok Roh | University of Pennsylvania (PICSL) |
| Nicholas Thomas-Low | Vanderbilt University |
| Symphony Wang | Weill Cornell Medicine |
| 黄海盟 | 安徽大学 |
Acknowledgements
This hackathon is supported by the National Institute of Mental Health (NIMH) of the National Institutes of Health (NIH) under the BRAIN Initiative award numbers 1RF1MH126732, 1U19MH114830-01, 5R24MH114793-02, 1U24MH114827-01.