Get Your Brain Together Hackathons

Get Your Brain Together HCK02

Welcome to the web page for the 2nd Get Your Brain Together Hackathon !


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:

When, where, how much?

If travelling to attend in-person,

How does it work?

Before the Hackathon

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.


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:

The primary goals for this hackathon is to ensure that everyone’s code can run on the dataset provided and can be replicated.


Tutorial sessions share how to work with open source registration tools, open access datasets, or neurodata

Monday 5/22

Tuesday 5/23

How to add a new tutorial?

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 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.


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
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


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.