Get Your Brain Straight Hackathons

Get Your Brain Straight HCK01

Welcome to the web page for the 1st Get Your Brain Straight Hackathon !

What?

The Get Your Brain Straight 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.

Example ways to participate:

When, where, how much?

How does it work?

Before the Hackathon

During the Hackathon

The week will start 8 AM Pacific Time, 11 AM Eastern Time, Monday, April 4th in an introductory all-hands videoconference. recording

Following the introduction, participate in the Reproducible Resource Challenge, join the tutorials, and participate BoF breakouts.

On Thursday, 11 AM Pacific Time, 2 PM Eastern Time, participants will delegate one member to present their registration processing pipelines, results, and discuss lessons learned. Recording

Who can attend?

Get Your Brain Straight 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 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.

In future hackathons, we will focus on:

How to add a new reproducible registration processing pipeline?

Challenge Dataset 1: fMOST Mouse Brain Registration to CCFv3

The fMOST brain volumes and CCFv3 atlas for the hackathon are available on the BIL here. The input is a single fMOST NIFTI brain volume. Details about this dataset can be found here.

Challenge Dataset 2: Light-Sheet Imaged Mouse Brain Registration to CCFv3

The Light-sheet imaged brain volumes are available on the BIL here. For this challenge set, the data and atlas is provided for a single brain hemisphere (for size considerations and to mimic most real world experiments). Multiple data replicates are provided. We provide one dataset subject0.zarr in full imaging resolution for those seeking a bigger challenge. As a convenience we provide the challenge sets at approximately atlas size as Nifti(subjectN_25.nii.gz) or OME-NGFF (subjectN_25.zarr). Participants may use either format but OME-NGFF is preferred because it allows more efficient memory usage for larger datasets.

Details on working with the data can be found here

Tutorials

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

Monday 4/4

Tuesday 4/5

Wednesday 4/6

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 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

Registered participants:

  1. Yufei Chen, AHU
  2. oylei, AHU
  3. Alice, Allen Institute for Brain Science
  4. Pamela Baker, Allen Institute for Brain Science
  5. Lydia Ng, Allen Institute for Brain Science
  6. Rachel Dalley, Allen Institute for Brain Science
  7. Li, Anhui University
  8. Yuxiao Zhang, Anhui University
  9. tingtinghan, Anhui University
  10. Tingting Han, Anhui University
  11. Jesse, Anhui University
  12. Liyunayuan, Anhui University
  13. Iana Vasylieva, Center for Biologic Imaging, University of Pittsburgh
  14. Adrian Arias Abreu, Centre for Genomic Regulation
  15. Stuart gano, Google
  16. John Bogovic, HHMI Janelia
  17. Bin Duan, Illinois Tech
  18. Can Ceritoglu, JHU Center for Imaging Science
  19. Kaitlin Stouffer, Johns Hopkins University
  20. Thomas Athey, Johns Hopkins University
  21. Brock Wester, Johns Hopkins University Applied Physics Laboratory
  22. Erik Johnson, Johns Hopkins University Applied Physics Laboratory
  23. Dzenan Zukic, Kitware
  24. Tom Birdsong, Kitware
  25. Will Schroeder, Kitware
  26. Matt McCormick, Kitware
  27. Paul Elliott, Kitware
  28. Ebrahim Ebrahim, Kitware
  29. Viktor van der Valk, LKEB - LUMC
  30. Brian Eastwood, MBF Bioscience
  31. Kara, N/A
  32. Fae Kronman, Penn State University
  33. Yongsoo Kim, Penn State University
  34. Art Wetzel, Pittsburgh Supercomputing Center
  35. Mariah Kenney, Pittsburgh Supercomputing Center
  36. Luke Tuite, Pittsburgh Supercomputing Center
  37. Greg Hood, Pittsburgh Supercomputing Center / CMU
  38. Alexander Ropelewski, PSC
  39. Xin Wu, RTI International
  40. Zhixi Yun, SEU
  41. Adam Aji, SonoVol
  42. Yufeng Liu, Southeast University
  43. Tony Reksoatmodjo, Translucence Biosystems
  44. Kate Lawson, UC Irvine
  45. Ricardo Azevedo, UC Irvine
  46. Negin, UC Irvine
  47. Jaclyn Beck, UC Irvine
  48. Zhongkai Wu, UC San Diego
  49. Christopher Choi, UCLA
  50. Daniel Tward, UCLA
  51. Ian Bowman, UCLA BRAIN
  52. Luis, UCLA BRAIN
  53. Karl Marrett, UCLA Computer Science, VAST lab
  54. Guorong Wu, UNC Chapel Hill
  55. Hyejin Yang, UNC Chapel Hill
  56. Sarah Khan, UNC Chapel Hill
  57. Marc Niethammer, UNC Chapel Hill
  58. Carolyn McCormick, UNC Chapel Hill
  59. Min Chen, University of Pennsylvania
  60. Jeffrey Duda, University of Pennsylvania
  61. Alan Watson, University of Pittsburgh
  62. Nick Tustison, University of Virginia
  63. brian, University of Virginia

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 and the BICCN.