Exploring the AHEAD brains together

[piloubazin]

Title

Exploring the AHEAD brains together

Short description and the goals for the OHBM BrainHack

We recently made available a post-mortem data set including quantitative MRI and microscopy reconstructed in 3D at 200µm (see this article for details). The data set is openly accessible on FigShare already, but we would like to do more to help integrate it in other open science platforms to promote collaborative exploration of the data.

Goals for the Brainhack:

• set up a version of the data set that fits into Brainbox
• check how the data is handled by various visualization tools, make recommendations
• import initial parcellations from automated tools (nighres so far, but others could be run) into the visualizations
• manually annotate errors, artifacts, inconsistencies
• delineate new structures collaboratively

Link to the Project

https://github.com/piloubazin/AHEAD-brains

Image for the OHBM brainhack website

https://uvaauas.figshare.com/ndownloader/files/27251792/preview/27251792/preview.jpg

Project lead

Pilou Bazin (github: piloubazin, discord: piloubazin, twitter: piloubazin)

Main Hub

Glasgow

Other Hub covered by the leaders

• [ ] Glasgow
• [ ] Asia / Pacific
• [ ] Europe / Middle East / Africa
• [ ] Americas

Skills

• enthusiasm for detail neuroanatomy
• dealing with data (re)formatting, header manipulation
• experience with various brain visualization tools
• ideas to increase collaboration in neuroanatomical atlasing

Recommended tutorials for new contributors

• [ ] Set up a brainhack friendly computing environment
• [ ] A introduction to Bash
• [ ] Python: Writing a script
• [ ] Python: Data analysis with Python
• [ ] Python: Visualisation
• [ ] Machine learning basics
• [ ] BIDS
• [ ] Machine learning for neuroimaging
• [ ] VCS: Using Git and Github
• [ ] VCS: Data management with Datalad
• [ ] Virtualization
• [ ] High Performance Computing: Oracle cloud resource

Good first issues

The data is rather big for neuroimaging viewers: ti would be good to test as many as possible among the popular ones and see what comes out. So far we tested MIPAV (works great :) and Katja Heuer pointed out that FSLeyes does weird things (thanks Katja!). What about ITKsnap, freeview, mrview, MRcron, Fiji, ...? Let's find out...

Twitter summary

Exploring the AHEAD brains together: setting up visualization and annotation tools https://github.com/piloubazin/AHEAD-brains @piloubazin

OHBMHackathon #Brainhack #OHBM2022

Short name for the Discord chat channel (~15 chars)

ahead-brains

Please read and follow the OHBM Code of Conduct

• [X] I agree to follow the OHBM Code of Conduct during the hackathon

[djarecka]

Thank you for submitting the project! We have 35 projects right now, woohoo! But that means the projects pitches will have to be short. We will give you tomorrow 2 minutes to pitch your project, you can have one slide or no slides! If you decide to use a slide, please include the link to the slide here.

And don't worry, you will still have more time to talk about your project during the BrainHack :-)

[piloubazin]

Great that there's a lot of projects once again :) Here's my slide: https://surfdrive.surf.nl/files/index.php/s/9TduzX0Vac0ZrzH Looking forward to this!