Cerebro: One tool to view them all

Title

Cerebro: One tool to view them all

Leaders

Sina Mansour L. (Twitter: @Sina_Mansour_L / Mattermost: @sina_mansour_l)

Collaborators

No response

Brainhack Global 2022 Event

Brainhack Australasia

Project Description

• What are you doing, for whom, and why? Cerebro aims to provide a visualization solution to advance the currently available methods to visualize neuroimaging and brain connectivity data. The existence of several different neuroimaging file formats produced by various neuroimaging software complicates the visualization of findings in one place. Furthermore, Cerebro will implement novel approaches to build advance existing methods and produce novel visualization techniques to better interpret study findings.

• What makes your project special and exciting? Were you ever stuck when trying to visualize your study findings? Did you want to visualize different data formats and notice there’s no software to visualize them ALL in one place? Have you thought about a different way to present your findings but couldn’t find a tool to do it? And finally, did you ever want to generate nice brain visualizations within your script (without launching third-party software)? Cerebro aims to provide a solution (in the form of a python package) that answers these needs.

• How to get started? Cerebro is at its early development stage and would hence require help in several aspects. There are several ways you could help.

In Brainhack Global 2022 we aim to:

1. Brainstorm different visualization approaches to come up with ideas.
2. List different file formats that Cerebro should be able to generate.
3. Try a hands-on session of visualizing some brains with Cerebro.
4. Submitting issues for feature requests.
5. And finally, if you like, contributing to the script.

• Where to find key resources? You can check the project repository to find more resources. Also, make sure to come to the project pitch on the first day to find out more.

Link to project repository/sources

https://github.com/sina-mansour/Cerebro_Viewer

Goals for Brainhack Global

1. Test the preliminary package release
2. Brainstorm different visualization approaches to consider
3. List different file formats that Cerebro should be able to generate.
4. Find various user demands from such a software
5. Try a hands-on session of visualizing some brains with Cerebro.
6. Submitting issues for feature requests to the git repository.

Good first issues

1. issue one: Come to our first-day discussion and let us know how and where you use visualization software

2. issue two: Install the package and give it a try

3. issue two: Feel free to clone the repository if you’d like to contribute code

Communication channels

https://mattermost.brainhack.org/brainhack/channels/cerebro-viewer

Skills

The project caters to different skills, you could join for discussions, help test the package, or contribute to documentation and code.

• Interest in visualizing neuroimaging data
• Using the Python programming language (some introduction will be included in the discussions)
• Writing documentation using Markdown or python docstrings (mainly for long-term contribution to code documentation)
• Advanced: Python expertise (mainly for the development of new features)

Onboarding documentation

No response

What will participants learn?

• Get familiar with different neuroimaging file formats and visual representations
• Learn to write python code that generates a 3D interactive brain

Data to use

No response

Number of collaborators

more

Credit to collaborators

All project contributors will be listed in the project’s git repository.

This project will continue to be an ongoing project to further develop the package in future brain hacks. Project contributors will be part of the potential publication originating from the project.

Image

Type

coding_methods, documentation, visualization

Development status

2_releases_existing

Topic

data_visualisation

Tools

Jupyter, other

Programming language

Python

Modalities

DWI, fMRI, MRI

Git skills

0_no_git_skills

Anything else?

No response

Things to do after the project is submitted and ready to review.

• Add a comment below the main post of your issue saying: Hi @brainhackorg/project-monitors my project is ready!
• Twitter-sized summary of your project pitch.