GSoC 2021 Project 20.1: Brainbox project - Brain Badges: Online certification for collaborative annotation and segmentation of brain imaging data

Problem: A wealth of open neuroimaging and histological data is publicly available, including data for subjects with different psychiatric disorders, different developmental stages, even different species. However, the data is not easy to find, is curated and analysed locally, in redundant, often wasteful and opaque ways.

Vision: Our vision is to create an interactive space where academic and citizen scientists can work together to curate public neuroimaging and histological data. The fruits of this common effort should be open, easy to find, access, and re-use. BrainBox and MicroDraw are our Web applications implementing this radical open science vision. BrainBox allows users to view, curate and annotate any neuroimaging dataset available on the Web, currently >13,000, and provides real-time interactive tools for manually segmenting and editing brain regions (3 min video about BrainBox: Open Neuroimaging Laboratory - YouTube). MicroDraw provides similar functionalities for high-resolution histological data.

Aim: For researchers to embrace this vision we need a way to assess and develop contributor’s expertise. Researchers leading a BrainBox or MicroDraw project, for example, need confidence about the quality of the results, and users need a clear path to begin contributing to a project. We propose to develop interactive training and certification modules: the Brain Badges. Using the training module, researchers will be able to explain the tasks that are required. Users will be proposed examples to practice, and then the evaluation module will test them on new data. Users will earn a badge for their achievement, which will be added, for example, to their BrainBox or MicroDraw profiles. Through the Brain Badges researchers will be able to recruit collaborators, weigh their contributions based on expertise, improving their confidence in the results. Users will have a precise idea of what is required to contribute to a project. The Brain Badges will increase their reputation, motivating them to keep learning.

Scope: We will design and code Brain Badges based on the Open Badges standard(https://openbadges.org). We will build 3 sample training and certification modules: data quality annotation, manual segmentation, and automatic segmentation correction.

Skills needed: Javascript, jQuery, Vuejs, Mocha, Chai, Webpack, HTML and CSS, Nodejs, MongoDB.

Mentors: Katja Heuer & Roberto Toro.
Lead mentor: Katja Heuer.
Co-mentor: Roberto Toro

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Hey @arnab1896!
I am Aditya R Rudra, a second year CSE undergraduate from NITK.
I am well versed with JS, jQuery, NodeJS, MongoDB and Webpack.
I went through the description and found the idea really interesting to work upon.
I have a quick read of the Open Badges Standard.
Any help regarding how to start contributing to the cause will be appreciated.

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Hi, @adityaofficial10 , tagging the mentors below. They will respond soon. In the meantime, feel free to start sharing any queries/questions you have after going through openbadges/Open Neuroimaging Laboratory

@katjaq @rto

Cheers!
Arnab

@arnab1896
Sure, I’ll try to gather as much information as possible and get a clear view of the project.

@katjaq @rto
I would like to know if there are any challenge tasks which I can complete to strengthen my application.

Hey @arnab1896 ,
Myself Uttkarsh , I am a 2nd year ICE undergraduate from NIT Jalandhar. I am a MERN developer having keen interest in solving real-world problems through development skills.
I have gone through the Brain Box project and the open badge and likes the idea of the current project : Brain Badges for certification. The idea looks quite interesting and inclines my interest towards this project. It would be very helpful if you could provide with the further discussion channel to get some more idea about the project.

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Hey @arnab1896 , can you please help me reaching out to mentors for clearing out some queries regarding the project …

Hello @adityaofficial10 , hello @Uttkarsh_Singh ,

Thank you for reaching out to us! :smiley: What do you think about doing a video call altogether, to clarify our objectives and see how we can help with your applications. Thank you for sharing your background and experiences with us, it sounds like you would both be a great fit for any of our 3 projects related to BrainBox. Maybe you like 2 different parts to focus on. Let’s find out :smiley: \ö//

Do we have a call all together next Monday, 15 March, after 11am GMT or Tuesday European morning (before 1pm GMT)? Would you be available?

Thanks again for choosing our projects and being interested in working with us. :smiling_face_with_three_hearts:

katja & roberto

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@katjaq
Thanks for the reply.
I am fine with the time slot and I look forward to it.

Thanks for the warm welcome…
I am also comfortable with the time slot i.e. Monday 15th anytime after 11am GMT😊
thanks again

Hello everyone! I am Abhir Raj Shrivastava, a 2nd year student from Jaypee Institute of Information Technology. I am a MERN stack developer and would like to know more and interact with the mentors about the project.

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@katjaq If you don’t mind I would also like to be a part of this meeting and discuss more about the project. :slightly_smiling_face:

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Hello @adityaofficial10 @Uttkarsh_Singh @Abhir-24

Thank you for your kind replies. I am sorry to ask for a slight change, but at the same time very excited to let you know that we will have amazing people from Sweden and Montreal join our video call who will additionally support our project :heart:
Please let me know if this Wednesday, March 17, at 1pm GMT, is possible for you. That would be early morning for Montreal, and I hope not too late for you. :slight_smile: Thank you.

best
katja & roberto

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Thanks for the reply @katjaq !
I am available on March 17 at 1 pm GMT. Looking forward to interact with you all :grinning: :upside_down_face:

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Wednesday at 1 pm would work really great for me :grin:
Looking forward to meet you all soon :slight_smile:

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Thanks for your time @katjaq
I look forward to this.

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Hello @adityaofficial10 @Uttkarsh_Singh @Abhir-24

Ok! Wednesday 1pm GMT it is! :smiley:
Let’s meet on the BrainWeb https://brain-web.github.io/videoconference .
See you all there! :slight_smile:
Looking forward to meeting you :blush:

katja and roberto

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sure @katjaq ,looking forward to the meeting :upside_down_face:

I am having problems in setting up the local environment for BrainBox. Can anyone please help me out?
As per the readme file I started the mongo server and changed the name of the repo to brainbox, created an OAuth application and did all other changes mentioned in files. But when I am running npm install, I am getting the following error.

@katjaq kindly help me out in resolving the errors.

Hi there mentors and fellow students.
I am Abdulbaasit a first year medicine and surgery student from LASU, Nigeria.
I am a Full Stack JavaScript Developer and I am very much interested in the idea of this project.
To quickly recap, there’s a large amount of neuroimaging and histological data available but there isn’t a publicly available way to access the data. The aim is to create an online certification web application that can match citizens and scientists to collaborate on projects.
@katjaq , could you please, maybe, post a link to the recorded meeting that was held some weeks back? If not no problem, I will try to set up the Brainbox and go through it myself and ask questions here.
Thank you very much and I look forward to speaking with the mentors

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