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( 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