This project aims at building special use case tutorials and refine a comprehensive documentation for our citizen science project BrainBox. We will use BrainBox, do a segmentation sprint and build our tutorials while we work :) Come and teach us how to teach BrainBox!
BrainBox is a web application to collaboratively annotate and segment neuroimaging data available on the web. This manual annotation step is time-consuming but very important: on its correctness depends that the results of any analysis downstream will be sound and accurate. Join us! Your contribution is invaluable!
We want to make it easy for anyone to participate in open science by launching or participating in collaborative projects using BrainBox. Automatic image-analysis algorithms still very often fail in tasks which are simple for humans. But the explosion in the number of data sets available prevents individual labs from engaging into time-consuming manual editing.
BrainBox makes it possible to work collaboratively, using real-time interaction on the Web. Our aim is to produce a series of simple tutorials to introduce citizen scientists to the basic steps to create a collaborative project, or to perform some of the most frequent types of segmentation and annotation required. We also aim at producing a tutorial showing how the resulting, human-curated data, can be queried and analysed using python.
We will be super happy to work with anyone who would love to join our effort.
While you can see in real-time what your collaborators are writing or drawing on a given data set, you can also chat with them, ask for help or approval of your work. By opening this scientific process to everyone, we will need to build tutorials that are teaching anyone from any background with any knowledge about the brain, how to see and label its structures. Join us! :)
It will be a project where we will be able to learn about our brain as much as about how to build comprehensive tutorials. We target video/screencast tutorials as well as clear short write ups supported by pictures on how to do certain things.
Specific tutorials we would love to focus on could include:
- How to check & fix automatically generated segmentations in large data sets with BrainBox
- Segmentation sprint of the brain of a brain of a dolphin, including the step of surface reconstruction
- How to get data from BrainBox and analyse it using python and the Jupyter notebook
- How to prepare your data for a BrainBox project
More information about BrainBox can be found in our 3 min video on the OpenNeuroLab’s YouTube channel:
“Open Neuroimaging Laboratory”
And in several smaller specific videos:
“Collaborative editing of brain masks in BrainBox”
“Collaborative creation of brain masks in BrainBox”
Join our project on github any time :) and join us also for the mozsprint – the global Mozilla sprint – June 1 & 2 2017! You can join us in person at the Institut Pasteur, Paris, on Github, or on our slack channel #brainboxtutorials. You can also e-mail us to get in touch at openneurobrainbox at gmail dot com!
We are looking forward to meeting you! :)