daniloisr / BrainBox

BrainBox is a web application that let's you annotate and segment 3D brain imaging data in real time, collaboratively.

BrainBox - An application from the Open Neuroimaging Laboratory

BrainBox is a web application that lets you annotate and segment 3D brain imaging data in real time, collaboratively. You can try it at http://brainbox.pasteur.fr.

BrainBox is a web application to share, visualise and annotate MRI brain data collaboratively. BrainBox will provide the means to create a layer of collaborative annotation over all the available MRI data without having to rely on a centralised data repository or the necessity of having to install software.

You can try it at http://brainbox.pasteur.fr. Log in with your github account and enter the URL to an MRI file you want to visualise, annotate and edit. You can also click one of the examples.

Developer instructions

If you want to work on BrainBox's code, you'll need a local installation:

Using Docker to install and run BrainBox

1. git clone this repository or download it
2. mv BrainBox brainbox to rename the directory
3. cd to brainbox
4. create a new OAuth application for your local brainbox url (http://localhost:3000 by default)
5. paste the keys into the github-keys.json.example file, change the callbackURL to "http://localhost:3000/auth/github/callback" and drop the .example
6. drop the .example from blacklist.json.example
7. drop the .example from whitelist.json.example
8. make sure Docker is installed
9. docker-compose up
10. Then open http://localhost:3000 in your browser.

Non docker developer install instructions

1. install and start mongo database
2. clone the repo and cd to the brainbox directory
3. mkdir public/data
4. create a new OAuth application for your local brainbox url (http://localhost:3000 by default)
5. paste the keys into the github-keys.json.example file, and drop the .example
6. drop the .example from blacklist.json.example
7. drop the .example from whitelist.json.example
8. npm install
9. npm start
10. To lint your files use npm test, you can use xo --fix to fix common mistakes, before committing, to do that install xo globally using npm i -g xo