alexlicohen / nbpapaya

View brain images in the ipython notebook using papaya.js

README

Want to see 3D brain data in the IPython notebook? Now you can by using Papaya, a Javascript library for viewing medical images in the browser, and this little bit of code.

Install

Clone this repository to your computer,

>>> git clone https://github.com/akeshavan/nbpapaya

then add submodules

>>> git submodule update --init --recursive

and run the setup script.

>>> python setup.py

Use

Open a new IPython notebook

from nbpapaya import Brain, clear_brain

Then show a brain:

Brain("/path/to/your/brain.nii",port=<your ipython notebook port. Default is 8888>)

Or show overlaid brains

Brain(["/path/to/brain1.nii","/path/to/brain2.nii"],8888)

You can play around with the color maps and intensity ranges on the Papaya javascript interface.

Also, some files are created in the directory of your notebook to make it work. When you're done, clean up:

clear_brain()

The file papaya_viewer.html and the papaya_data folder are deleted.

Troubleshoot

Things might go wrong because I wrote this quickly. If you don't see anything, make sure you called Brain with the correct port. If you did, make sure that papaya.js and papaya.css exist in ~/.ipython/profile_default/static/custom/. If nothing is there, move the files in there. Also email me: [e-mail].