BrainBrowser

Neurological Visualization for the Web

Tarek Sherif

What is BrainBrowser?

• A suite of web-enabled visualization tools for neurology data
  • Volume Viewer: Slice-by-slice visualization of volumetric data
  • Surface Viewer: Real-time 3D visualization of surface data
• At a lower level:
  • A set of JavaScript libraries to run data visualizers on a web page

Motivation

• Visualizing your data generally means:
• Having all data on your machine
• Installing visualization software on your machine
  • E.g. Display, Register
  • Make sure it works with your:
    • Operating System
    • Installed Libraries
• If everything works: VISUALIZE!

BrainBrowser is a Web Application

• Web as a platform
  • Integrate into existing web pages
  • Interact with anything else on the web
    • Data
    • APIs
    • Facebook? Twitter?
• All users need is a modern web browser
  • No other software to install on their machines

Standards Compliant

• BrainBrowser uses standards-compliant web technologies
  • HTML5
  • CSS
  • JavaScript
  • Canvas
  • WebGL (three.js)
• Standard technologies for developers
• No plugins to install for users
  • No Java, Flash, Unity, etc.

Volume Viewer

• Navigate volumetric data in a slice-by-slice manner
  • Load one or more volumes
  • Navigate through the data

Load Volumes

• Currently, only MINC data is supported
  • Load raw and header data
  • Plugin architecture leaves door open for other formats
• Structural or functional data
• Multiple volumes can be overlayed

Navigate

• Sagittal, Coronal and Transverse slices are displayed for a given point in 3D space
• Manipulate the point being viewed by moving a cursor with the mouse
• Step through time increments for functional data

Demos

• Structural Data
• Functional Data

Surface Viewer

• Manipulate surface data in real-time 3D
  • Load one or more surfaces
  • Load intensity data
  • Manipulate the data

Load Surfaces

• Supported formats:
  • MNI Object (polygon or line data)
  • Wavefront Object
  • Freesurfer ASCII
• Extensible plugin architecture
  • If you write a parser for another file format, it can simply be added to BrainBrowser

Load Intensity Data

• MNI TXT and Freesurfer ASC currently supported
• Extensible plugin architecture
  • If you write a parser for another file format, it can simply be added to BrainBrowser
  • Essentially any per-vertex data format
• Optionally tie other data to vertices
  • Region information
  • Text descriptions
  • Images

Manipulate the Data

• Rotate, pan, zoom
• Change range of intensities displayed
• Adjust transparency on different parts of the surface
• View mesh

Demos

• Surface Viewer
• The MACACC dataset

Using BrainBrowser

• Try out the demos: https://brainbrowser.cbrain.mcgill.ca
  • Try out your own data!
• Download the JavaScript library and add it to your website
  • Fine-grained control over configuration
  • Extend with plugins
  • Must be programmed
• Use the web service
  • Loads all libraries and dependencies
  • Some aspects can be configured without programming
  • Surface Viewer only

Thanks!