Web-based Visualization of Scientific Data


Daniel Haehn

Daniel Haehn

  • PhD Student in Computer Science,
    Harvard University (Hanspeter Pfister)

  • Studied Medical Computer Science (M.S.),
    Heidelberg University, Germany

Daniel Haehn (2)

  • Signal- and Image Processing background

  • Medical Imaging / Radiology
    • UPenn
    • Brigham and Women's Hospital
    • Boston Children's Hospital

http://slicer.org

http://slicedrop.com

Daniel Haehn (3)

  • 2011 Back to Web Development
    • Mainly Visualization

  • Everything Open Source

Web-based visualization

  • JavaScript

  • Rendering on the Client

  • HTML5 Canvas for 2D and 3D (WebGL)


Canvas 2D

WebGL?

Challenges

  • Browser Compatibility     :D

  • Performance

  • Limitations

Advantages

  • No Installation

  • Up-to-date

  • Reachability

3D Slicer and others

Slice:Drop


http://slicedrop.com

XTK

http://goXTK.com

Connectome

  • Large Electron Microscopy Data (nanoscale, TB, PB)
  • Automatically Annotated
  • Manual Proofreading required (~1.5 corrections per cell required)

Connectome (2)

Standalone Proofreading Tool

http://www.rhoana.org/

Connectome (3)

First Approach: IIP Image Server + OpenSeaDragon

http://monster.krash.net/dojo/_legacy/frontend/zstack_hack.html

Connectome (4)

Second Approach: Custom Image Server + OpenSeaDragon

http://monster.krash.net:1338/dojo/

Connectome (5)

Final Approach: Custom Image Server + Custom Viewer

http://monster.krash.net:1337/dojo/

demos

demos

knee atlas


http://demos.goxtk.com/knee_atlas/

demos

brain atlas


http://demos.goxtk.com/brain_atlas/

demos

Semantic Movies


http://gallantlab.org/semanticmovies/ Huth, Nishimoto, Vu and Gallant (2012), "A continuous semantic space describes the representation of thousands of object and action categories across the human brain", Neuron 2012

demos

stackdrop


http://stackdrop.org

demos

fetal mri


http://fetalmri.org

demos

3d slicer webGl export


https://github.com/xtk/SlicerWebGLExport

thank you

http://danielhaehn.com/p/mit2014