17urn:lsid:arphahub.com:pub:8E638694-B4E0-570A-856A-746FF325BF6BResearch Ideas and OutcomesRIO2367-7163Pensoft Publishers10.3897/rio.3.e12358123586960Project ReportInteractive online brain shape visualizationKeshavanAnishaanishakeshavan@gmail.com1KleinArnoCipolliniBenUniversity of California, San Francisco, San Francisco, CA, United States of AmericaUniversity of California, San FranciscoSan Francisco, CAUnited States of America
2017230220173e1235858DF45F4-F06E-59AB-940C-72AD4C2A15D632187821022017Anisha Keshavan, Arno Klein, Ben CipolliniThis is an open access article distributed under the terms of the Creative Commons Attribution License 4.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.three.jsVTKmorphometryd3.jsIntroduction
Our goal for the hackathon was to create an interactive Web browser application to visualize human brain image data processed by the Mindboggle software package (Klein and Hirsch 2005, Klein et al. 2017). The Mindboggle project was initiated to improve the labeling as well as morphometry of brain imaging data, and to promote open science by making all data, software, and documentation freely and openly available. An interface for interactive visualization is essential for assessing issues in brain image processing and analysis, including surface reconstruction, labeling, and morphometry. Mindboggle processes human brain cortical surface meshes in the VTK format, and generates label and shape information for each anatomical region, where labels follow the Desikan-Killiany-Tourville protocol (Klein and Tourville 2012).
Approach
Over the course of two afternoons at the Human Brain Mapping 2015 conference’s hackathon, we evaluated several JavaScript libraries for creating browser-based WebGL visualizations of brain surfaces, including three.js, XTK, and BrainBrowser. Three.js was chosen for ease of use and degree of active development and community support. To accompany these surface visualizations with graphical plots, we chose the d3 JavaScript library for its flexibility and widespread use.
Results
We completed an initial version of our browser-based interactive visualization tool; a left hemisphere of a human brain is available at http://roygbiv.mindboggle.info. Click and drag to rotate this brain, scroll to zoom in and out, and click on any region of the brain while pressing the shift key to produce an accompanying plot of shape measures for that region Fig. 1. This will render all other regions transparent. Fig. 2 shows the distributions of travel depth, geodesic depth, mean curvature, freesurfer curvature, and freesurfer cortical thickness for the selected region. Shift-click outside the brain to return opacity to all regions.
After the hackathon, we refactored the code to use an object-based approach. This allows multiple brains to be shown simultaneously. This approach was used to create a master-slave interaction (Fig. 3): selection of a ROI in one hemisphere loads data for display on a second hemisphere. This approach was used in a dynamic poster presented at Society for Neuroscience in 2015 (Cipollini et al. 2015).
Conclusions
We have received very positive feedback for our efforts at the hackathon, and have since received several requests and encouragement to build this visualization out to accommodate other data besides shape information and to enable the visual evaluation of thousands of brains. We hope to continue this work with the help of others! To contribute to this project, please send pull requests to https://github.com/akeshavan/roygbiv (Cipollini et al. 2017).
Acknowledgements
This work was completed during the OHBM 2015 Brainhack. The authors would like to thank the 2015 Brainhack organizers and Roberto Toro for his javsacript expertise.
ReferencesCipolliniBBartschHCottrellG2015ChicagoCipolliniBenKleinArnoKeshavanAnishaWhiteCurt2017akeshavan/roygbiv: Initial ReleaseZenodohttp://doi.org/10.5281/zenodo.268541KleinArnoHirschJoy2005Mindboggle: a scatterbrained approach to automate brain labeling242261280http://dx.doi.org/10.1016/j.neuroimage.2004.09.01610.1016/j.neuroimage.2004.09.016KleinArnoTourvilleJason2012101 Labeled Brain Images and a Consistent Human Cortical Labeling Protocol6http://dx.doi.org/10.3389/fnins.2012.0017110.3389/fnins.2012.00171KleinAGhoshSSBaoFSGiardJHameYStavskyELeeNRossaBReuterMNetoECKeshavanA2017Mindboggling morphometry of human brains13310.1371/journal.pcbi.1005350
Example visualization
Example of a selected region and its accompanying boxplot.