Neuroimaging in the Browser using the X Toolkit

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

“…In neuroimaging, a number of open source, browser-based visualization tools have been developed. Javascript brain viewers like BrainBrowser (Sherif et al, 2015), papaya.js 43 , XTK.js 44 (Haehn et al, 2014), and AMI library (Bernal-Rusiel et al, 2017) enable researchers visualize neuroimaging data in the browser. Interactive, linked data dashboards have been built as outputs of neuroimaging software, like ROYGBIV 45 (Keshavan et al, 2017b; Klein et al, 2017), AFQ-Browser 46 (Yeatman et al, 2018), and MRIQC has a web-based viewer to visually inspect outputs (Esteban et al, 2017).…”

“…Overview of discussed scientific communication web resources. General resources for data sharing include (1) D3.js https://d3js.org; 2) Plotly: https://plotly.com/; General neuroimaging data visualization libraries include 3) XTK (Haehn et al, 2014) 4) BrainBrowser (Sherif et al, 2015) 5) AMI.js (Bernal-Rusiel et al, 2017) 6) papaya.js https://github.com/rii-mango/papaya; 7) Open Anatomy Browser (Halle et al, 2017) Some neuroimaging packages that release associated web-viewers: 8) AFQ-Browser (Yeatman et al, 2018) 9) ROYGBIV/Mindboggle (Keshavan et al, 2017b; Klein et al, 2017) 10) MRIQC (Esteban et al, 2017) For scholarly publishing and review: 11) Stencila https://stenci.la; 12) hypothes.is https://hypothes.is; In education: 13) EdX https://www.edx.org/; 14) Coursera https://www.coursera.org/; For neuroimaging-specific courses and resources: 15) YouTube channels of Dr. Jeanette Mumford and Dr. Dirk Ostwald 16) ReproNim training modules http://www.reproducibleimaging.org/; 17) Neurostars forum https://neurostars.org; Web resources for learning how to communicate to the general public: 18) Alda-Kavli Learning Center online resources https://www.aldacenter.org/AKLC…”

A Survey of Macroscopic Brain Network Visualization Technology

“…Meanwhile, the issues of burdensome configuration of runtime environment are also overcome because the applications will run in a web browser as a web service and some native JavaScript programs which execute on a built-in JavaScript engine. Haehn et al [58] contributed "The X Toolkit"(XTK), the first JavaScriptbased framework for visualizing and interacting with medical imaging data using WebGL. The toolkit is geared towards powerful scientific visualization and provides a simple Application programming interface (API) which hides low-level elements of WebGL from users.…”

Scalable Interactive Visualization for Connectomics

“…Ginsburg et al [32] propose a rendering system which combines brain surfaces with tractography fibers to render a 3D network of connected brain regions. Similar visualizations can be created using the X toolkit [35], which offers WebGL rendering for neuroimaging data, and SliceDrop [36], which is a Web-based viewer for medical imaging data including volume rendering and axis-aligned slice views. Neuroglancer [33] provides different 2D and 3D visualizations for large datasets.…”

“…We use Websockets to support collaborative editing and to synchronize any changes among all proofreaders. For volume rendering, we use the XTK WebGL library [35], which enables volume rendering of medical imaging data.…”