NeuroCave: A web-based immersive visualization platform for exploring connectome datasets

Abstract

We introduce NeuroCave, a novel immersive visualization system that facilitates the visual inspection of structural and functional connectome datasets. The representation of the human connectome as a graph enables neuroscientists to apply network-theoretic approaches in order to explore its complex characteristics. With NeuroCave, brain researchers can interact with the connectome—either in a standard desktop environment or while wearing portable virtual reality headsets (such as Oculus Rift, Samsung Gear, or Google Daydream VR platforms)—in any coordinate system or topological space, as well as cluster brain regions into different modules on-demand. Furthermore, a default side-by-side layout enables simultaneous, synchronized manipulation in 3D, utilizing modern GPU hardware architecture, and facilitates comparison tasks across different subjects or diagnostic groups or longitudinally within the same subject. Visual clutter is mitigated using a state-of-the-art edge bundling technique and through an interactive layout strategy, while modular structure is optimally positioned in 3D exploiting mathematical properties of platonic solids. NeuroCave provides new functionality to support a range of analysis tasks not available in other visualization software platforms.

PRAGMA: Interactively Constructing Functional Brain Parcellations

“…Network-based neuroscience visualization tools have demonstrated how to gain insight from connectome datasets, some at the level of functional modules, e.g. NeuroCave [16] and Tem-poCave [33], and some at the level of individual neurons, e.g. Brain-Trawler [8].…”

Visual Link Routing in Immersive Visualisations

“…Halpin et al [16] show that the use of virtual reality leads to better insight regarding social network exploration. Finally, Fiber-Clay [21] and NeuroCave [25] uses bundling in immersive environments. However, in most of these cases, users are looking at the graph from the outside (i.e.…”

TempoCave: Visualizing Dynamic Connectome Datasets to Support Cognitive Behavioral Therapy

“…TempoCave is inspired by previous approaches for visualizing networks [4], comparing graphs [15], and exploring connectome datasets [27]. Keiriz et al [18] survey the landscape of connectome visualization, focusing mainly on static datasets, and characterizing them in terms of their main visualization modality (emphasizing volume, surface, or graph representations), as well as identifying tools that include support for virtual reality (VR) environments. TempoCave presents connectomes as 3D networks, similar to approaches presented in Connectome Visualization Utility [22], Brain-Net Viewer [35], Connectome Viewer Toolkit [14], and the AlloBrain project [32].…”

“…Other recent brain visualization tools focus on neurobiological tasks, such as Ganglberger et al's [13] BrainTrawler, which provides tools to conduct integrated analyses of genomic data and mesoscale neuroscience datasets at the level of individual neurons. TempoCave aims to support tasks T1-T5 relevant to diagnosing and treating patients with neurological disorders, extending previous work that focused on static connectomes [18], which also presents a 3D view and enables a user to explore data immersively [8,11].…”