ViSimpl: Multi-View Visual Analysis of Brain Simulation Data

Abstract

After decades of independent morphological and functional brain research, a key point in neuroscience nowadays is to understand the combined relationships between the structure of the brain and its components and their dynamics on multiple scales, ranging from circuits of neurons at micro or mesoscale to brain regions at macroscale. With such a goal in mind, there is a vast amount of research focusing on modeling and simulating activity within neuronal structures, and these simulations generate large and complex datasets which have to be analyzed in order to gain the desired insight. In such context, this paper presents ViSimpl, which integrates a set of visualization and interaction tools that provide a semantic view of brain data with the aim of improving its analysis procedures. ViSimpl provides 3D particle-based rendering that allows visualizing simulation data with their associated spatial and temporal information, enhancing the knowledge extraction process. It also provides abstract representations of the time-varying magnitudes supporting different data aggregation and disaggregation operations and giving also focus and context clues. In addition, ViSimpl tools provide synchronized playback control of the simulation being analyzed. Finally, ViSimpl allows performing selection and filtering operations relying on an application called NeuroScheme. All these views are loosely coupled and can be used independently, but they can also work together as linked views, both in centralized and distributed computing environments, enhancing the data exploration and analysis procedures.

SynCoPa: Visualizing Connectivity Paths and Synapses Over Detailed Morphologies

“…To achieve all these goals, particle rendering has been implemented here using an improved version of PReFr (Galindo et al, 2015 ), a general-purpose framework that provides a high level abstraction API for controlling how particles behave and appear. PReFr has been successfully applied to the purpose of visualizing neuronal circuits' simulations (Galindo et al, 2016 ). Having the capability of rendering up to one million particles on multi-core CPUs, PReFr serves as a stable base for the implementation of the methods proposed in this article.…”

Simulation, visualization and analysis tools for pattern recognition assessment with spiking neuronal networks

“…The visualization and analysis framework used in this work was ViSimpl [6]. As described in a previous paper, it is composed of different applications designed to perform both quantitative and qualitative analysis of brain simulation data.…”

“…Recently, software packages have emerged aiming to facilitate the analysis and processing of neuronal activity [5] in both simulated and experimental frameworks. Similarly, other software packages, including StackViz and SimPart, have been proposed to allow researchers fast visual analysis of the network activity [6].…”

A Method for the Symbolic Representation of Neurons

“…The circular dendrograms presented here have been developed within an exploratory analysis framework, conceived with the analysis of neuronal morphology in mind, although this framework has already also been extended to deal with functional data (Galindo et al, 2016; Toharia et al, 2016; NeuroLOTs, 2018). In this framework, operators can use a number of tools to carry out procedures such as cluster analysis, search by content, analysis of the spatial variation of specific features, etc.…”