Left: The main view of NeuroBlocks, comprising a scalable "pixelbased" visualization of the current segmentation state on top, and a timeline for exploring the project's evolution at the bottom. Top right: Detailed view of a segmentation task assigned to a user, showing recent modifications and thumbnails of the corresponding tool states. Bottom right: Linked petascale volume rendering of the underlying microscopy data and the selected segmented object. Abstract-In the field of connectomics, neuroscientists acquire electron microscopy volumes at nanometer resolution in order to reconstruct a detailed wiring diagram of the neurons in the brain. The resulting image volumes, which often are hundreds of terabytes in size, need to be segmented to identify cell boundaries, synapses, and important cell organelles. However, the segmentation process of a single volume is very complex, time-intensive, and usually performed using a diverse set of tools and many users. To tackle the associated challenges, this paper presents NeuroBlocks, which is a novel visualization system for tracking the state, progress, and evolution of very large volumetric segmentation data in neuroscience. NeuroBlocks is a multi-user web-based application that seamlessly integrates the diverse set of tools that neuroscientists currently use for manual and semi-automatic segmentation, proofreading, visualization, and analysis. NeuroBlocks is the first system that integrates this heterogeneous tool set, providing crucial support for the management, provenance, accountability, and auditing of large-scale segmentations. We describe the design of NeuroBlocks, starting with an analysis of the domain-specific tasks, their inherent challenges, and our subsequent task abstraction and visual representation. We demonstrate the utility of our design based on two case studies that focus on different user roles and their respective requirements for performing and tracking the progress of segmentation and proofreading in a large real-world connectomics project.
More recently, Neuroblocks REF proposed an online-system for tracking the progress and evolution of a large-scale segmentation project.
NeuroBlocks – Visual Tracking of Segmentation and Proofreading for Large Connectomics Projects
IEEE Transactions on Visualization and Computer Graphics
IEEE Transactions on Visualization and Computer Graphics
Computer Science Medicine