Interactive Atlas Viewer

The Human Brain Project hosts a rich web-based 3D atlas viewer („NeHuBa“), that is capable of displaying very large brain volumes, including oblique slicing, a whole brain overview, surface meshes, and maps. It allows to interactively choose different template spaces and reference parcellations, find brain areas by name or visual selection, and browse additional region-specific multimodal data. The rendering of large volumetric data builds on the opensource project neuroglancer. Some important atlases and templates can be directly accessed, including the „Big Brain“ (Amunts et al., Science 2013) the JulichBrain cytoarchitectonic atlas and the Waxholm Space Atlas of the Sprague Dawley Rat Brain.

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Source Code
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TD DG XG PC

Other Tools

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siibra-explorer

siibra-explorer is built around an interactive 3D view of the brain displaying a unique selection of detailed templates and parcellation maps for the human, macaque, rat or mouse brain, including BigBrain as a microscopic resolution human brain model at its full resolution of 20 micrometres.

Collaboratory

The EBRAINS Collaboratory offers researchers and developers a secure environment to work with others. You control the level of collaboration by sharing your projects with specific users, teams or all of the Internet. Many researchers are sharing their work already; several services, tools, datasets and other resources are publicly available, and many more are available for registered users.

MeshView

MeshView is a web application for real-time 3D display of surface mesh data representing structural parcellations from volumetric atlases, such as the Waxholm Space Atlas of the Sprague Dawley Rat Brain. MeshView is available as an EBRAINS community app, accessible via a collab (further info: https://wiki.ebrains.eu/bin/view/Collabs/image-registration-and-analysis-demo/) Key features: orbiting view with toggleable opaque/transparent/hidden parcellation meshes rendering user defined cut surface as if meshes were solid objects rendering point-clouds (simple type-in, or loaded from a JSON format) coordinate system is compatible with QuickNII (https://www.nitrc.org/projects/quicknii)

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