QUINT-Online

The QUINT workflow is an analysis solution for 2D rodent microscopy data, answering the need for brain-wide mapping and regional quantification. The workflow is used to quantify cells and establish maps of cell distribution, receptor densities, connectivity patterns or pathological protein accumulation in the brain. For more information see here: https://ebrains.eu/data-tools-services/tools/labellled-features-analysis

The QUINT-Online workflow is one of the featured EBRAINS workflow (https://ebrains.eu/impact/ebrains-in-use/featured-workflows).  The online workbench offers tighter integration of the tools, shareable viewer links, and metadata management.

Tool suite: CreateZoom, WebAlign, WebWarp, WebIlastik, WebNutil, MeshView

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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. 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://meshview-for-brain-atlases.readthedocs.io)

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