ZetaStitcher

ZetaStitcher was designed to stitch the large volumetric datasets that are produced, for example, with Light-Sheet Microscopy when imaging large samples (such as a whole mouse brain) at high resolution. This tool computes optimal alignment of adjacent tiles by evaluating the cross-correlation of overlapping areas at selected stack depths. This ensures a high throughput, since a large dataset need not be processed in its entirety. Cross-correlation is computed efficiently by means of FFT. The software is fully written in Python and exposes an Application Programming Interface (API) that can be used to perform queries on the stitched dataset for further processing.

Launch online
Source Code
Contributors
GM

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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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