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Brain atlases provide spatial reference systems for neuroscience, giving the ability to navigate, characterise and analyse information on the basis of anatomical location. Atlases define shape, location and variability of brain regions in common coordinate spaces, and allow interpretation, integration, and comparison of observations and measurements collected from different sources and different brains. EBRAINS develops open access 3D atlases for the human, rat, and mouse brainEBRAINS develops open access 3D atlases for the human, rat, and mouse brain. Explore brain regions in an interactive 3D viewer at microscopic detail and discover related multimodal data features from the EBRAINS Knowledge Graph. Programmatic access via a Python client, HTTP API, and command line interface is in development, coming soon to EBRAINS. Integrate your own data of different scale and type to EBRAINS atlases to make them available in a common spatial framework for reuse and quantitative analysis. Use EBRAINS atlas analysis tools to extract, quantify, and compare data in specific brain regions AtlasesServices
Open access 3D anatomical reference atlases for the human, rat, and mouse brain.
The first step of integrating neuroscience data is to relate them to a common anatomical location. Image data can be spatially aligned with a 3D reference atlas using linear or non-linear deformations. The transformations needed to bring atlas and images into spatial registration are stored as spatial metadata. EBRAINS provides two tools for registration of 2D images to atlases: QuickNII, tailored for efficient spatial registration of serial 2D (microscopic) image data, and Visualign, tailored for non-linear alignment images to optimize spatial registration after using the QuickNII tool.
By spatially registering images to a 3D atlas, it becomes possible to perform analyses based on regions of interest that are specified by the atlas maps. The QUINT workflow employs a suite of tools to efficiently extract, locate and quantify labelled features in serial 2D images. Roadmap2021, Q2Launch of an integrated toolsuite which brings together the 3D interactive atlas viewer and the new Python client and HTTP API Viewing of 2D image series with brain atlas overlays available through the EBRAINS Knowledge Graph 2021, Q3Atlas viewer supports overlaying local Nifti files with atlases and 'virtual dissections' in BigBrain Initial release of non-human primate (NHP) atlas. Parcellation maps and functional data will be linked in the future Waxholm space rat atlas update with 45 new delineations in cerebral cortex, basal ganglia, thalamus 2021, Q4Human brain atlas supports freesurfer space and spatial relationships between complementary parcellation maps 2022, Q1First release of an atlasing toolbox for neuroimaging, allowing probabilistic assignment of whole-brain signals to anatomical regions Alpha release of EBRAINS/nilearn interface for connectivity analysis ilastik accessible as an EBRAINS web service, allowing to perform interactive image segmentation on EBRAINS image data Release of WebAlign, combining QuickNII and VisuAlign in a web-accessible tool 2022, Q2New workflow allowing to project individual MRI scans to the human brain atlas for analysis Alpha release of datalad accessibility layer for EBRAINS atlas datasets 2022, Q3Beta release of EBRAINS/nipy software interface for connectivity analysis Beta release of Neuron Morphology registration pipeline integrated to EBRAINS QUINT workflow available as web-based workflow VoluBA updated with basic nonlinear registration capabilities 2022, Q4Interactive segmentation of user supplied files in web-ilastik, with the possibility to submit results to EBRAINS curation services Major release of updated human and rodent atlases with online documentation and tutorials WebAlign and VoluBA allow submission of registration results to EBRAINS curation 2023, Q1Stable and fully documented release of EBRAINS/nilearn interface for connectivity analysis neurogenpy library integrated with EBRAINS which allows analysis of gene expression data and learning of gene regulatory networks Stable release of Neuron Morphology registration pipeline, allowing submission of outputs to EBRAINS data curation QUINT workflow provides Nutil as a web service and direct links to Knowledge graph dataset cards Stable release of datalad accessibility layer for EBRAINS datasets Release of non-human primate (NHP) atlas integrated in EBRAINS |
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