Atlases

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 brain

EBRAINS 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


Atlases

Services

    • Atlases

    Multilevel Human Brain Atlas A three-dimensional atlas that integrates the different facets of human brain organisation at the millimeter and micrometer level

    • Atlases

    Rat Brain Atlas Explore open access 3D anatomical atlas for the rat brain

    • Atlases

    Mouse Brain Atlas Explore open access 3D anatomical atlas for the mouse brain

    • Atlases

    QUINT Extract, quantify and analyse labelled features from rodent histological images

    • Atlases

    QuickNII and VisuAlign Spatially register mouse and rat serial 2D brain images to 3D reference atlases

    • Atlases

    VoluBA Spatially register high-resolution volumes of interest to 3D reference atlases

    • Atlases

    JuGEx Gene expression analysis in human brain atlas regions

Open access 3D anatomical reference atlases for the human, rat, and mouse brain.

    • Atlases

    Multilevel Human Brain Atlas A three-dimensional atlas that integrates the different facets of human brain organisation at the millimeter and micrometer level

    • Atlases

    Rat Brain Atlas Explore open access 3D anatomical atlas for the rat brain

    • Atlases

    Mouse Brain Atlas Explore open access 3D anatomical atlas for the 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.

    • Atlases

    QuickNII and VisuAlign Spatially register mouse and rat serial 2D brain images to 3D reference atlases

    • Atlases

    VoluBA Spatially register high-resolution volumes of interest to 3D reference atlases

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.

    • Atlases

    QUINT Extract, quantify and analyse labelled features from rodent histological images

    • Atlases

    JuGEx Gene expression analysis in human brain atlas regions


Roadmap

2021, Q2

Launch 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, Q3

Atlas 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, Q4

Human brain atlas supports freesurfer space and spatial relationships between complementary parcellation maps

2022, Q1

First 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, Q2

New 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, Q3

Beta 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, Q4

Interactive 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, Q1

Stable 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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