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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.

DataBrain atlasesModelling and simulationValidation and inference

Human Brain Atlas

The EBRAINS multilevel human brain atlas provides detailed information on anatomy, connectivity, and function. It links macroanatomical concepts and their intersubject variability with measurements of the microstructural composition and intrinsic variance of brain regions.

Brain atlases


Ilastik is a simple, user-friendly tool for interactive image classification, segmentation and analysis. It is built as a modular software framework, which currently has workflows for automated (supervised) pixel- and object-level classification, automated and semi automated object tracking, semi-automated segmentation and object counting without detection. Most analysis operations are performed lazily, which enables targeted interactive processing of data subvolumes, followed by complete volume analysis in offline batch mode. Using it requires no experience in image processing.

Data analysis and visualisationBrain atlases

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.

Brain atlases


JuGEx is a tool that combines data from two repositories, the Allen Human Brain Atlas and the EBRAINS Human Brain Atlas, to provide detailed insights into how gene activities and microanatomical architectures contribute to brain function and dysfunction. The Allen Human Brain Atlas contains regional gene expression data, while the EBRAINS human brain atlas offers three-dimensional cytoarchitectonic maps reflecting interindividual variability. JuGEx integrates tissue transcriptome and probabilistic brain segregation data, allowing researchers to explore the complex relationships between genetic expression, brain structure, and function. With JuGEx, researchers can gain a deeper understanding of the intricate connections between genes and cognition, which can inform the development of new treatments for brain disorders and improve our understanding of brain function in health and disease.

Brain atlases


LocaliZoom allows the viewing and exploring of high-resolution images with superimposed atlas overlays, and the extraction of coordinates of annotated points within those images for viewing in 3D brain atlas space. It is well suited for the extraction of a limited number of coordinates, e.g. representing an electrode track or labelling within a small region of interest.

Data analysis and visualisationBrain atlases

Multilevel Macaque Monkey Brain Atlas

The EBRAINS Monkey Brain Atlas is a comprehensive resource that provides in-depth insights into the anatomy, connectivity, and functions of the macaque monkey brain. It includes detailed information about the organization of the monkey brain at multiple levels, ranging from the microscopic level to the macroscopic level of the entire brain.

Brain atlases

Mouse Brain Atlas

The Allen mouse brain atlas is a comprehensive digital resource that provides detailed information on the structure and function of the mouse brain. A wide range of structural and functional experimental data mapped to the Allen mouse brain atlas are shared via the EBRAINS research infrastructure.

Brain atlases


Nutil aims to simplify the pre-and-post processing of 2D brain section image data from mouse, rat and other small animal models. It can be used to preprocess images in preparation for analysis, and used as part of the QUINT workflow to perform spatial analysis of labelled features relative to a reference brain atlas. Nutil is developed as a stand-alone application with a simple user-interface, requiring little-to-no experience to execute.

Brain atlasesData analysis and visualisation


QCAlign was developed to support the use of the QUINT workflow for high-throughput studies. The QUINT workflow supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to a reference atlas.

Brain atlasesAnalysis


Software for 2D image registration to 3D atlas.

Brain atlasesData integration

Extract, quantify and analyse features from rodent histological images

The QUINT workflow comprises a suite of software designed to support atlas-based quantification. All the software have user interfaces, with no coding ability required. It generates object counts and percentage coverage per atlas-region, in addition to point clouds for visualising the features in 3D.

Brain atlases

Rat Brain Atlas

The Waxholm Space rat brain atlas is a detailed volumetric atlas of the rat brain, to which a wide range of anatomical and functional data have been registered, including detailed data showing cellular distributions, axonal pathways, and gene expression patterns. EBRAINS provides a visualization interface, enabling researchers to explore and compare different aspects of the rat brain in 3D space.

Brain atlases


siibra-api is an HTTP API for querying and retrieving contents of EBRAINS atlases. Originally built as a backend service for the interactive atlas viewer siibra-explorer, the API has been documented for connecting the brain atlases to other applications and web services.

Brain atlases


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.

Data analysis and visualisationBrain atlases


The Python library siibra-python is designed for integrating EBRAINS atlases into scripts and computational workflows. Besides providing programmatic access to all functionalities available in the interactive viewer siibra-explorer, it enables more advanced utilization of atlas information.

Brain atlases

TVB Brain Atlas Viewer

A viewer that allows users to view brain atlasses on top of a 3d brain model. The Brain Atlas Viewer allows users to inspect the location and shape of different brain regions and their associated function. Brain regions can be selected by anatomy or by function. Descriptions are available in English, Arabic, Hebrew, and German. Regions are annotated with their function. TVB Brain Atlas Viewer is an interactive software that can be operated via touch screen. It was part of the HBP Travelling Exhibition that started in July 2019 at Bloomfield Museum in Jerusalem organized by the HBP Museum Program (SP11). An overview over TVB-on-EBRAINS services is provided in the preprint

Whole-brain simulationModelling and simulationBrain atlases

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