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BigBrain Tools & Services

The BigBrain project develops a highly compatible and unified resource across Canadian and European neuroscience IT ecosystems to host high-resolution human brain models and connect them with different neuroinformatics services. We also foster co-development of solutions for viewing and annotating large volumetric data, and improving the cross-continental compatibility of datasets and neuroinformatics APIs


Partner and community developed BigBrain tools

Visualization and Annotation

by: David MacDonald et al
Display is designed to visualize and manipulate three dimensional objects, such as human cortical surfaces and sulcal curves.
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by: Louis Borgeat, Philippe Massicotte, et al
Atelier3D is a visualisation and annotation tool from NRC Computer Vision and Graphics
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ebrains siibra explorer
by: Various
Browser-based viewer for visually exploring the EBRAIN atlases, including the BigBrain.
Open ebrains siibra explorer
by: Tarek Sherif et al
BrainBrowser is a set of web-based 3D visualization tools primarily used for viewing neurological data, such as MRI scans. The surface viewer was modified by Natacha Beck and Lindsay B Lewis to handle the BigBrain surfaces created by C Lepage, A Altinkaya, and various contributors.
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by: Roberto Toro et al
MicroDraw is a web application to visualise and annotate collaboratively high resolution histology data.
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Neuroinformatics Infrastructure

by: CBRAIN team
CBRAIN is an infrastructure that connects researchers and data from all walks of science to high performance and cloud computing in an easy to manage, reproducible, and user-friendly manner.
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by: LORIS team
(Longitudinal Online Research and Imaging System) is a web-based data and project management software for neuroimaging research studies. It is an OPEN SOURCE framework for storing and processing behavioural, clinical, neuroimaging and genetic data.
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When publishing data, merely providing file access is insufficient for a simple reason: data are not static. Released data often (and should!) continue to evolve; file formats can change, bugs will be fixed, new data are added, and derived data needs to be integrated.
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NeuroHub allows access to powerful computational tools for data processing and streamlined systems for secure storage and sharing of multi-disciplinary data.
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A python client for interacting with multilevel brain atlases in particular for accessing the EBRAINS human brain atlas.
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Computing Services

Calcul Québec
Calcul Québec’s supercomputers, located in various universities, are available to researchers from across Quebec and Canada. Our systems total over 80 000 cores in a variety of configurations.
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Compute Canada
High performance computing
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Juelich Supercomputing Centre
The Jülich Supercomputing Centre (JSC) at Forschungszentrum Jülich enables scientists and engineers to solve highly complex, grand challenges in science and engineering within collaborative infrastructures for both supercomputing and grid technologies.
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Community Contributed Tools

BigBrain Warp
by: Casey Paquola et al.
Integrating BigBrain with multi-modal imaging.
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Featured: BigBrain Warp
date: Apr 01 2021
Our featured tool developed by Casey Paquola and Boris Bernhardt.
go to the project
The Human Brain in Chimera
by: Tom Goddard
A tutorial on how to visualize the BigBrain in Chimera using the MINC format.
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The BrainBox
by: Various
BrainBox allows you to visualise, segment and annotate collaboratively any brain MRI dataset available online.
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The Virtual Brain
by: Viktor Jirsa et al
A multiscale integration and simulation platform for brain network computation.
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Base Infrastructure

EBRAINS is a digital research infrastructure by the Human Brain Project encompassing a range of tools and services for brain research and technology development. These assist scientists to analyse and integrate brain data and to simulate brain function.
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Huron Scanners
High resolution scanners from Huron Digital Pathology.
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Supported Standards

The EBRAINS Knowledge Graph
The EBRAINS Knowledge Graph is a metadata management system that hosts data from various brain research fields. A graph database tracks the linkage between experimental and neuroscientific data science supporting wide data reuse and complex computational research.
Go to EBRAINS Knowledge Graph
International Neuroinformatics Coordinating Facility
The mission of the International Neuroinformatics Coordinating Facility (INCF) is to develop, evaluate, and endorse standards and best practices that embrace the principles of Open, FAIR, and Citable neuroscience.
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by: Tristan Glatard et al
A cross-platform descriptive command-line framework for applications.
Open in Github