Atlas-driven analysis resources

Course in Neuroscience data integration

This course contains an introduction to currently available reference atlases for mouse and rat brain. It will demonstrate how the 3D brain templates for the reference atlases are acquired, how they are used as a basis for delineating the structures of the brain, how they can be enriched by other data modalities, and how they can be used as a basis for assigning location (coordinate based or semantic) to a wide range of structural and functional data collected from the brain.

Brain atlases

Tools and services tutorials

The single entry point to tutorials for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials.

Tutorials

Investigating cellular diversity in a novel Alzheimer’s disease mouse model using the optimized QUINT workflow (v1)

This study includes 40 mice (20 at 6 months(m), 20 at 14 months(m); 2 males and 38 females). Of the mice, 29 are from 14 AD-BXD strains, 2 are the C57B1/6J founder strain, 6 are the F1 B6/DBA/2J (D2) 5XFAD founder strain, and 3 are nontransgenic (Ntg)-BXD.

Brain atlases

ilastik: interactive machine learning for (bio) image analysis

We present ilastik, an easy-to-use interactive tool that brings machine-learning-based (bio)image analysis to end users without substantial computational expertise.

Brain atlases

MeshView user manual

MeshView is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the human and rodent brain.

Brain atlases

LocaliZoom user manual

EBRAINS LocaliZoom serial section image viewer provides an intuitive way of navigating high-resolution 2D image series coupled with segmentation overlay, from a web browser.

Brain atlases

QuickNII user manual

QuickNII is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas-based analysis and integration of experimental data and knowledge about the human and rodent brain.

Brain atlases

VisuAlign user manual

VisuAlign is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the human and rodent brain.

Brain atlases

QCAlign user manual

QCAlign was developed to support the use of the QUINT workflow for high-throughput studies

Brain atlases

WebAlign user manual

WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.

Brain atlases

WebWarp user manual

WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases.

Brain atlases

Atlas-based data integration for mapping the connections and architecture of the brain

Here, we review approaches for integrating data describing neural connections and other modalities in rodent brain atlases and discuss how atlas-based workflows can facilitate brainwide analyses of neural network organization in relation to other facets of neuroarchitecture.

Brain atlases

WHS rat brain atlas v4 (Kleven et al., 2023)

Volumetric brain atlases are increasingly used to integrate and analyse diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present the new Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource.

Brain atlases

WHS rat brain atlas v3 (Osen et al., 2019)

The mammalian auditory system comprises a complex network of brain regions. Interpretations and comparisons of experimental results from this system depend on appropriate anatomical identification of auditory structures.

Brain atlases

WHS rat brain atlas v2 (Kjonigsen et al., 2015)

Atlases of the rat brain are widely used as reference for orientation, planning of experiments, and as tools for assigning location to experimental data. Improved quality and use of magnetic resonance imaging (MRI) and other tomographical imaging techniques in rats have allowed the development of new three-dimensional (3-D) volumetric brain atlas templates.

Brain atlases

WHS rat brain atlas v1.01 (Papp et al., 2015)

The main focus of our original article was to describe the anatomical delineations constituting the first version of the WHS Sprague Dawley atlas, apply the Waxholm Space coordinate system, and publish the associated MRI/DTI template and segmentation volume in their original format. To increase usability of the dataset, we have recently shared an updated version of the volumetric image material (v1.01). The aims of this addendum are to inform about the improvements in the updated dataset, in particular related to navigation in the WHS coordinate system, and provide guidance for transforming coordinates acquired in the first version of the atlas.

Brain atlases

WHS rat brain atlas v1 (Papp et al., 2014)

Three-dimensional digital brain atlases represent an important new generation of neuroinformatics tools for understanding complex brain anatomy, assigning location to experimental data, and planning of experiments. We have acquired a microscopic resolution isotropic MRI and DTI atlasing template for the Sprague Dawley rat brain with 39 μm isotropic voxels for the MRI volume and 78 μm isotropic voxels for the DTI.

Brain atlases

Exploring EBRAINS brain atlases using siibra-explorer

Exploring the EBRAINS brain atlases using the siibra-explorer, an interactive online 3D atlas viewer, and learning how the human brain atlas is structured.

Brain atlases

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