Brain Atlas Resources

The project was initiated to determine the projections of the orbital frontal cortex (OFC) to the parahippocampal region in the rat, using the anterograde tracers biotinylated dextran amine (BDA) and Phaseolus vulgaris-leucoagglutinin (PHA-L).

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.

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.

Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain. 2021, iScience. https://doi.org/10.1016/j.isci.2020.101906

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

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

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.

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.

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.

Navigating the murine brain: towards best practices for determining and documenting neuroanatomical locations in experimental studies. Frontiers in Neuroanatomy. 2018 Nov 2; 12: article 82. https://doi.org/10.3389/fnana.2018.00082

Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 2020,14:37. https://doi.org/10.3389/fninf.2020.00037

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

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.

The QUINT workflow comprises a flexible suite of software designed to support atlas-based quantification of labelled features in series of histological images from mouse or rat brain.

The QUINT workflow takes you through a series of steps developed to enable researchers to quantify and analyse labelled features in a series of histological images of rodent brain sections within a known atlas space.

QUINT: Workflow for quantification and spatial analysis of features in histological images from rodent brain. Front Neuroinform. 2019 Dec 3;13:75. https://doi.org/10.3389/fninf.2019.00075.

This dataset contains a brain-wide overview of the efferent neural projections from the orbitofrontal, posterior parietal and insular areas in the rat cerebral cortex.

Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLosONE, 2019, 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796

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.

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.

A tutorial on how to anchor partial volumetric data to BigBrain using voluba.

voluba is a browser-based tool for interactive alignment of volumes of interest to 3D atlases.

In this tutorial, you will warp an example MRI scan to MNI ICBM 152 2009c Nonlinear Asymmetric space and analyze a point of the input space in the detailed anatomical context of the EBRAINS Human Brain Atlas.

voluba-mriwarp is a desktop application for aligning human MRI scans to MNI152 template and analyzing brain regions.

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

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

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.

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.

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.

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.

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.