Resources

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

Anterogradely labeled axonal projections from the orbitofrontal cortex in rat

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).

Brain atlases

Semiquantitative overview of efferent projections from the orbitofrontal, posterior parietal and insular cortices in rat

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.

Brain atlases

QUINT user manual

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.

Brain atlases

QUINT workflow tutorial

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.

Brain atlases

Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse 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

Brain atlases

Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images

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

Brain atlases

Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies

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

Brain atlases

QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain

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.

Brain atlases

Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool

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

Brain atlases

Waxholm Space atlas of the Sprague Dawley rat brain.

Papp E.A., Leergaard T.B., Calabrese E., Johnson G.A., Bjaalie J.G. (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386. https://doi.org/10.1016/j.neuroimage.2014.04.001

Brain atlases

Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging.

Osen K.K., Imad J., Wennberg A.E., Papp E.A., Leergaard T.B. (2019) Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 199, 38-56. https://doi.org/10.1016/j.neuroimage.2019.05.016

Brain atlases

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