Waxholm Space atlas of the rat brain: A 3D atlas supporting data analysis and integration

Leergaard, Trygve B.; Kleven, Heidi; Bjerke, Ingvild Elise; Clascá, Francisco; Groenewegen, H.J.; Bjaalie, Jan G.

doi:10.21203/rs.3.rs-2466303/v1

Cited by 10 publications

(11 citation statements)

References 42 publications

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“…The computational mesh used for the simulations in this paper was constructed from the "Waxholm Space Atlas of the Sprague Dawley Rat Brain v4" (RRID: SCR_017124) [73][74][75], available under the licence CC-BY-SA 4.0 (https://creativecommons.org/licenses/by-sa/4.0/) at https://www.nitrc.org/projects/whs-sd-atlas. The atlas provides a detailed segmentation of different regions within the rat brain.…”

Section: Computational Mesh Solution Methods and Verificationmentioning

confidence: 99%

Multi-compartmental model of glymphatic clearance of solutes in brain tissue

Poulain

Riseth²,

Vinje³

2023

PLoS ONE

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The glymphatic system is the subject of numerous pieces of research in biology. Mathematical modelling plays a considerable role in this field since it can indicate the possible physical effects of this system and validate the biologists’ hypotheses. The available mathematical models that describe the system at the scale of the brain (i.e. the macroscopic scale) are often solely based on the diffusion equation and do not consider the fine structures formed by the perivascular spaces. We therefore propose a mathematical model representing the time and space evolution of a mixture flowing through multiple compartments of the brain. We adopt a macroscopic point of view in which the compartments are all present at any point in space. The equations system is composed of two coupled equations for each compartment: One equation for the pressure of a fluid and one for the mass concentration of a solute. The fluid and solute can move from one compartment to another according to certain membrane conditions modelled by transfer functions. We propose to apply this new modelling framework to the clearance of 14C-inulin from the rat brain.

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Section: Computational Mesh Solution Methods and Verificationmentioning

confidence: 99%

Multi-compartmental model of glymphatic clearance of solutes in brain tissue

Poulain

Riseth²,

Vinje³

2023

PLoS ONE

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“…This is important because widespread variations in brain atlas ontologies have been developed to represent the molecular, chemical, genetic, and electrophysiological signals being measured across institutions. With different levels of granularity and different intended applications, multiple atlases per species now exist and are continuing to emerge [1,2,41,42,43,44]. While some atlases have been defined in the same coordinate framework-often achieved through existing methods of image registration or manual alignment [28]many exist in different coordinate frameworks.…”

Section: Generalizing the Methodology To Compare Atlas To Atlasmentioning

confidence: 99%

A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming

Stouffer

Trouvé²,

Younes

et al. 2023

Preprint

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This paper explicates a solution to the problem of building correspondences between molecular-scale transcriptomics and tissue-scale atlases. The central model represents spatial transcriptomics as generalized functions encoding molecular position and high-dimensional transcriptomic-based (gene, cell type) identity. We map onto low-dimensional atlas ontologies by modeling each atlas compartment as a homogeneous random field with unknown transcriptomic feature distribution. The algorithm presented solves simultaneously for the minimizing geodesic diffeomorphism of coordinates and latent atlas transcriptomic feature fractions by alternating LDDMM optimization for coordinate transformations and quadratic programming for the latent transcriptomic variables. We demonstrate the universality of the algorithm in mapping tissue atlases to gene-based and cell-based MERFISH datasets as well as to other tissue scale atlases. The joint estimation of diffeomorphisms and latent feature distributions allows integration of diverse molecular and cellular datasets into a single coordinate system and creates an avenue of comparison amongst atlas ontologies for continued future development.

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“…Registration with a three-dimensional rat brain reference atlas. To provide a starting point for analysis of anatomical location, all images were spatially registered to the three-dimensional Waxholm Space atlas of the Sprague Dawley rat brain 96,97,99,100 (WHS rat brain atlas, RRID: SCR_017124, Fig. 1c), using the QuickNII Fig.…”

Section: Microscopic Imagingmentioning

confidence: 99%

“…H200 and H441 were horizontally sectioned and split into subseries of Timm-dark and Nissl, while H201 was sagittally sectioned and stained with Timm-light, Timm-dark and Nissl. (c) The TIFF images of the different subseries of sections, here exemplified with subject H108 (Timm-light, Timm-dark, Nissl), were pre-processed and spatially registered to the Waxholm Space atlas of Sprague Dawley rat brain v4 100 101 (RRID: SCR_016854). This tool allows the user to create custom made atlas plates, in any plane of orientation, based on the global match of multiple anatomical landmarks and affine transformation (scaling, panning and rotation).…”

Section: Microscopic Imagingmentioning

confidence: 99%

“…Section images are shared in standard TIFF format, compatible for display and analyses through a range of tools. The pre-processing and image registration software, Nutil 98 (RRID: SCR_017183), QuickNII 101 (RRID: SCR_016854) and VisuAlign (RRID: SCR_017978), as well as the Waxholm Space atlas of the Sprague Dawley rat brain 96,97,99,100 (WHS rat brain atlas, RRID: SCR_017124), are available for download via NITRC, NeuroImaging Tools and Resources Collaboratory (https://nitrc.org/). Spatial relationships between images and the WHS rat brain atlas, available in JSON files, can be inspected and manipulated with the QuickNII tool presuming that PNG versions of the images is present in the same folder as the related JSON file.…”

Section: Code Availabilitymentioning

confidence: 99%

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A Timm-Nissl multiplane microscopic atlas of rat brain zincergic terminal fields and metal-containing glia

et al. 2023

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The ability of Timm’s sulphide silver method to stain zincergic terminal fields has made it a useful neuromorphological marker. Beyond its roles in zinc-signalling and neuromodulation, zinc is involved in the pathophysiology of ischemic stroke, epilepsy, degenerative diseases and neuropsychiatric conditions. In addition to visualising zincergic terminal fields, the method also labels transition metals in neuronal perikarya and glial cells. To provide a benchmark reference for planning and interpretation of experimental investigations of zinc-related phenomena in rat brains, we have established a comprehensive repository of serial microscopic images from a historical collection of coronally, horizontally and sagittally oriented rat brain sections stained with Timm’s method. Adjacent Nissl-stained sections showing cytoarchitecture, and customised atlas overlays from a three-dimensional rat brain reference atlas registered to each section image are included for spatial reference and guiding identification of anatomical boundaries. The Timm-Nissl atlas, available from EBRAINS, enables experimental researchers to navigate normal rat brain material in three planes and investigate the spatial distribution and density of zincergic terminal fields across the entire brain.

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Waxholm Space atlas of the rat brain: A 3D atlas supporting data analysis and integration

Cited by 10 publications

References 42 publications

Multi-compartmental model of glymphatic clearance of solutes in brain tissue

Multi-compartmental model of glymphatic clearance of solutes in brain tissue

A Universal Method for Crossing Molecular and Atlas Modalities using Simplex-Based Image Varifolds and Quadratic Programming

A Timm-Nissl multiplane microscopic atlas of rat brain zincergic terminal fields and metal-containing glia

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