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

Unveiling the potential of ultrasound in brain imaging: Innovations, challenges, and prospects

Within medical imaging, ultrasound serves as a crucial tool, particularly in the realms of brain imaging and disease diagnosis. It offers superior safety, speed, and wider applicability compared to Magnetic Resonance Imaging (MRI) and X-ray Computed Tomography (CT). Nonetheless, conventional transcranial ultrasound applications in adult brain imaging face challenges stemming from the significant acoustic impedance contrast between the skull bone and soft tissues. Recent strides in ultrasound technology encompass a spectrum of advancements spanning tissue structural imaging, blood flow imaging, functional imaging, and image enhancement techniques. Structural imaging methods include traditional transcranial ultrasound techniques and ultrasound elastography. Transcranial ultrasound assesses the structure and function of the skull and brain, while ultrasound elastography evaluates the elasticity of brain tissue. Blood flow imaging includes traditional transcranial Doppler (TCD), ultrafast Doppler (UfD), contrast-enhanced ultrasound (CEUS), and ultrasound localization microscopy (ULM), which can be used to evaluate the velocity, direction, and perfusion of cerebral blood flow. Functional ultrasound imaging (fUS) detects changes in cerebral blood flow to create images of brain activity. Image enhancement techniques include full waveform inversion (FWI) and phase aberration correction techniques, focusing on more accurate localization and analysis of brain structures, achieving more precise and reliable brain imaging results. These methods have been extensively studied in clinical animal models, neonates, and adults, showing significant potential in brain tissue structural imaging, cerebral hemodynamics monitoring, and brain disease diagnosis. They represent current hotspots and focal points of ultrasound medical research. This review provides a comprehensive summary of recent developments in brain imaging technologies and methods, discussing their advantages, limitations, and future trends, offering insights into their prospects.

Comparison of basal ganglia regions across murine brain atlases using metadata models and the Waxholm Space

The murine basal ganglia regions are targets for research into complex brain functions such as motor control and habit formation. However, there are several ways to name and annotate these regions, posing challenges for interpretation and comparison of data across studies. Here, we give an overview of basal ganglia terms and boundaries in the literature and reference atlases, and describe the criteria used for annotating these regions in the Waxholm Space rat brain atlas. We go on to compare basal ganglia annotations in stereotaxic rat brain atlases and the Allen Mouse brain Common Coordinate Framework to those in the Waxholm Space rat brain atlas. We demonstrate and describe considerable differences in the terms and boundaries of most basal ganglia regions across atlases and their versions. We also register information about atlases and regions in the openMINDS metadata framework, facilitating integration of data in neuroscience databases. The comparisons of terms and boundaries across rat and mouse atlases support analysis and interpretation of existing and new data from the basal ganglia.

Development and advancements in rodent MRI-based brain atlases

Rodents, particularly mice and rats, are extensively utilized in fundamental neuroscience research. Brain atlases have played a pivotal role in this field, evolving from traditional printed histology atlases to digital atlases incorporating diverse imaging datasets. Magnetic resonance imaging (MRI)-based brain atlases, also known as brain maps, have been employed in specific studies. However, the existence of numerous versions of MRI-based brain atlases has impeded their standardized application and widespread use, despite the consensus within the academic community regarding their significance in mice and rats. Furthermore, there is a dearth of comprehensive and systematic reviews on MRI-based brain atlases for rodents. This review aims to bridge this gap by providing a comprehensive overview of the advancements in MRI-based brain atlases for rodents, with a specific focus on mice and rats. It seeks to explore the advantages and disadvantages of histologically printed brain atlases in comparison to MRI brain atlases, delineate the standardized methods for creating MRI brain atlases, and summarize their primary applications in neuroscience research. Additionally, this review aims to assist researchers in selecting appropriate versions of MRI brain atlases for their studies or refining existing MRI brain atlas resources, thereby facilitating the development and widespread adoption of standardized MRI-based brain atlases in rodents.

The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases

Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.

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

Volumetric brain atlases are increasingly used to integrate and analyze 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 an update of the Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource. This brain atlas features annotations of 222 structures, of which 112 are new and 57 revised compared to previous versions. It provides a detailed map of the cerebral cortex, hippocampal region, striatopallidal areas, midbrain dopaminergic system, thalamic cell groups, the auditory system and main fiber tracts. We document the criteria underlying the annotations and demonstrate how the atlas with related tools and workflows can be used to support interpretation, integration, analysis and dissemination of experimental rat brain data.

The efferent connections of the orbitofrontal, posterior parietal, and insular cortex of the rat brain

The orbitofrontal, posterior parietal, and insular cortices are sites of higher-order cognitive processing implicated in a wide range of behaviours, including working memory, attention guiding, decision making, and spatial navigation. To better understand how these regions contribute to such functions, we need detailed knowledge about the underlying structural connectivity. Several tract-tracing studies have investigated specific aspects of orbitofrontal, posterior parietal and insular connectivity, but a digital resource for studying the cortical and subcortical projections from these areas in detail is not available. We here present a comprehensive collection of brightfield and fluorescence microscopic images of serial coronal sections from 49 rat brain tract-tracing experiments, in which discrete injections of the anterograde tracers biotinylated dextran amine and/or Phaseolus vulgaris leucoagglutinin were placed in the orbitofrontal, parietal, or insular cortex. The images are spatially registered to the Waxholm Space Rat brain atlas. The image collection, with corresponding reference atlas maps, is suitable as a reference framework for investigating the brain-wide efferent connectivity of these cortical association areas.

AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures

Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.

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

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.

A neuroscientist's guide to using murine brain atlases for efficient analysis and transparent reporting

Brain atlases are widely used in neuroscience as resources for conducting experimental studies, and for integrating, analyzing, and reporting data from animal models. A variety of atlases are available, and it may be challenging to find the optimal atlas for a given purpose and to perform efficient atlas-based data analyses. Comparing findings reported using different atlases is also not trivial, and represents a barrier to reproducible science. With this perspective article, we provide a guide to how mouse and rat brain atlases can be used for analyzing and reporting data in accordance with the FAIR principles that advocate for data to be findable, accessible, interoperable, and re-usable. We first introduce how atlases can be interpreted and used for navigating to brain locations, before discussing how they can be used for different analytic purposes, including spatial registration and data visualization. We provide guidance on how neuroscientists can compare data mapped to different atlases and ensure transparent reporting of findings. Finally, we summarize key considerations when choosing an atlas and give an outlook on the relevance of increased uptake of atlas-based tools and workflows for FAIR data sharing.

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

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.

Histological E-data Registration in rodent Brain Spaces

Recording technologies for rodents have seen huge advances in the last decade, allowing users to sample thousands of neurons simultaneously from multiple brain regions. This has prompted the need for digital tool kits to aid in curating anatomical data, however, existing tools either provide limited functionalities or require users to be proficient in coding to use them. To address this we created HERBS (Histological E-data Registration in rodent Brain Spaces), a comprehensive new tool for rodent users that offers a broad range of functionalities through a user-friendly graphical user interface. Prior to experiments, HERBS can be used to plan coordinates for implanting electrodes, targeting viral injections or tracers. After experiments, users can register recording electrode locations (e.g. Neuropixels and tetrodes), viral expression, or other anatomical features, and visualize the results in 2D or 3D. Additionally, HERBS can delineate labeling from multiple injections across tissue sections and obtain individual cell counts.Regional delineations in HERBS are based either on annotated 3D volumes from the Waxholm Space Atlas of the Sprague Dawley Rat Brain or the Allen Mouse Brain Atlas, though HERBS can work with compatible volume atlases from any species users wish to install. HERBS allows users to scroll through the digital brain atlases and provides custom-angle slice cuts through the volumes, and supports free-transformation of tissue sections to atlas slices. Furthermore, HERBS allows users to reconstruct a 3D brain mesh with tissue from individual animals. HERBS is a multi-platform open-source Python package that is available on PyPI and GitHub, and is compatible with Windows, macOS, and Linux operating systems.

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

Detailed knowledge about the neural connections among regions of the brain is key for advancing our understanding of normal brain function and changes that occur with aging and disease. Researchers use a range of experimental techniques to map connections at different levels of granularity in rodent animal models, but the results are often challenging to compare and integrate. Three-dimensional reference atlases of the brain provide new opportunities for cumulating, integrating, and reinterpreting research findings across studies. 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.

Age-Specific Adult Rat Brain MRI Templates and Tissue Probability Maps

Age-specific resources in human MRI mitigate processing biases that arise from structural changes across the lifespan. There are fewer age-specific resources for preclinical imaging, and they only represent developmental periods rather than adulthood. Since rats recapitulate many facets of human aging, it was hypothesized that brain volume and each tissue's relative contribution to total brain volume would change with age in the adult rat. Data from a longitudinal study of rats at 3, 5, 11, and 17 months old were used to test this hypothesis. Tissue volume was estimated from high resolution structural images using a priori information from tissue probability maps. However, existing tissue probability maps generated inaccurate gray matter probabilities in subcortical structures, particularly the thalamus. To address this issue, gray matter, white matter, and CSF tissue probability maps were generated by combining anatomical and signal intensity information. The effects of age on volumetric estimations were then assessed with mixed-effects models. Results showed that herein estimation of gray matter volumes better matched histological evidence, as compared to existing resources. All tissue volumes increased with age, and the tissue proportions relative to total brain volume varied across adulthood. Consequently, a set of rat brain templates and tissue probability maps from across the adult lifespan is released to expand the preclinical MRI community's fundamental resources.

A multicontrast MR atlas of the Wistar rat brain

We describe a multi-contrast, multi-dimensional atlas of the Wistar rat acquired at microscopic spatial resolution using magnetic resonance histology (MRH). Diffusion weighted images, and associated scalar images were acquired of a single specimen with a fully sampled Fourier reconstruction, 61 angles and b=3000 s/mm2 yielding 50 um isotropic spatial resolution. The higher angular sampling allows use of the GQI algorithm improving the angular invariance of the scalar images and yielding an orientation distribution function to assist in delineating subtle boundaries where there are crossing fibers  and track density images providing insight into local fiber architecture.  A multigradient echo image of the same specimen was acquired at 25 um isotropic spatial resolution. A quantitative susceptibility map enhances fiber architecture relative to the magnitude images.  An accompanying multi-specimen atlas (n=6) was acquired with compressed sensing with the same diffusion protocol as used for the single specimen atlas.  An average was created using diffeomorphic mapping. Scalar volumes from the diffusion data, a T2* weighted volume, a quantitative susceptibility map, and a track density volume, all registered to the same space provide multiple contrasts to assist in anatomic delineation. The new template  provides significantly increased contrast in the scalar DTI images when compared to previous atlases. A compact interactive viewer based on 3D Slicer is provided to facilitate comparison among the contrasts in the multiple volumes. The single volume and average atlas with multiple 3D volumes provide an improved template for anatomic interrogation of the Wistar rat brain. The improved contrast to noise in the scalar DTI images and the addition of other volumes (eg. QA,QSM,TDI ) will facilitate automated label registration for MR histology and preclinical imaging.

Ratlas-LH: An MRI template of the Lister hooded rat brain with stereotaxic coordinates for neurosurgical implantations

There is currently no brain atlas available to specifically determine stereotaxic coordinates for neurosurgery in Lister hooded rats despite the popularity of this strain for behavioural neuroscience studies in the United Kingdom and elsewhere. We have created a dataset, which we refer to as ‘Ratlas-LH’ (for Lister hooded). Ratlas-LH combines in vivo magnetic resonance images of the brain of young adult male Lister hooded rats with ex vivo micro-computed tomography images of the ex vivo skull, as well as a set of delineations of brain regions, adapted from the Waxholm Space Atlas of the Sprague Dawley Rat Brain. Ratlas-LH was produced with an isotropic resolution of 0.15 mm. It has been labelled in such a way as to provide a stereotaxic coordinate system for the determination of distances relative to the skull landmark of bregma. We have demonstrated that the atlas can be used to determine stereotaxic coordinates to accurately target brain regions in the Lister hooded rat brain. Ratlas-LH is freely available to facilitate neurosurgical procedures in the Lister hooded rat.

Structural Alterations in a Rat Model of Short-Term Conductive Hearing Loss Are Associated With Reduced Resting State Functional Connectivity

Conductive hearing loss (CHL) results in attenuation of air conducted sound reaching the inner ear. How a change in air conducted sound alters the auditory system resulting in cortical alterations is not well understood. Here, we have assessed structural and functional magnetic resonance imaging (MRI) in an adult (P60) rat model of short-term conductive hearing loss (1 week). Diffusion tensor imaging (DTI) revealed fractional anisotropy (FA) and axial diffusivity alterations after hearing loss that circumscribed the auditory cortex (AC). Tractography found the lateral lemniscus tract leading to the bilateral inferior colliculus (IC) was reduced. For baseline comparison, DTI and tractography alterations were not found for the somatosensory cortex. To determine functional connectivity changes due to hearing loss, seed-based analysis (SBA) and independent component analysis (ICA) were performed. Short term conductive hearing loss altered functional connectivity in the AC and IC, but not the somatosensory cortex. The results present an exploratory neuroimaging assessment of structural alterations coupled to a change in functional connectivity after conductive hearing loss. The results and implications for humans consist of structural-functional brain alterations following short term hearing loss in adults.

Enzymes of acetylcholine metabolism in the rat inferior colliculus

Although there is strong evidence for cholinergic projections to the rat inferior colliculus, especially from the pedunculopontine tegmental nucleus (Noftz et al., 2020), there is a lack of information about the quantitative prevalence of the enzymes of acetylcholine metabolism in its various portions. We have used microdissection of freeze-dried sections combined with radiometric assays to map the distributions in the rat inferior colliculus of the activities of choline acetyltransferase (ChAT), which catalyzes synthesis of acetylcholine, and acetylcholinesterase (AChE), which catalyzes its breakdown by hydrolysis. Both enzyme activities were present throughout the inferior colliculus. Average ChAT activity was consistently somewhat higher in the external cortex, excluding its most superficial layer, than in the dorsal cortex or central nucleus. Within the external cortex, ChAT activity was about half as high laterally in its most superficial layer as elsewhere. The distribution of AChE activity was more uniform than that of ChAT. Overall, ChAT activity in the rat inferior colliculus was relatively low, about a fifth of that in whole brain of rat and lower than in other central auditory regions, whereas AChE activity was about two-thirds that of rat whole brain and about average for central auditory regions. The results are compared to previous measurements for cat and hamster inferior colliculus. They are consistent with a modest role for cholinergic neurotransmission in the inferior colliculus, to modulate the activity of its major neuronal types.

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

With recent technological advances in microscopy and image acquisition of tissue sections, further developments of tools are required for viewing, transforming, and analyzing the ever-increasing amounts of high-resolution data produced. In the field of neuroscience, histological images of whole rodent brain sections are commonly used for investigating brain connections as well as cellular and molecular organization in the normal and diseased brain, but present a problem for the typical neuroscientist with no or limited programming experience in terms of the pre- and post-processing steps needed for analysis. To meet this need we have designed Nutil, an open access and stand-alone executable software that enables automated transformations, post-processing, and analyses of 2D section images using multi-core processing (OpenMP). The software is written in C++ for efficiency, and provides the user with a clean and easy graphical user interface for specifying the input and output parameters. Nutil currently contains four separate tools: (1) A transformation toolchain named “Transform” that allows for rotation, mirroring and scaling, resizing, and renaming of very large tiled tiff images. (2) “TiffCreator” enables the generation of tiled TIFF images from other image formats such as PNG and JPEG. (3) A “Resize” tool completes the preprocessing toolset and allows downscaling of PNG and JPEG images with output in PNG format. (4) The fourth tool is a post-processing method called “Quantifier” that enables the quantification of segmented objects in the context of regions defined by brain atlas maps generated with the QuickNII software based on a 3D reference atlas (mouse or rat). The output consists of a set of report files, point cloud coordinate files for visualization in reference atlas space, and reference atlas images superimposed with color-coded objects. The Nutil software is made available by the Human Brain Project (https://www.humanbrainproject.eu) at https://www.nitrc.org/projects/nutil/.

Database of literature derived cellular measurements from the murine basal ganglia

Quantitative measurements and descriptive statistics of different cellular elements in the brain are typically published in journal articles as text, tables, and example figures, and represent an important basis for the creation of biologically constrained computational models, design of intervention studies, and comparison of subject groups. Such data can be challenging to extract from publications and difficult to normalise and compare across studies, and few studies have so far attempted to integrate quantitative information available in journal articles. We here present a database of quantitative information about cellular parameters in the frequently studied murine basal ganglia. The database holds a curated and normalised selection of currently available data collected from the literature and public repositories, providing the most comprehensive collection of quantitative neuroanatomical data from the basal ganglia to date. The database is shared as a downloadable resource from the EBRAINS Knowledge Graph (https://kg.ebrains.eu), together with a workflow that allows interested researchers to update and expand the database with data from future reports.