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1.
Nat Methods ; 20(11): 1822-1829, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37783883

RESUMEN

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.


Asunto(s)
Mapeo Encefálico , Encéfalo , Ratas , Animales , Corteza Cerebral , Dopamina , Análisis de Datos , Imagen por Resonancia Magnética
2.
PLoS Biol ; 21(6): e3002133, 2023 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-37390046

RESUMEN

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.


Asunto(s)
Encéfalo , Neurociencias , Animales , Humanos , Ratones , Ecosistema , Neuronas
3.
Development ; 149(5)2022 03 01.
Artículo en Inglés | MEDLINE | ID: mdl-35262177

RESUMEN

Axonal projections from layer V neurons of distinct neocortical areas are topographically organized into discrete clusters within the pontine nuclei during the establishment of voluntary movements. However, the molecular determinants controlling corticopontine connectivity are insufficiently understood. Here, we show that an intrinsic cortical genetic program driven by Nr2f1 graded expression is directly implicated in the organization of corticopontine topographic mapping. Transgenic mice lacking cortical expression of Nr2f1 and exhibiting areal organization defects were used as model systems to investigate the arrangement of corticopontine projections. By combining three-dimensional digital brain atlas tools, Cre-dependent mouse lines and axonal tracing, we show that Nr2f1 expression in postmitotic neurons spatially and temporally controls somatosensory topographic projections, whereas expression in progenitor cells influences the ratio between corticopontine and corticospinal fibres passing the pontine nuclei. We conclude that cortical gradients of area-patterning genes are directly implicated in the establishment of a topographic somatotopic mapping from the cortex onto pontine nuclei.


Asunto(s)
Mapeo Encefálico , Puente , Animales , Axones , Corteza Cerebral , Ratones , Vías Nerviosas/fisiología , Neuronas , Puente/fisiología
4.
Cereb Cortex ; 34(2)2024 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-38314581

RESUMEN

Neural circuits support behavioral adaptations by integrating sensory and motor information with reward and error-driven learning signals, but it remains poorly understood how these signals are distributed across different levels of the corticohippocampal hierarchy. We trained rats on a multisensory object-recognition task and compared visual and tactile responses of simultaneously recorded neuronal ensembles in somatosensory cortex, secondary visual cortex, perirhinal cortex, and hippocampus. The sensory regions primarily represented unisensory information, whereas hippocampus was modulated by both vision and touch. Surprisingly, the sensory cortices and the hippocampus coded object-specific information, whereas the perirhinal cortex did not. Instead, perirhinal cortical neurons signaled trial outcome upon reward-based feedback. A majority of outcome-related perirhinal cells responded to a negative outcome (reward omission), whereas a minority of other cells coded positive outcome (reward delivery). Our results highlight a distributed neural coding of multisensory variables in the cortico-hippocampal hierarchy. Notably, the perirhinal cortex emerges as a crucial region for conveying motivational outcomes, whereas distinct functions related to object identity are observed in the sensory cortices and hippocampus.


Asunto(s)
Corteza Perirrinal , Ratas , Animales , Hipocampo/fisiología , Percepción Visual/fisiología , Lóbulo Parietal , Recompensa
5.
Cereb Cortex ; 33(13): 8247-8264, 2023 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-37118890

RESUMEN

Cortical computations require coordination of neuronal activity within and across multiple areas. We characterized spiking relationships within and between areas by quantifying coupling of single neurons to population firing patterns. Single-neuron population coupling (SNPC) was investigated using ensemble recordings from hippocampal CA1 region and somatosensory, visual, and perirhinal cortices. Within-area coupling was heterogeneous across structures, with area CA1 showing higher levels than neocortical regions. In contrast to known anatomical connectivity, between-area coupling showed strong firing coherence of sensory neocortices with CA1, but less with perirhinal cortex. Cells in sensory neocortices and CA1 showed positive correlations between within- and between-area coupling; these were weaker for perirhinal cortex. All four areas harbored broadcasting cells, connecting to multiple external areas, which was uncorrelated to within-area coupling strength. When examining correlations between SNPC and spatial coding, we found that, if such correlations were significant, they were negative. This result was consistent with an overall preservation of SNPC across different brain states, suggesting a strong dependence on intrinsic network connectivity. Overall, SNPC offers an important window on cell-to-population synchronization in multi-area networks. Instead of pointing to specific information-coding functions, our results indicate a primary function of SNPC in dynamically organizing communication in systems composed of multiple, interconnected areas.


Asunto(s)
Corteza Perirrinal , Ratas , Animales , Hipocampo , Neuronas/fisiología , Región CA1 Hipocampal/fisiología , Lóbulo Parietal
6.
Neuroimage ; 251: 118973, 2022 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-35131433

RESUMEN

The Virtual Brain (TVB) is now available as open-source services on the cloud research platform EBRAINS (ebrains.eu). It offers software for constructing, simulating and analysing brain network models including the TVB simulator; magnetic resonance imaging (MRI) processing pipelines to extract structural and functional brain networks; combined simulation of large-scale brain networks with small-scale spiking networks; automatic conversion of user-specified model equations into fast simulation code; simulation-ready brain models of patients and healthy volunteers; Bayesian parameter optimization in epilepsy patient models; data and software for mouse brain simulation; and extensive educational material. TVB cloud services facilitate reproducible online collaboration and discovery of data assets, models, and software embedded in scalable and secure workflows, a precondition for research on large cohort data sets, better generalizability, and clinical translation.


Asunto(s)
Encéfalo , Nube Computacional , Animales , Teorema de Bayes , Encéfalo/diagnóstico por imagen , Simulación por Computador , Humanos , Imagen por Resonancia Magnética/métodos , Ratones , Programas Informáticos
7.
PLoS Biol ; 17(7): e3000344, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-31260438

RESUMEN

The Human Brain Project (HBP) is a European flagship project with a 10-year horizon aiming to understand the human brain and to translate neuroscience knowledge into medicine and technology. To achieve such aims, the HBP explores the multilevel complexity of the brain in space and time; transfers the acquired knowledge to brain-derived applications in health, computing, and technology; and provides shared and open computing tools and data through the HBP European brain research infrastructure. We discuss how the HBP creates a transdisciplinary community of researchers united by the quest to understand the brain, with fascinating perspectives on societal benefits.


Asunto(s)
Encéfalo/anatomía & histología , Informática Médica/métodos , Neurociencias/métodos , Tecnología/métodos , Encéfalo/diagnóstico por imagen , Diagnóstico por Imagen/métodos , Humanos , Procesamiento de Imagen Asistido por Computador/métodos , Informática Médica/tendencias , Neurociencias/tendencias , Reproducibilidad de los Resultados , Tecnología/tendencias
8.
Glia ; 67(2): 393-403, 2019 02.
Artículo en Inglés | MEDLINE | ID: mdl-30485540

RESUMEN

Transgenic Tg2576 mice expressing human amyloid precursor protein (hAPP) with the Swedish mutation are among the most frequently used animal models to study the amyloid pathology related to Alzheimer's disease (AD). The transgene expression in this model is considered to be neuron-specific. Using a novel hAPP-specific antibody in combination with cell type-specific markers for double immunofluorescent labelings and laser scanning microscopy, we here report that-in addition to neurons throughout the brain-astrocytes in the corpus callosum and to a lesser extent in neocortex express hAPP. This astrocytic hAPP expression is already detectable in young Tg2576 mice before the onset of amyloid pathology and still present in aged Tg2576 mice with robust amyloid pathology in neocortex, hippocampus, and corpus callosum. Surprisingly, hAPP immunoreactivity in cortex is restricted to resting astrocytes distant from amyloid plaques but absent from reactive astrocytes in close proximity to amyloid plaques. In contrast, neither microglial cells nor oligodendrocytes of young or aged Tg2576 mice display hAPP labeling. The astrocytic expression of hAPP is substantiated by the analyses of hAPP mRNA and protein expression in primary cultures derived from Tg2576 offspring. We conclude that astrocytes, in particular in corpus callosum, may contribute to amyloid pathology in Tg2576 mice and thus mimic this aspect of AD pathology.


Asunto(s)
Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/patología , Precursor de Proteína beta-Amiloide/genética , Precursor de Proteína beta-Amiloide/metabolismo , Astrocitos/metabolismo , Encéfalo/patología , Factores de Edad , Animales , Proteínas de Unión al Calcio/genética , Proteínas de Unión al Calcio/metabolismo , Células Cultivadas , Modelos Animales de Enfermedad , Regulación de la Expresión Génica/genética , Proteína Ácida Fibrilar de la Glía/metabolismo , Gutatión-S-Transferasa pi/metabolismo , Humanos , Ratones , Ratones Endogámicos C57BL , Proteínas de Microfilamentos/genética , Proteínas de Microfilamentos/metabolismo , Proteínas Musculares , Neuronas/metabolismo , Neuronas/patología , Fosfopiruvato Hidratasa/genética , Fosfopiruvato Hidratasa/metabolismo , ARN Mensajero/metabolismo , Factor de Crecimiento Transformador beta/genética , Factor de Crecimiento Transformador beta/metabolismo
9.
Neuroimage ; 108: 441-9, 2015 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-25585022

RESUMEN

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 rat hippocampal region is a commonly used model for basic research on memory and learning, and for preclinical investigations of brain disease. The region features a complex anatomical organization with multiple subdivisions that can be identified on the basis of specific cytoarchitectonic or chemoarchitectonic criteria. We here investigate the extent to which it is possible to identify boundaries of divisions of the hippocampal region on the basis of high-resolution MRI contrast. We present the boundaries of 13 divisions, identified and delineated based on multiple types of image contrast observed in the recently published Waxholm Space MRI/DTI template for the Sprague Dawley rat brain (Papp et al., Neuroimage 97:374-386, 2014). The new detailed delineations of the hippocampal formation and parahippocampal region (Waxholm Space atlas of the Sprague Dawley rat brain, v2.0) are shared via the INCF Software Center (http://software.incf.org/), where also the MRI/DTI reference template is available. The present update of the Waxholm Space atlas of the rat brain is intended to facilitate interpretation, analysis, and integration of experimental data from this anatomically complex region.


Asunto(s)
Mapeo Encefálico , Imagen de Difusión Tensora , Hipocampo/anatomía & histología , Imagenología Tridimensional , Imagen por Resonancia Magnética , Animales , Masculino , Ratas , Ratas Sprague-Dawley
10.
Neuroimage ; 105: 561-2, 2015 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-25635280

RESUMEN

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.


Asunto(s)
Atlas como Asunto , Encéfalo/anatomía & histología , Ratas Sprague-Dawley/anatomía & histología , Animales , Masculino
11.
Hippocampus ; 25(7): 838-57, 2015 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-25533645

RESUMEN

The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource.


Asunto(s)
Mapeo Encefálico , Hipocampo/anatomía & histología , Imagenología Tridimensional , Imagen por Resonancia Magnética , Animales , Femenino , Masculino , Proteínas del Tejido Nervioso/metabolismo , Ratas , Ratas Long-Evans , Ratas Wistar
12.
Neuroimage ; 97: 374-86, 2014 Aug 15.
Artículo en Inglés | MEDLINE | ID: mdl-24726336

RESUMEN

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. Building on this template, we have delineated 76 major anatomical structures in the brain. Delineation criteria are provided for each structure. We have applied a spatial reference system based on internal brain landmarks according to the Waxholm Space standard, previously developed for the mouse brain, and furthermore connected this spatial reference system to the widely used stereotaxic coordinate system by identifying cranial sutures and related stereotaxic landmarks in the template using contrast given by the active staining technique applied to the tissue. With the release of the present atlasing template and anatomical delineations, we provide a new tool for spatial orientation analysis of neuroanatomical location, and planning and guidance of experimental procedures in the rat brain. The use of Waxholm Space and related infrastructures will connect the atlas to interoperable resources and services for multi-level data integration and analysis across reference spaces.


Asunto(s)
Atlas como Asunto , Encéfalo/anatomía & histología , Ratas Sprague-Dawley/anatomía & histología , Animales , Imagen de Difusión por Resonancia Magnética , Sustancia Gris/anatomía & histología , Procesamiento de Imagen Asistido por Computador , Difusión de la Información , Internet , Masculino , Ratas , Médula Espinal/anatomía & histología , Sustancia Blanca/anatomía & histología
13.
Front Neuroinform ; 18: 1284107, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38421771

RESUMEN

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.

14.
Commun Biol ; 7(1): 605, 2024 May 20.
Artículo en Inglés | MEDLINE | ID: mdl-38769398

RESUMEN

Alzheimer's disease (AD) is broadly characterized by neurodegeneration, pathology accumulation, and cognitive decline. There is considerable variation in the progression of clinical symptoms and pathology in humans, highlighting the importance of genetic diversity in the study of AD. To address this, we analyze cell composition and amyloid-beta deposition of 6- and 14-month-old AD-BXD mouse brains. We utilize the analytical QUINT workflow- a suite of software designed to support atlas-based quantification, which we expand to deliver a highly effective method for registering and quantifying cell and pathology changes in diverse disease models. In applying the expanded QUINT workflow, we quantify near-global age-related increases in microglia, astrocytes, and amyloid-beta, and we identify strain-specific regional variation in neuron load. To understand how individual differences in cell composition affect the interpretation of bulk gene expression in AD, we combine hippocampal immunohistochemistry analyses with bulk RNA-sequencing data. This approach allows us to categorize genes whose expression changes in response to AD in a cell and/or pathology load-dependent manner. Ultimately, our study demonstrates the use of the QUINT workflow to standardize the quantification of immunohistochemistry data in diverse mice, - providing valuable insights into regional variation in cellular load and amyloid deposition in the AD-BXD model.


Asunto(s)
Enfermedad de Alzheimer , Encéfalo , Modelos Animales de Enfermedad , Variación Genética , Animales , Enfermedad de Alzheimer/genética , Enfermedad de Alzheimer/patología , Enfermedad de Alzheimer/metabolismo , Ratones , Encéfalo/metabolismo , Encéfalo/patología , Ratones Transgénicos , Péptidos beta-Amiloides/metabolismo , Péptidos beta-Amiloides/genética , Masculino
15.
Hum Brain Mapp ; 34(2): 327-46, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23169482

RESUMEN

Water diffusion magnetic resonance imaging (dMRI) is a powerful tool for studying biological tissue microarchitectures in vivo. Recently, there has been increased effort to develop quantitative dMRI methods to probe both length scale and orientation information in diffusion media. Diffusion spectrum imaging (DSI) is one such approach that aims to resolve such information based on the three-dimensional diffusion propagator at each voxel. However, in practice, only the orientation component of the propagator function is preserved when deriving the orientation distribution function. Here, we demonstrate how a straightforward extension of the linear spherical deconvolution (SD) model can be used to probe tissue orientation structures over a range (or "spectrum") of length scales with minimal assumptions on the underlying microarchitecture. Using high b-value Cartesian q-space data on a rat brain tissue sample, we demonstrate how this "restriction spectrum imaging" (RSI) model allows for separating the volume fraction and orientation distribution of hindered and restricted diffusion, which we argue stems primarily from diffusion in the extraneurite and intraneurite water compartment, respectively. Moreover, we demonstrate how empirical RSI estimates of the neurite orientation distribution and volume fraction capture important additional structure not afforded by traditional DSI or fixed-scale SD-like reconstructions, particularly in gray matter. We conclude that incorporating length scale information in geometric models of diffusion offers promise for advancing state-of-the-art dMRI methods beyond white matter into gray matter structures while allowing more detailed quantitative characterization of water compartmentalization and histoarchitecture of healthy and diseased tissue.


Asunto(s)
Encéfalo/anatomía & histología , Imagen de Difusión Tensora/métodos , Algoritmos , Animales , Axones/fisiología , Agua Corporal/fisiología , Mapeo Encefálico , Membrana Celular/fisiología , Cerebelo/anatomía & histología , Cerebelo/citología , Corteza Cerebral/anatomía & histología , Corteza Cerebral/citología , Cuerpo Calloso/fisiología , Imagen de Difusión Tensora/instrumentación , Globo Pálido/anatomía & histología , Globo Pálido/citología , Procesamiento de Imagen Asistido por Computador , Modelos Anatómicos , Método de Montecarlo , Neostriado/anatomía & histología , Neostriado/citología , Neuritas/fisiología , Neuritas/ultraestructura , Ratas , Ratas Sprague-Dawley , Procesamiento de Señales Asistido por Computador
16.
Sci Data ; 10(1): 645, 2023 09 21.
Artículo en Inglés | MEDLINE | ID: mdl-37735463

RESUMEN

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.


Asunto(s)
Encéfalo , Corteza Insular , Animales , Ratas , Conocimiento , Memoria a Corto Plazo , Procesos Mentales
17.
Sci Data ; 10(1): 150, 2023 03 21.
Artículo en Inglés | MEDLINE | ID: mdl-36944675

RESUMEN

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.


Asunto(s)
Encéfalo , Neuroglía , Ratas , Animales , Encéfalo/anatomía & histología , Encéfalo/citología , Metales , Neuroglía/citología , Neuroglía/metabolismo , Zinc
18.
Sci Data ; 10(1): 486, 2023 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-37495585

RESUMEN

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.


Asunto(s)
Atlas como Asunto , Encéfalo , Animales , Humanos , Ratones , Ratas , Encéfalo/anatomía & histología , Imagen por Resonancia Magnética/métodos , Flujo de Trabajo
19.
Nat Commun ; 14(1): 5884, 2023 09 21.
Artículo en Inglés | MEDLINE | ID: mdl-37735467

RESUMEN

Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.


Asunto(s)
Ascomicetos , Animales , Ratones , Encéfalo/diagnóstico por imagen , Redes Neurales de la Computación , Sistemas de Lectura , Neuroimagen
20.
Front Neuroinform ; 17: 1154080, 2023.
Artículo en Inglés | MEDLINE | ID: mdl-36970659

RESUMEN

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.

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