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PubMed2002

MR microscopy and high resolution small animal MRI: applications in neuroscience research.

The application of magnetic resonance (MR) imaging in the study of human disease using small animals has steadily evolved over the past two decades and strongly established the fields of "small animal MR imaging" and "MR microscopy." An increasing number of neuroscience related investigations now implement MR microscopy in their experiments. Research areas of growth pertaining to MR microscopy studies are focused on (1). phenotyping of genetically engineered mice models of human neurological diseases and (2). rodent brain atlases. MR microscopy can be performed in vitro on tissue specimens, ex vivo on brain slice preparations and in vivo (typically on rodents). Like most new imaging technologies, MR microscopy is technologically demanding and requires broad expertise. Uniform guidelines or "standards" of a given MR microscopy experiment are non-existent. The main focus therefore of this review will be on biological applications of MR microscopy and the experimental requirements. We also take a critical look at the biological information that small animal (rodent) MR imaging has provided in neuroscience research.

Animals↗
PubMedDate not supplied

Spatial registration of digital brain atlases based on fuzzy set theory.

We present a semiautomatic method based on fuzzy set theory for adjusting a computerized brain atlas to magnetic resonance images (MRIs) of the human cerebral cortex. The atlas was registered to three-dimensional MRI data sets of 10 healthy volunteers. After a global matching using the external contour of the brain, several local procedures were performed regarding selected primary furrows and cytoarchitectonic areas. The final transformation matrix was calculated with respect to these anatomical structures and to their local matrices. Evaluation revealed an increase in accuracy as expressed by a reduction of the visible mismatch with respect to the registration of cortical and subcortical brain structures.

Atlases as Topic↗
PubMed1998

The use of a computerized brain atlas to support knowledge-based training in radiology.

Trainers of radiologists face the particular challenges of teaching normal and abnormal appearance for a variety of imaging modalities, providing access to a large appropriately-indexed case library, and teaching a consistent approach to the reporting of cases. The computer has the potential to address these issues, to supplement conventional teaching of radiology by providing case-based tutoring and diagnostic support based on a large library of images of normal and abnormal anatomy, described in a consistent terminology. The paper presents a new approach to computer-based training in radiology that combines a knowledge-based tutor with an on-line medical atlas. It describes two existing computer systems, the MR Tutor and ATLAS, and discusses the medical, computational, epistemic, and pedagogic issues involved in developing a combined Atlas-Tutor. Integrating an atlas with a training system could significantly improve the teaching and support offered, but practical difficulties include the need to merge knowledge representations and to incorporate techniques for registering atlas plates on images that exhibit abnormalities. The paper addresses these problems, and concludes by indicating how the Atlas-Tutor might be employed in practical radiology training.

Atlases as Topic↗
PubMed2003

The Cerefy Neuroradiology Atlas: a Talairach-Tournoux atlas-based tool for analysis of neuroimages available over the internet.

The article introduces an atlas-assisted method and a tool called the Cerefy Neuroradiology Atlas (CNA), available over the Internet for neuroradiology and human brain mapping. The CNA contains an enhanced, extended, and fully segmented and labeled electronic version of the Talairach-Tournoux brain atlas, including parcelated gyri and Brodmann's areas. To our best knowledge, this is the first online, publicly available application with the Talairach-Tournoux atlas. The process of atlas-assisted neuroimage analysis is done in five steps: image data loading, Talairach landmark setting, atlas normalization, image data exploration and analysis, and result saving. Neuroimage analysis is supported by a near-real-time, atlas-to-data warping based on the Talairach transformation. The CNA runs on multiple platforms; is able to process simultaneously multiple anatomical and functional data sets; and provides functions for a rapid atlas-to-data registration, interactive structure labeling and annotating, and mensuration. It is also empowered with several unique features, including interactive atlas warping facilitating fine tuning of atlas-to-data fit, navigation on the triplanar formed by the image data and the atlas, multiple-images-in-one display with interactive atlas-anatomy-function blending, multiple label display, and saving of labeled and annotated image data. The CNA is useful for fast atlas-assisted analysis of neuroimage data sets. It increases accuracy and reduces time in localization analysis of activation regions; facilitates to communicate the information on the interpreted scans from the neuroradiologist to other clinicians and medical students; increases the neuroradiologist's confidence in terms of anatomy and spatial relationships; and serves as a user-friendly, public domain tool for neuroeducation. At present, more than 700 users from five continents have subscribed to the CNA.

Atlases as Topic↗
PubMed2003

Establishing a normative atlas of the human lung: intersubject warping and registration of volumetric CT images.

RATIONALE AND OBJECTIVES: To establish the range of normal values for quantitative CT-based measures of lung structure and function, the authors developed a method for matching pulmonary structures across individuals and creating a normative human lung atlas. MATERIALS AND METHODS: A computerized human lung atlas was synthesized from computed tomographic (CT) images from six subjects by means of three-dimensional image registration. The authors identified a set of reproducible feature points for each CT image and used these points to establish correspondences across subjects, used a landmark- and intensity-based consistent image registration algorithm to register a template image volume from the population to the rest of the pulmonary CT volumes in the population, averaged these transformations, and constructed an atlas by deforming the template with the average transformation. RESULTS: The effectiveness of the authors' method was evaluated and visualized by means of both gray-level and segmented CT images. The method reduced the average landmark registration error from 10.5 mm to 0.4 mm and the average relative volume overlap error from 0.7 to 0.11 for the six data sets studied. CONCLUSION: The method, and the computerized human lung atlas constructed and visualized by the authors with this method, provides a basis for establishing regional ranges of normative values for structural and functional measures of the human lung.

Algorithms↗
PubMed2001

Building 3D sulcal models using local geometry.

This paper presents a series of 3D statistical models of the cortical sulci. They are built from points located automatically over the sulcal fissures, and corresponded automatically using variants on the iterative closest point algorithm. The models are progressively improved by adding in more and more structural and configural information, and the final results are consistent with findings from other anatomical studies. The models can be used to locate and label anatomical features automatically in 3D MR images of the head, for analysis, visualisation, classification, and normalisation.

Atlases as Topic↗
PubMed1975

Specialized reference works and their users. A preliminary study.

An examination of the use of three specialized reference works was made to identify users of the reference tools and the benefits from their use. The feasibility of locating and interviewing users was tested, and an attempt was made to determine the situations in which the works are used. Methods of locating users are described. Users were interviewed to determine the value of each work and alternative sources of information. The works were compared with alternative sources to test their comprehensiveness. Conclusions are: (1) identification of users and their needs is complex, and requires the combination of a number of research methods; (2) the availability and accessibility of alternate information sources varies with both the reference work and the type of user.

Alkaloids↗
PubMed2021

Comparative cellular analysis of motor cortex in human, marmoset and mouse.

The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.

Animals↗
PubMed2025

The new frontier in understanding human and mammalian brain development.

Neurodevelopmental disorders that cause cognitive, behavioural or motor impairments affect around 15% of children and adolescents worldwide1, with diagnoses of profound autism and attention deficit hyperactivity disorder increasing in the USA and contributing to a major economic burden2,3. Yet the origins and mechanisms of these conditions remain poorly understood, limiting progress in therapies. Comprehensive cell atlases of the developing human brain, alongside those of model organisms such as mice and non-human primates, are now providing high-resolution measures of gene expression, cell-type abundance and spatial distribution. In this Perspective, we highlight recent studies that have identified novel developmental cell populations, revealed conserved and divergent patterns of cell genesis, migration and maturation across species, and begun testing hypotheses that link them to processes ranging from transcriptional control of cell fate specification to the emergence of complex behaviours. We present remaining conceptual and technical challenges and provide an outlook on how further studies of human and mammalian brain development can empower a deeper understanding of neurodevelopmental and neuropsychiatric disorders. Future efforts expanding to additional developmental stages, including adolescence, as well as whole-brain, multimodal and cross-species integration, will yield new insights into how development shapes the brain. These atlases promise to serve as essential references for unravelling mechanisms of brain function and disease vulnerability, and for advancing precision medicine.

Humans↗
PubMed2003

Examining geographic patterns of mortality: the atlas of mortality in small areas in Spain (1987-1995).

BACKGROUND: Small-area mortality atlases have been demonstrated to be a useful tool for both showing general geographical patterns in mortality data and identifying specific high-risk locations. In Spain no study has so far systematically examined geographic patterns of small-area mortality for the main causes of death. This paper presents the main features, contents and potential uses of the Spanish Atlas of Mortality in small areas (1987-1995). METHODS: Population data for 2,218 small areas were drawn from the 1991 Census. Aggregated mortality data for 14 specific causes of death for the period 1987-1995 were obtained for each small area. Empirical Bayes-model-based estimates of age-adjusted relative risk were displayed in small-area maps for each cause/gender/age group (0-64 or 65 and over) combination using the same range of values (i.e. septiles) and colour schemes. RESULTS: The 'Spanish Atlas of Mortality' includes multiple choropleth (area-shaded) small-area maps and graphs to answer different questions about the data. The atlas is divided into three main sections. Section 1 includes the methods and comments on the main maps. Section 2 presents a two-page layout for each leading cause of death by gender including 1) a large map with relative risk estimates, 2) a map that indicates high- and low-risk small areas, 3) a graph with median and interquartile range of relative risk estimates for 17 large regions of Spain, and 4) relative-risk maps for two age groups. Section 3 provides specific information on the geographical units of analysis, statistical methods and other supplemental maps. CONCLUSION: The 'Spanish Atlas of Mortality' is a useful tool for examining geographical patterns of mortality risk and identifying specific high-risk areas. Mortality patterns displayed in the atlas may have important implications for research and social/health policy planning purposes.

Adolescent↗