Constructing the rodent stereotaxic brain atlas: a survey.

The stereotaxic brain atlas is a fundamental reference tool commonly used in the field of neuroscience. Here we provide a brief history of brain atlas development and clarify three key conceptual elements of stereotaxic brain atlasing: brain image, atlas, and stereotaxis. We also refine four technical indices for evaluating the construction of atlases: the quality of staining and labeling, the granularity of delineation, spatial resolution, and the precision of spatial location and orientation. Additionally, we discuss state-of-the-art technologies and their trends in the fields of image acquisition, stereotaxic coordinate construction, image processing, anatomical structure recognition, and publishing: the procedures of brain atlas illustration. We believe that the use of single-cell resolution and micron-level location precision will become a future trend in the study of the stereotaxic brain atlas, which will greatly benefit the development of neuroscience.

Evolution of Human Brain Atlases in Terms of Content, Applications, Functionality, and Availability.

Human brain atlases have been evolving tremendously, propelled recently by brain big projects, and driven by sophisticated imaging techniques, advanced brain mapping methods, vast data, analytical strategies, and powerful computing. We overview here this evolution in four categories: content, applications, functionality, and availability, in contrast to other works limited mostly to content. Four atlas generations are distinguished: early cortical maps, print stereotactic atlases, early digital atlases, and advanced brain atlas platforms, and 5 avenues in electronic atlases spanning the last two generations. Content-wise, new electronic atlases are categorized into eight groups considering their scope, parcellation, modality, plurality, scale, ethnicity, abnormality, and a mixture of them. Atlas content developments in these groups are heading in 23 various directions. Application-wise, we overview atlases in neuroeducation, research, and clinics, including stereotactic and functional neurosurgery, neuroradiology, neurology, and stroke. Functionality-wise, tools and functionalities are addressed for atlas creation, navigation, individualization, enabling operations, and application-specific. Availability is discussed in media and platforms, ranging from mobile solutions to leading-edge supercomputers, with three accessibility levels. The major application-wise shift has been from research to clinical practice, particularly in stereotactic and functional neurosurgery, although clinical applications are still lagging behind the atlas content progress. Atlas functionality also has been relatively neglected until recently, as the management of brain data explosion requires powerful tools. We suggest that the future human brain atlas-related research and development activities shall be founded on and benefit from a standard framework containing the core virtual brain model cum the brain atlas platform general architecture.

A comprehensive atlas of white matter tracts in the chimpanzee.

Chimpanzees (Pan troglodytes) are, along with bonobos, humans' closest living relatives. The advent of diffusion MRI tractography in recent years has allowed a resurgence of comparative neuroanatomical studies in humans and other primate species. Here we offer, in comparative perspective, the first chimpanzee white matter atlas, constructed from in vivo chimpanzee diffusion-weighted scans. Comparative white matter atlases provide a useful tool for identifying neuroanatomical differences and similarities between humans and other primate species. Until now, comprehensive fascicular atlases have been created for humans (Homo sapiens), rhesus macaques (Macaca mulatta), and several other nonhuman primate species, but never in a nonhuman ape. Information on chimpanzee neuroanatomy is essential for understanding the anatomical specializations of white matter organization that are unique to the human lineage.

Spatial and temporal tools for building a human cell atlas.

Improvements in the sensitivity, content, and throughput of microscopy, in the depth and throughput of single-cell sequencing approaches, and in computational and modeling tools for data integration have created a portfolio of methods for building spatiotemporal cell atlases. Challenges in this fast-moving field include optimizing experimental conditions to allow a holistic view of tissues, extending molecular analysis across multiple timescales, and developing new tools for 1) managing large data sets, 2) extracting patterns and correlation from these data, and 3) integrating and visualizing data and derived results in an informative way. The utility of these tools and atlases for the broader scientific community will be accelerated through a commitment to findable, accessible, interoperable, and reusable data and tool sharing principles that can be facilitated through coordination and collaboration between programs working in this space.

A 3D molecular atlas of the chick embryonic heart.

We present a detailed analysis of gene expression in the 2-day (HH12) embryonic chick heart. RNA-seq of 13 micro-dissected regions reveals regionalised expression of 15,570 genes. Of these, 132 were studied by in situ hybridisation and a subset (38 genes) was mapped by Optical Projection Tomography or serial sectioning to build a detailed 3-dimensional atlas of expression. We display this with a novel interactive 3-D viewer and as stacks of sections, revealing the boundaries of expression domains and regions of overlap. Analysis of the expression domains also defines some sub-regions distinct from those normally recognised by anatomical criteria at this stage of development, such as a previously undescribed subdivision of the atria into two orthogonal sets of domains (dorsoventral and left-right). We also include a detailed comparison of expression in the chick with the mouse and other species.

Learning Acetabular Fracture Classification using a Three-Dimensional Interactive Software: A Randomized Controlled Trial.

Acetabular fractures are a real challenge for junior doctors as well as experienced orthopedic surgeons. Correct fracture classification is crucial for appreciating the fracture type, surgical planning, and predicting prognosis. Although three-dimensional (3D) tutorial is believed to improve the understanding of the complex anatomy structure, there have been few applications and randomized controlled trials to confirm it in orthopedics. This study aims to develop a 3D interactive software system for teaching acetabular fracture classification and evaluate its efficacy. Participants were randomly but evenly allocated into either the experimental group (who learned the acetabular fracture classification using a 3D software) or the control group (who used a traditional two-dimensional [2D] tutorial). Both groups were then tasked to classify 10 acetabular fractures and complete a five-point Likert scale on their satisfaction of each learning modality. To calculate significance (P < 0.05), independent t-test was used for normally distributed data whereas Mann-Whitney U test for non-normally distributed data. The experimental group significantly outperformed the control group (t (28) = 2.526, P = 0.017) with identifying correct acetabular fracture classification. Moreover, Likert scale score in the experimental group was also significantly higher than in the control group (Z = 2.477, P = 0.013). This 3D classification software has objectively and subjectively showed an advantage over the traditional 2D tutorial, resulting in an improved classification accuracy and higher Likert scale score. The 3D software has the potential to improve both clinical knowledge as well as identifying correct patient management in orthopedics.

Teaching by stealth: utilising the hidden curriculum through body painting within anatomy education

This study considers the hidden curriculum within anatomy education, with a specific focus on body painting. Body painting is not only utilised within anatomy education for teaching surface anatomy and clinical examination, but also to provide a platform for the development of other skills, primarily through the hidden curriculum. The hidden curriculum is the unplanned curriculum transmitting tacit messages to students on values, attitudes, principles and organisation. This may lend itself to deliver values in line with General Medical Council UK registration requirements of 'safety and quality', 'communication', 'partnership and teamwork', and 'maintaining trust' in the undergraduate medical curriculum. This qualitative study explored faculty perceptions of the use of body painting as a teaching tool. The hidden curriculum appeared spontaneously as a major advantage of utilising painting. Four major themes emerged; trait development, socialisation, tacit learning and script formation. Anatomy education lends itself to an environment in which to study the hidden curriculum. Results from this study demonstrate faculty awareness of, and deliberate use of, the hidden curriculum as a method to 'teach by stealth', and therefore by actively employing the term pushing at the boundaries of the hidden curriculum concept

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Description of 'Ponticular Artery' at the atlas: an anatomical case report with potential clinical relevance

The atlas plays an important role as a characteristic connective bony element between the cervical spine and the occiput. Its details and variations are of special interest to neurosurgeons - e.g., in a far lateral transcondylar approach. We investigated 121 atlases and their variations. During our investigations, we periodically found atlases with a complete arcuate foramen (canal for vertebral artery) and an additional foramen in the bony roof of a complete arcuate foramen. Different structures passing through this additional foramen are described in the literature, but no artery. We found a macroscopically clear verified artery in a 67-year-old male cadaver passing through the foramen in the bony roof of a complete arcuate foramen. Such an artery is of clinical importance to neurosurgeons or musculoskeletal surgeons, but unmentioned in literature until now. A potential name for this artery could be 'ponticular artery'. The discovered artery is most likely a branch to the neck muscles. The knowledge of a possible existence of such an artery is necessary to prevent complications during surgical procedures in the region of the upper cervical spine. Furthermore, the special course of this artery could be the reason for atrophy and imbalance of deep cervical muscles and consequently headaches

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Discrepancies in stereotaxic coordinate publications and improving precision using an animal-specific atlas.

Rodent brain atlases have traditionally been used to identify brain structures in three-dimensional space for a variety of stereotaxic procedures. As neuroscience becomes increasingly sophisticated, higher levels of precision and consistency are needed. Observations of various atlases currently in use across labs reveal numerous coordinate discrepancies. Here we provide examples of inconsistencies by comparing the coordinates of the boundaries of various brain structures across six atlas publications. We conclude that the coordinates determined by any particular atlas should be considered as only a first approximation of the actual target coordinates for the experimental animal for a particular study. Furthermore, the coordinates determined by one research team cannot be assumed to be universally applicable and accurate in other experimental settings. To optimize precision, we describe a simple protocol for the construction of a customized atlas that is specific to the surgical approach and to the species, gender, and age of the animal used in any given study.

Development and Implementation of a Corriedale Ovine Brain Atlas for Use in Atlas-Based Segmentation.

Segmentation is the process of partitioning an image into subdivisions and can be applied to medical images to isolate anatomical or pathological areas for further analysis. This process can be done manually or automated by the use of image processing computer packages. Atlas-based segmentation automates this process by the use of a pre-labelled template and a registration algorithm. We developed an ovine brain atlas that can be used as a model for neurological conditions such as Parkinson's disease and focal epilepsy. 17 female Corriedale ovine brains were imaged in-vivo in a 1.5T (low-resolution) MRI scanner. 13 of the low-resolution images were combined using a template construction algorithm to form a low-resolution template. The template was labelled to form an atlas and tested by comparing manual with atlas-based segmentations against the remaining four low-resolution images. The comparisons were in the form of similarity metrics used in previous segmentation research. Dice Similarity Coefficients were utilised to determine the degree of overlap between eight independent, manual and atlas-based segmentations, with values ranging from 0 (no overlap) to 1 (complete overlap). For 7 of these 8 segmented areas, we achieved a Dice Similarity Coefficient of 0.5-0.8. The amygdala was difficult to segment due to its variable location and similar intensity to surrounding tissues resulting in Dice Coefficients of 0.0-0.2. We developed a low resolution ovine brain atlas with eight clinically relevant areas labelled. This brain atlas performed comparably to prior human atlases described in the literature and to intra-observer error providing an atlas that can be used to guide further research using ovine brains as a model and is hosted online for public access.

Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design.

BACKGROUND: A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable. RESULTS: I first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures. CONCLUSIONS: This collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.

Mapping neuroplastic potential in brain-damaged patients.

It is increasingly acknowledged that the brain is highly plastic. However, the anatomic factors governing the potential for neuroplasticity have hardly been investigated. To bridge this knowledge gap, we generated a probabilistic atlas of functional plasticity derived from both anatomic magnetic resonance imaging results and intraoperative mapping data on 231 patients having undergone surgery for diffuse, low-grade glioma. The atlas includes detailed level of confidence information and is supplemented with a series of comprehensive, connectivity-based cluster analyses. Our results show that cortical plasticity is generally high in the cortex (except in primary unimodal areas and in a small set of neural hubs) and rather low in connective tracts (especially associative and projection tracts). The atlas sheds new light on the topological organization of critical neural systems and may also be useful in predicting the likelihood of recovery (as a function of lesion topology) in various neuropathological conditions-a crucial factor in improving the care of brain-damaged patients.

Uncovered secret of a Vasseur-Tramond wax model.

The technique of anatomical wax modelling reached its heyday in Italy during the 18th century, through a fruitful collaboration between sculptors and anatomists. It soon spread to other countries, and prestigious schools were created in England, France, Spain and Austria. Paris subsequently replaced Italy as the major centre of manufacture, and anatomical waxes were created there from the mid-19th century in workshops such as that of Vasseur-Tramond. This workshop began to sell waxes to European Faculties of Medicine and Schools of Surgery around 1880. Little is known of the technique employed in the creation of such artefacts as this was deemed a professional secret. To gain some insight into the methods of construction, we have studied a Vasseur-Tramond wax model in the Valladolid University Anatomy Museum, Spain, by means of multi-slice computerised tomography and X-ray analysis by means of environmental scanning electron microscopy. Scanning electron microscopy was used to examine the hair. These results have revealed some of the methods used to make these anatomical models and the materials employed.

Relationship between pedographic analysis and the Manchester scale in hallux valgus.

OBJECTIVE: The aim of this study was to evaluate the correlation between the Manchester scale and foot pressure distribution in patients with hallux valgus deformity. METHODS: The study included 152 feet of 87 patients with hallux valgus and a control group of 391 feet of 241 individuals without hallux valgus deformity. The severity of hallux valgus was determined using the Manchester scale grading system. Plantar loading patterns in 10 foot areas were determined for all participants. RESULTS: According to the Manchester scale, 72% of the participants had no, 12.9% mild, 10.7% moderate and 4.4% severe deformity. The Manchester scale grade was highly correlated with both hallux valgus angle and first intermetatarsal angle (p=0.00). Significant differences between the four grades were present for mean pressure under the hallux and the first and second metatarsal heads only (p=0.00). The load distribution under these areas was higher as the hallux valgus progressed from mild to more severe. In all groups, the highest pressure was observed under the second metatarsal head. CONCLUSION: The Manchester scale was strongly associated with both the hallux valgus angle and the first intermetatarsal angle. The progression from mild to moderate and severe deformation is associated with peak pressure raise at the hallux, first and second metatarsal heads. The Manchester scale appears to be a useful tool to provide information for the degree of deformity and the pressure under painful foot areas.

Derivation of high-resolution MRI atlases of the human cerebellum at 3T and segmentation using multiple automatically generated templates.

The cerebellum has classically been linked to motor learning and coordination. However, there is renewed interest in the role of the cerebellum in non-motor functions such as cognition and in the context of different neuropsychiatric disorders. The contribution of neuroimaging studies to advancing understanding of cerebellar structure and function has been limited, partly due to the cerebellum being understudied as a result of contrast and resolution limitations of standard structural magnetic resonance images (MRI). These limitations inhibit proper visualization of the highly compact and detailed cerebellar foliations. In addition, there is a lack of robust algorithms that automatically and reliably identify the cerebellum and its subregions, further complicating the design of large-scale studies of the cerebellum. As such, automated segmentation of the cerebellar lobules would allow detailed population studies of the cerebellum and its subregions. In this manuscript, we describe a novel set of high-resolution in vivo atlases of the cerebellum developed by pairing MR imaging with a carefully validated manual segmentation protocol. Using these cerebellar atlases as inputs, we validate a novel automated segmentation algorithm that takes advantage of the neuroanatomical variability that exists in a given population under study in order to automatically identify the cerebellum, and its lobules. Our automatic segmentation results demonstrate good accuracy in the identification of all lobules (mean Kappa [κ]=0.731; range 0.40-0.89), and the entire cerebellum (mean κ=0.925; range 0.90-0.94) when compared to "gold-standard" manual segmentations. These results compare favorably in comparison to other publically available methods for automatic segmentation of the cerebellum. The completed cerebellar atlases are available freely online (http://imaging-genetics.camh.ca/cerebellum) and can be customized to the unique neuroanatomy of different subjects using the proposed segmentation pipeline (https://github.com/pipitone/MAGeTbrain).

A powerful way of teaching anatomy.

I read the article entitled "A plea for the use of drawing in human anatomy teaching", by Clavert et al. with great interest. I was glad to read that, in France, anatomy is initially taught by building each structure or region on a blackboard with colored chalk. I find this method quite efficient for this purpose. I believe that drawing is a powerful way of teaching anatomy and therefore the blackboard deserves its rightful place beside other 'high-tech' media. I agree with the authors that the blackboard and the chalk constitute wonderful and powerful educational media, and that appropriate simplification and transposing (of anatomical information) in daily practice are necessary for a sufficient educational result. Among other 'modern' media, movies of surgical procedures could easily attract the students' attention.