Automated morphological phenotyping using learned shape descriptors and functional maps: A novel approach to geometric morphometrics.

The methods of geometric morphometrics are commonly used to quantify morphology in a broad range of biological sciences. The application of these methods to large datasets is constrained by manual landmark placement limiting the number of landmarks and introducing observer bias. To move the field forward, we need to automate morphological phenotyping in ways that capture comprehensive representations of morphological variation with minimal observer bias. Here, we present Morphological Variation Quantifier (morphVQ), a shape analysis pipeline for quantifying, analyzing, and exploring shape variation in the functional domain. morphVQ uses descriptor learning to estimate the functional correspondence between whole triangular meshes in lieu of landmark configurations. With functional maps between pairs of specimens in a dataset we can analyze and explore shape variation. morphVQ uses Consistent ZoomOut refinement to improve these functional maps and produce a new representation of shape variation, area-based and conformal (angular) latent shape space differences (LSSDs). We compare this new representation of shape variation to shape variables obtained via manual digitization and auto3DGM, an existing approach to automated morphological phenotyping. We find that LSSDs compare favorably to modern 3DGM and auto3DGM while being more computationally efficient. By characterizing whole surfaces, our method incorporates more morphological detail in shape analysis. We can classify known biological groupings, such as Genus affiliation with comparable accuracy. The shape spaces produced by our method are similar to those produced by modern 3DGM and to auto3DGM, and distinctiveness functions derived from LSSDs show us how shape variation differs between groups. morphVQ can capture shape in an automated fashion while avoiding the limitations of manually digitized landmarks, and thus represents a novel and computationally efficient addition to the geometric morphometrics toolkit.

Communication, collaboration and contagion: "Virtualisation" of anatomy during COVID-19.

COVID-19 has generated a global need for technologies that enable communication, collaboration, education and scientific discourse whilst maintaining physical distance. University closures due to COVID-19 and physical distancing measures disrupt academic activities that previously occurred face-to-face. Restrictions placed on universities due to COVID-19 have precluded most conventional forms of education, assessment, research and scientific discourse. Anatomists now require valid, robust and easy-to-use communication tools to facilitate remote teaching, learning and research. Recent advances in communication, video conferencing and digital technologies may facilitate continuity of teaching and research activities. Examples include highly-interactive video conferencing technology, collaborative tools, social media and networking platforms. In this narrative review, we examine the utility of these technologies in supporting effective communication and professional activities of anatomists during COVID-19 and after.

Virtual Anatomy Museum: Facilitating Public Engagement Through an Interactive Application.

Digitisation has become a common practice in the preservation of museum collections. Recent development of photogrammetry techniques allows for more accessible acquisition of three-dimensional (3D) models that serve as accurate representations of their originals. One of the potential applications of this is presenting digital collections as virtual museums to engage the public. Medical museums, particularly, would benefit from digitisation of their collections as many of them are closed to the public.The aim of this project was to design and create an interactive virtual museum which would represent the Anatomy Museum at the University of Glasgow with key specimens digitised using photogrammetry techniques. Members of the general public (25 participants) were asked to evaluate the usability and effectiveness of the interactive application by completing questionnaires.A process to digitise anatomical specimens using photogrammetry and convert them into game-ready 3D models was developed. The results demonstrated successful generation of 3D models of specimens preserved using different techniques, including specimens preserved in fluid and glass jars. User tests and evaluation of the application by members of the general public were positive, with participants agreeing that they would now consider visiting the real museum after using the virtual version.

Applying Geometric Morphometrics to Digital Reconstruction and Anatomical Investigation.

Virtual imaging, image manipulation and morphometric methods are increasingly used in medicine and the natural sciences. Virtual imaging hardware and image manipulation software allows us to readily visualise, explore, alter, repair and study digital objects. This suite of equipment and tools combined with statistical tools for the study of form variation and covariation using Procrustes based analyses of landmark coordinates, geometric morphometrics, makes possible a wide range of studies of human variation pertinent to biomedicine. These tools for imaging, quantifying and analysing form have already led to new insights into organismal growth, development and evolution and offer exciting prospects in future biomedical applications. This chapter presents a review of commonly used methods for digital acquisition, extraction and landmarking of anatomical structures and of the common geometric morphometric statistical methods applied to investigate them: generalised Procrustes analysis to derive shape variables, principal component analysis to examine patterns of variation, multivariate regression to examine how form is influenced by meaningful factors and partial least squares analysis to examine associations among structures or between these and other interesting variables. An example study of human facial and maxillary sinus ontogeny illustrates these approaches.

Seeing with Sound: How Ultrasound Is Changing the Way We Look at Anatomy.

Ultrasound uses high frequency sound waves and their rebounding echoes to capture live images of the structures beneath the skin. Thanks to recent technological advances, contemporary ultrasound machines offer excellent image resolution packaged in smaller, highly portable devices, which has allowed ultrasound to expand into new areas, both within the hospital as well as across non-traditional settings. Ultrasound is an incredibly powerful visualization tool in medicine, allowing physicians to safely see and interrogate the most relevant parts of their patient's internal anatomy instantly. Point-of-care ultrasound, a focused ultrasound evaluation performed at the patient's bedside, is now common across medical specialties, encompassing a vast array of diagnostic, procedural and screening applications. The impressive expansion of point-of-care ultrasound has resulted in an increased demand for ultrasound training earlier during medical school. As a non-invasive and non-destructive way to see inside the living body, ultrasound is an ideal tool to teach anatomy. It allows both medical and non-medical students the ability to improve their understanding and retention of anatomical form and function. The widespread and still expanding use of ultrasound in healthcare today, as well as its adoption into the anatomy classroom, is a testament to the power of ultrasound for achieving real-time visualization of the hidden aspects of our bodies.

Towards Advanced Interactive Visualization for Virtual Atlases.

An atlas is generally defined as a bound collection of tables, charts or illustrations describing a phenomenon. In an anatomical atlas for example, a collection of representative illustrations and text describes anatomy for the purpose of communicating anatomical knowledge. The atlas serves as reference frame for comparing and integrating data from different sources by spatially or semantically relating collections of drawings, imaging data, and/or text. In the field of medical image processing, atlas information is often constructed from a collection of regions of interest, which are based on medical images that are annotated by domain experts. Such an atlas may be employed, for example, for automatic segmentation of medical imaging data. The combination of interactive visualization techniques with atlas information opens up new possibilities for content creation, curation, and navigation in virtual atlases. With interactive visualization of atlas information, students are able to inspect and explore anatomical atlases in ways that were not possible with the traditional method of presenting anatomical atlases in book format, such as viewing the illustrations from other viewpoints. With advanced interaction techniques, it becomes possible to query the data that forms the basis for the atlas, thus empowering researchers to access a wealth of information in new ways. So far, atlas-based visualization has been employed mainly for medical education, as well as biological research. In this survey, we provide an overview of current digital biomedical atlas tasks and applications and summarize relevant visualization techniques. We discuss recent approaches for providing next-generation visual interfaces to navigate atlas data that go beyond common text-based search and hierarchical lists. Finally, we reflect on open challenges and opportunities for the next steps in interactive atlas visualization.

Three-Dimensional Visualisation of Skeletal Cavities.

Bones contain spaces within them. The extraction and the analysis of those cavities are crucial in the study of bone tissue function and can inform about pathologies or past traumatic events. The use of medical imaging techniques allows a non-invasive visualisation of skeletal cavities opening a new frontier in medical inspection and diagnosis. Here, we report the application of a new mesh-based approach for the isolation of skeletal cavities of different size and geometrical structure. We apply a mesh-based approach to extract (i) the main virtual cavities inside the human skull, (ii) a complete human endocast, (iii) the inner vasculature of the malleus bone and (iv) the medullary of a human femur. The detailed description of the mesh-based isolation method and its pioneristic application to four different case-studies show the potential of this approach in medical visualisation.

Statistical Shape Models: Understanding and Mastering Variation in Anatomy.

In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression.Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated.We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) Statistical Shape Models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods or machine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring.

Anatomy Visualizations Using Stereopsis: Current Methodologies in Developing Stereoscopic Virtual Models in Anatomical Education.

Technology for developing three-dimensional (3D) virtual models in anatomical sciences education has seen a great improvement in recent years. Various data used for creating stereoscopic virtual models have also been constantly improving. This paper focuses specifically on the methodologies of creating stereoscopic virtual models and the techniques and materials used in developing stereoscopic virtual models from both our previous studies and other published literature. The presentation and visualization of stereoscopic models are highlighted, and the benefits and limitations of stereoscopic models are discussed. The practice of making 3D measurements on the lengths, angles, and volumes of models can potentially be used to help predict typical measurement parameters of anatomical structures and for the placement of surgical instruments. Once stereoscopic virtual models have been constructed, their visualization and presentation can be implemented in anatomy education and clinical surgical trainings.

Reporting sex or gender in anatomical research: Which is appropriate?

Sex- and gender-based differences need to be considered in evidence-based medical research as there are anatomical and physiological differences between males and females. Females are underrepresented in studies, with results from males often generalized to both sexes. The Sex and Gender Equity in Research (SAGER) guidelines were published in 2016 to address sex- and gender-bias in research. Correct understanding and appropriate use of the terms "sex" and "gender" are essential. These terms are discussed in an anatomical context and recommendations are made as to how the SAGER guidelines can guide the reporting of anatomical studies to minimize the risk of reporting bias. Clin. Anat. 32:697-698, 2019. © 2019 Wiley Periodicals, Inc.

Feedback on the usefulness of an illustrated guidebook in an anatomical dissection course.

PURPOSE: Dissection provides direct experience in anatomy, which constitutes an essential discipline for medical students. For this purpose, we created a dissection guide for students in the 2nd-year of medical studies at the Grenoble University School of Medicine. The objective was to evaluate this tool of reverse pedagogy in terms of student satisfaction and educational interest. METHODS: Every 2nd-year student takes four sessions of limb dissection. To assist this dissection course, we developed a photographic guide launched in 2013. It includes an introduction presenting a methodology for dissection, followed by detailed protocols for each dissection area. Each step is illustrated with captioned photographs associated with a concise explanatory text. A questionnaire was then sent to 242 students to assess the impact of this tool and their overall satisfaction. RESULTS: Overall student satisfaction with this guidebook was rated 8.1 out of 10 with a 93.2% with significant improvement (p = 0.0137) and 78.7% of them declaring they had a better understanding of anatomy and mastery of the dissection techniques, respectively. In addition, students assessed the usefulness of the dissection guide at 3.6 out of 4 with the relevance of the content and presentation judged at 3.4 out of 4. Finally, the exam scores increased significantly with use of the guidebook (p < 0.0001). CONCLUSIONS: Students deemed the organization of this anatomy tutorial as highly satisfactory, and using the guidebook as a reference in dissection sessions allowed students to prepare for the dissection and improve their knowledge of anatomy, as demonstrated by improved exam scores.

A concise survey on 3D modeling in the science of anatomy.

This report provides a concise overview of the rendering and utilization of three-dimensional models in the field of anatomy. Anatomical three-dimensional virtual models are widely used for educational purposes, preoperative planning, and surgical simulations because they simply allow for interactive three-dimensional navigation across the human organs or entire body. Virtual three-dimensional models have been recently fabricated as accurate replicas of the anatomical structures thanks to advances in rapid prototyping technology.

Adoption of azygos, hemiazygos, and dartos.

Exceptions to the anatomical nomenclature rule that names must be in proper Latin include a few terms that contain borrowed Greek adjectives that are not declined like Latin words. Adoption of these adjectives into Latin would change about a half-dozen terms, e.g., vena azyga, vena hemiazyga, and fascia darta. The anatomical nomenclature rules apply only to the Latin terms, so there is no requirement to alter the way azygos, hemiazygos, and dartos are used in equivalent terms in other languages. Clin. Anat. 30:450-451, 2017. © 2017 Wiley Periodicals, Inc.

Size, shape, and form: concepts of allometry in geometric morphometrics.

Allometry refers to the size-related changes of morphological traits and remains an essential concept for the study of evolution and development. This review is the first systematic comparison of allometric methods in the context of geometric morphometrics that considers the structure of morphological spaces and their implications for characterizing allometry and performing size correction. The distinction of two main schools of thought is useful for understanding the differences and relationships between alternative methods for studying allometry. The Gould-Mosimann school defines allometry as the covariation of shape with size. This concept of allometry is implemented in geometric morphometrics through the multivariate regression of shape variables on a measure of size. In the Huxley-Jolicoeur school, allometry is the covariation among morphological features that all contain size information. In this framework, allometric trajectories are characterized by the first principal component, which is a line of best fit to the data points. In geometric morphometrics, this concept is implemented in analyses using either Procrustes form space or conformation space (the latter also known as size-and-shape space). Whereas these spaces differ substantially in their global structure, there are also close connections in their localized geometry. For the model of small isotropic variation of landmark positions, they are equivalent up to scaling. The methods differ in their emphasis and thus provide investigators with flexible tools to address specific questions concerning evolution and development, but all frameworks are logically compatible with each other and therefore unlikely to yield contradictory results.

Measurement error in geometric morphometrics.

Geometric morphometrics-a set of methods for the statistical analysis of shape once saluted as a revolutionary advancement in the analysis of morphology -is now mature and routinely used in ecology and evolution. However, a factor often disregarded in empirical studies is the presence and the extent of measurement error. This is potentially a very serious issue because random measurement error can inflate the amount of variance and, since many statistical analyses are based on the amount of "explained" relative to "residual" variance, can result in loss of statistical power. On the other hand, systematic bias can affect statistical analyses by biasing the results (i.e. variation due to bias is incorporated in the analysis and treated as biologically-meaningful variation). Here, I briefly review common sources of error in geometric morphometrics. I then review the most commonly used methods to measure and account for both random and non-random measurement error, providing a worked example using a real dataset.

The development of anatomy: from macroscopic body dissections to stem cell-derived organoids.

Anatomy as a descriptive topic of research and instruction in medicine has been increasingly influenced by discoveries in molecular cell and developmental biology and most recently the advent of human induced pluripotent stem cells and organoids. We summarize here how anatomy has been influenced by developmental and stem cell biologists, and how in vitro modelling of the three-dimensional body environment is emerging to understand structure and function of cells during differentiation processes in development and disease.

Hamiltonian Systems and Optimal Control in Computational Anatomy: 100 Years Since D'Arcy Thompson.

The Computational Anatomy project is the morphome-scale study of shape and form, which we model as an orbit under diffeomorphic group action. Metric comparison calculates the geodesic length of the diffeomorphic flow connecting one form to another. Geodesic connection provides a positioning system for coordinatizing the forms and positioning their associated functional information. This article reviews progress since the Euler-Lagrange characterization of the geodesics a decade ago. Geodesic positioning is posed as a series of problems in Hamiltonian control, which emphasize the key reduction from the Eulerian momentum with dimension of the flow of the group, to the parametric coordinates appropriate to the dimension of the submanifolds being positioned. The Hamiltonian viewpoint provides important extensions of the core setting to new, object-informed positioning systems. Several submanifold mapping problems are discussed as they apply to metamorphosis, multiple shape spaces, and longitudinal time series studies of growth and atrophy via shape splines.

A comparative study of vascular injection fluids in fresh-frozen and embalmed human cadaver forearms.

Over the years, various vascular injection products have been developed to facilitate anatomical dissections. This study aimed to compare the most commonly used vascular injection products in fresh-frozen and formalin-embalmed cadaver specimens. An overview of the properties, advantages and limitations of each substance was given, and a comparison of vascular infusion procedures in both preservation methods was made. A literature search was performed in order to identify the most commonly used vascular injection products. Acrylic paint, latex, gelatin, silicone, Araldite F and Batson's No. 17 were selected for the study. One fresh-frozen and one embalmed cadaver forearm were infused with each injection product according to a uniform protocol. The curing time, skin- and subcutaneous tissue penetration, degree of filling of the arterial tree, extravasations, consistency of the injected vessels during dissection, and the costs of each injection fluid were noted. There was a large variation between the injection fluids in processing- and curing time, colour intensity, flexibility, fragility, elasticity, strength, toxicity and costs. All fluids were suitable for infusion. The penetration of injection fluid into the skin and subcutaneous tissue was significantly better in fresh-frozen specimens (P = 0.002 and P = 0.009, respectively), with significantly smaller branches casted (P = 0.004). Vascular infusion of fresh-frozen cadaver specimens results in a significantly better filled coloured arterial tree, enabling more detail to be achieved and smaller branches casted. The biomechanical properties of fresh-frozen soft tissues are less affected compared with formalin fixation. All the injection fluids studied are suitable for vascular infusion, but their different properties ensure that certain products and procedures are more suitable for specific study purposes.