Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

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Open data and digital morphology

Phenotypic integration and modularity are ubiquitous features of complex organisms, describing the magnitude and pattern of relationships among biological traits. A key prediction is that these relationships, reflecting genetic, developmental, and functional interactions, shape evolutionary processes by governing evolvability and constraint. Over the last 60 years, a rich literature of research has quantified patterns of integration and modularity across a variety of clades and systems. Only recently has it become possible to contextualize these findings in a phylogenetic framework to understand how trait integration interacts with evolutionary tempo and mode. Here, we review the state of macroevolutionary studies of integration and modularity, synthesizing empirical and theoretical work into a conceptual framework for predicting the effects of integration on evolutionary rate and disparity: a fly in a tube. While magnitude of integration is expected to influence the potential for phenotypic variation to be produced and maintained, thus defining the shape and size of a tube in morphospace, evolutionary rate, or the speed at which a fly moves around the tube, is not necessarily controlled by trait interactions. Finally, we demonstrate this reduced disparity relative to the Brownian expectation for a given rate of evolution with an empirical example: the avian cranium.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/evo.13608

A fly in a tube: Macroevolutionary expectations for integrated phenotypes.

Nanoscale Metal‐Organic Frameworks: Synthesis, Biocompatibility, Imaging Applications, and Thermal and Dynamic Therapy of Tumors

Cardiac arrhythmias and conduction disturbances are accompanied by structural remodelling of the specialised cardiomyocytes known collectively as the cardiac conduction system. Here, using contrast enhanced micro-computed tomography, we present, in attitudinally appropriate fashion, the first 3-dimensional representations of the cardiac conduction system within the intact human heart. We show that cardiomyocyte orientation can be extracted from these datasets at spatial resolutions approaching the single cell. These data show that commonly accepted anatomical representations are oversimplified. We have incorporated the high-resolution anatomical data into mathematical simulations of cardiac electrical depolarisation. The data presented should have multidisciplinary impact. Since the rate of depolarisation is dictated by cardiac microstructure, and the precise orientation of the cardiomyocytes, our data should improve the fidelity of mathematical models. By showing the precise 3-dimensional relationships between the cardiac conduction system and surrounding structures, we provide new insights relevant to valvar replacement surgery and ablation therapies. We also offer a practical method for investigation of remodelling in disease, and thus, virtual pathology and archiving. Such data presented as 3D images or 3D printed models, will inform discussions between medical teams and their patients, and aid the education of medical and surgical trainees.

High resolution 3-Dimensional imaging of the human cardiac conduction system from microanatomy to mathematical modeling

Recent developments within micro-computed tomography (μCT) imaging have combined to extend our capacity to image tissue in three (3D) and four (4D) dimensions at micron and sub-micron spatial resolutions, opening the way for virtual histology, live cell imaging, subcellular imaging and correlative microscopy. Pivotal to this has been the development of methods to extend the contrast achievable for soft tissue. Herein, we review the new capabilities within the field of life sciences imaging, and consider how future developments in this field could further benefit the life sciences community.

/pdf/x-ray-computed-tomography-in-life-sciences-3su02v52ju.pdf

X-ray computed tomography in life sciences.

Morphologists have historically had to rely on destructive procedures to visualize the three-dimensional (3-D) anatomy of animals. More recently, however, non-destructive techniques have come to the forefront. These include X-ray computed tomography (CT), which has been used most commonly to examine the mineralized, hard-tissue anatomy of living and fossil metazoans. One relatively new and potentially transformative aspect of current CT-based research is the use of chemical agents to render visible, and differentiate between, soft-tissue structures in X-ray images. Specifically, iodine has emerged as one of the most widely used of these contrast agents among animal morphologists due to its ease of handling, cost effectiveness, and differential affinities for major types of soft tissues. The rapid adoption of iodine-based contrast agents has resulted in a proliferation of distinct specimen preparations and scanning parameter choices, as well as an increasing variety of imaging hardware and software preferences. Here we provide a critical review of the recent contributions to iodine-based, contrast-enhanced CT research to enable researchers just beginning to employ contrast enhancement to make sense of this complex new landscape of methodologies. We provide a detailed summary of recent case studies, assess factors that govern success at each step of the specimen storage, preparation, and imaging processes, and make recommendations for standardizing both techniques and reporting practices. Finally, we discuss potential cutting-edge applications of diffusible iodine-based contrast-enhanced computed tomography (diceCT) and the issues that must still be overcome to facilitate the broader adoption of diceCT going forward.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/joa.12449

Diffusible iodine‐based contrast‐enhanced computed tomography (diceCT): an emerging tool for rapid, high‐resolution, 3‐D imaging of metazoan soft tissues

Abstract: A 20-year-old male Moluccan eclectus (Eclectus roratus) was presented with a history of falling off the perch, ataxia, unilateral blindness, hyporexia, and progressive lethargy. The eclectus was found to have a leukocytosis (52 × 103 cells/µL), characterized by an absolute and relative heterophilia (42.6 × 103 cells/µL and 82%, respectively), relative lymphopenia (18%), elevated bile acids (88 µmol/L), and elevated triglycerides (236 mg/dL). Radiographic images revealed a mass effect within the caudal coelom. After 13 days of outpatient supportive care, the patient was rechecked and had normalized bile acids (<35 µmol/L), static triglycerides (232 mg/ dL), and hyperuricemia (18.6 mg/dL). Computed tomography was performed antemortem with and without iodinated contrast agent, 4 mL/kg IV over 2 minutes, and a mass was found associated with the left kidney. Due to worsening neurologic signs and involvement with surrounding structures, the owner elected euthanasia. Before the postmortem examination, a postmortem intravascular contrast agent was used to provide a more thorough visualization of internal anatomical structures, including left renal vasculature disruption, mass vasculature, caudal coelomic organ displacement, and increased irregular optic chiasm radiodensity. Postmortem, a 4 × 4.1 × 5.1-cm white to tan mass was identified. Histopathology confirmed a seminoma with metastasis to the kidneys and optic chiasm. Seminomas have been described in avian species; however, seminoma metastasis in an eclectus parrot confirmed by histopathology has not been reported, and optic chiasm metastasis of a seminoma has not been described in any avian species. This report describes postmortem computed tomographic angiography of metastatic seminoma in a Moluccan eclectus with metastasis to the optic chiasm.

Diagnosis of Seminoma With Metastasis to the Brain and Kidneys in a Moluccan Eclectus (Eclectus roratus) Using Advanced Contrast Based Imaging

Veterinary students and practicing technicians will find this book to be an important bench manual as well as an educated tool to have on their desk. Also included in the package is a free online resource for testing and additional information. 

Laboratory Manual for Clinical Veterinary Technology

Innovations in three‐dimensional (3D) imaging and segmentation have facilitated unprecedented levels of anatomical investigation into the detailed structures of the respiratory system that are often difficult to study in situ. Recent hypotheses of homology between crocodilians and birds have facilitated quantitative comparative analyses of bronchial trees and in situ models reveal new complexities in the relationship between the respiratory and skeletal systems. Here we quantitatively compare the bronchial trees of two crocodilians, the American alligator (Alligator mississippiensis) and Cuvier’s dwarf caiman (Paleosuchus palpebrosus) with select birds, including the ostrich (Struthio camelus), the African gray parrot (Psittacus erithacus), and the red‐tailed hawk (Buteo jamaicensis). Notably, the relative distances from the carina to the secondary bronchi measured are conserved, indicating a possible ancestral or constrained trait. With respect to interspecific avian comparisons, we found grossly observable variation within a single taxon in air sac morphology (e.g., P. erithacus), as well as substantial differences between the individual taxa via segmented surface models – particularly in the expansions of the interclavicular sacs, the extent of the diverticula, and the size of the abdominal sacs. Furthermore, we found that specific sac contribution to postcranial pneumatization varies substantially across our dataset. Individual specimens imaged for this study also revealed multiple pathologies, including scoliosis, foreign objects inside the animals, and broken bones, which have been incorporated into the anatomical models for clinical surgical atlases that are under development. While these data are preliminary, they provide a framework for larger scale comparisons and hypotheses of the ancestral archosaurian pulmonary system.

Intra‐ and interspecific structural variation in the archosaur lung: insights from 3D imaging and segmentation

The avian respiratory system is composed of a unidirectionally ventilated, volume‐constant gas‐exchanging lung, and a series of compliant, flexible air sacs. Diverticula from the lungs and air sacs invade adjacent bone and create air‐filled cavities within the skeleton through the process of pneumatization. While previous studies have addressed the presence or absence of pneumatic bones in multiple species, the pattern of pneumatization has been vaguely generalized with respect to which lung elements are responsible for pneumatizing different skeleton regions. Here, we aim to address which components of the avian respiratory system are pneumatizing each component of the postcranial skeleton and how the patterns vary between different taxa. Computed tomography (CT) and microCT data are used to visualize the pneumatized bones and to segment 3D digital surface models of the skeletal and respiratory systems. Specimens used in this study include the African grey parrot (Psittacus erithacus), ostrich (Struthio camelus), red‐tailed hawk. (Buteo jamaicensis), and tundra swan (Cygnus columbianus). We found substantial differences in the pneumatization patterns between the birds. In all taxa examined, there is an extensive supramedullary diverticulum that travels through the vertebral canal which directly pneumatizes each vertebra in the parrots but does not contribute to any pneumatization in the swan or hawk. The sacral, pelvic, and femoral elements are pneumatized solely by pelvic diverticula in the ostrich, but predominantly by the abdominal sacs in parrots. These data indicate that the pneumatization patterns in birds are highly variable and warrant further study.

M. Scott Echols

Papers

Diffusible iodine‐based contrast‐enhanced computed tomography (diceCT): an emerging tool for rapid, high‐resolution, 3‐D imaging of metazoan soft tissues

Diagnosis of Seminoma With Metastasis to the Brain and Kidneys in a Moluccan Eclectus (Eclectus roratus) Using Advanced Contrast Based Imaging

Laboratory Manual for Clinical Veterinary Technology

Intra‐ and interspecific structural variation in the archosaur lung: insights from 3D imaging and segmentation

Interspecific variation in avian postcranial pneumaticity: A pilot study