A rapid and cost-effective pipeline for digitization of museum specimens with 3D photogrammetry

"Spine to the future"-A narrative review of anatomy engagement

Anatomy has been integral to medical and health education for centuries, it has also had a significant role in wider public life, as an educational resource, a link to their health, and also as a darker deterrent. Historically, public engagement in anatomy is hallmarked by public dissections of convicted criminals across the globe. Artists, specifically non-medical men, such as Leonardo da Vinci, are reported to have participated in public dissection. Dissection would later rekindle public interest in anatomy as graverobbing led to the reform and regulation of anatomy in many countries. In recent years, there has been growing interest from the public in learning more about their bodies as health and well-being become of paramount importance, particularly following the COVID-19 pandemic. Anatomy sits in a prime position to direct and instigate conversations around health, well-being, and body image. Every human on earth possesses a perfect resource to look at and learn about. Models, art-based anatomical activities, and crafts provide active learning opportunities for the wider public around anatomy. Most recently, apps, games, and extended reality provide novel and insightful learning opportunities for the public relating to the body. Finally, training and resources must also be made available from institutions and professional bodies to anatomists to enable them to deliver engagement in an already congested and educationally heavy schedule. This resurgence of interest in anatomical public engagement sees anatomy re-enter the public spotlight, with more appropriate resources and educational settings to offer engagement with the aim of benefiting the public.

Increasing the impact of vertebrate scientific collections through 3D imaging: The openVertebrate (oVert) Thematic Collections Network

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens.

Recording animal-view videos of the natural world using a novel camera system and software package

Plants, animals, and fungi display a rich tapestry of colors. Animals, in particular, use colors in dynamic displays performed in spatially complex environments. Although current approaches for studying colors are objective and repeatable, they miss the temporal variation of color signals entirely. Here, we introduce hardware and software that provide ecologists and filmmakers the ability to accurately record animal-perceived colors in motion. Specifically, our Python codes transform photos or videos into perceivable units (quantum catches) for animals of known photoreceptor sensitivity. The plans and codes necessary for end-users to capture animal-view videos are all open source and publicly available to encourage continual community development. The camera system and the associated software package will allow ecologists to investigate how animals use colors in dynamic behavioral displays, the ways natural illumination alters perceived colors, and other questions that remained unaddressed until now due to a lack of suitable tools. Finally, it provides scientists and filmmakers with a new, empirically grounded approach for depicting the perceptual worlds of nonhuman animals.

Rapid imaging in the field followed by photogrammetry digitally captures the otherwise lost dimensions of plant specimens

Premise

We recognized the need for a customized imaging protocol for plant specimens at the time of collection for the purpose of three-dimensional (3D) modeling, as well as the lack of a broadly applicable photogrammetry protocol that encompasses the heterogeneity of plant specimen geometries and the challenges introduced by processes such as wilting.

Methods and Results

We developed an equipment list and set of detailed protocols describing how to capture images of plant specimens in the field prior to their deformation (e.g., with pressing) and how to produce a 3D model from the image sets in Agisoft Metashape Professional.

Conclusions

The equipment list and protocols represent a foundation on which additional improvements can be made for specimen geometries outside of the range of the six types considered, and an easy entry into photogrammetry for those who have not previously used it.

A workflow for the creation of photorealistic 3D cadaveric models using photogrammetry

Three-dimensional (3D) representations of anatomical specimens are increasingly used as learning resources. Photogrammetry is a well-established technique that can be used to generate 3D models and has only been recently applied to produce visualisations of cadaveric specimens. This study has developed a semi-standardised photogrammetry workflow to produce photorealistic models of human specimens. Eight specimens, each with unique anatomical characteristics, were successfully digitised into interactive 3D models using the described workflow and the strengths and limitations of the technique are described. Various tissue types were reconstructed with apparent preservation of geometry and texture which visually resembled the original specimen. Using this workflow, an institution could digitise their existing cadaveric resources, facilitating the delivery of novel educational experiences.

New Method for Rapid 3D Reconstruction of Semi-Transparent Underwater Animals and Structures

Morphological features are the primary identifying properties of most animals and key to many comparative physiological studies, yet current techniques for preservation and documentation of soft-bodied marine animals are limited in terms of quality and accessibility. Digital records can complement physical specimens, with a wide array of applications ranging from species description to kinematics modeling, but options are lacking for creating models of soft-bodied semi-transparent underwater animals. We developed a lab-based technique that can live-scan semi-transparent, submerged animals, and objects within seconds. To demonstrate the method, we generated full three-dimensional reconstructions (3DRs) of an object of known dimensions for verification, as well as two live marine animals-a siphonophore and an amphipod-allowing detailed measurements on each. Techniques like these pave the way for faster data capture, integrative and comparative quantitative approaches, and more accessible collections of fragile and rare biological samples.

Temporal stability of the hybrid zone between Calocitta magpie-jays revealed through comparison of museum specimens and iNaturalist photos

Hybrid zones are natural experiments for the study of avian evolution. Hybrid zones can be dynamic, moving as species adjust to new climates and habitats, with unknown implications for species and speciation. There are relatively few studies that have comparable modern and historic sampling to assess change in hybrid zone location and width over time, and those studies have generally found mixed results, with many hybrid zones showing change over time, but others showing stability. The white-throated magpie-jay (Calocitta formosa) and black-throated magpie-jay (Calocitta colliei) occur along the western coast of Mexico and Central America. The two species differ markedly in throat color and tail length, and prior observation suggests a narrow hybrid zone in southern Jalisco where individuals have mixed throat color. This study aims to assess the existence and temporal stability of this putative hybrid zone by comparing throat color between georeferenced historical museum specimens and modern photos from iNaturalist with precise locality information. Our results confirm the existence of a narrow hybrid zone in Jalisco, with modern throat scores gradually increasing from the parental ends of the cline toward the cline center in a sigmoidal curve characteristic of hybrid zones. Our temporal comparison suggests that the hybrid zone has not shifted its position between historical (pre-1973) and modern (post-2005) time periods-a surprising result given the grand scale of habitat change to the western Mexican lowlands during this time. An anomalous pocket of white-throated individuals in the northern range of the black-throated magpie-jay hints at the possibility of prehistorical long-distance introduction. Future genomic data will help disentangle the evolutionary history of these lineages and better characterize how secondary contact is affecting both the DNA and the phenotype of these species.

Studying flowers in 3D using photogrammetry

Flowers are intricate and integrated three-dimensional (3D) structures predominantly studied in 2D due to the difficulty in quantitatively characterising their morphology in 3D. Given the recent development of analytical methods for high-dimensional data, the reconstruction of flower models in three dimensions represents the limiting factor to studying flowers in 3D. We developed a floral photogrammetry protocol to reconstruct 3D models of flowers based on images taken with a digital single-lens reflex camera, a turntable and a portable lightbox. We demonstrate that photogrammetry allows a rapid and accurate reconstruction of 3D models of flowers from 2D images. It can reconstruct all visible parts of flowers and has the advantage of keeping colour information. We illustrated its use by studying the shape and colour of 18 Gesneriaceae species. Photogrammetry is an affordable alternative to micro-computed tomography (micro-CT) that requires minimal investment and equipment, allowing it to be used directly in the field. It has the potential to stimulate research on the evolution and ecology of flowers by providing a simple way to access 3D morphological data from a variety of flower types.

Phototank setup and focus stack imaging method for reptile and amphibian specimens (Amphibia, Reptilia)

Fluid-preserved reptile and amphibian specimens are challenging to photograph with traditional methods due to their complex three-dimensional forms and reflective surfaces when removed from solution. An effective approach to counteract these issues involves combining focus stack photography with the use of a photo immersion tank. Imaging specimens beneath a layer of preservative fluid eliminates glare and risk of specimen desiccation, while focus stacking produces sharp detail through merging multiple photographs taken at successive focal steps to create a composite image with an extended depth of field. This paper describes the wet imaging components and focus stack photography workflow developed while conducting a large-scale digitization project for targeted reptile and amphibian specimens housed in the University of Colorado Museum of Natural History Herpetology Collection. This methodology can be implemented in other collections settings and adapted for use with fluid-preserved specimen types across the Tree of Life to generate high-quality, taxonomically informative images for use in documenting biodiversity, remote examination of fine traits, inclusion in publications, and educational applications.

A high-throughput multispectral imaging system for museum specimens

We present an economical imaging system with integrated hardware and software to capture multispectral images of Lepidoptera with high efficiency. This method facilitates the comparison of colors and shapes among species at fine and broad taxonomic scales and may be adapted for other insect orders with greater three-dimensionality. Our system can image both the dorsal and ventral sides of pinned specimens. Together with our processing pipeline, the descriptive data can be used to systematically investigate multispectral colors and shapes based on full-wing reconstruction and a universally applicable ground plan that objectively quantifies wing patterns for species with different wing shapes (including tails) and venation systems. Basic morphological measurements, such as body length, thorax width, and antenna size are automatically generated. This system can increase exponentially the amount and quality of trait data extracted from museum specimens.

A Novel Technique for Producing Three-Dimensional Data Using Serial Sectioning and Semi-Automatic Image Classification

The three-dimensional characterization of internal features, via metrics such as orientation, porosity, and connectivity, is important to a wide variety of scientific questions. Many spatial and morphological metrics only can be measured accurately through direct in situ three-dimensional observations of large (i.e., big enough to be statistically representative) volumes. For samples that lack material contrast between phases, serial grinding and imaging—which relies solely on color and textural characteristics to differentiate features—is a viable option for extracting such information. Here, we present the Grinding, Imaging, Reconstruction Instrument (GIRI), which automatically serially grinds and photographs centimeter-scale samples at micron resolution. Although the technique is destructive, GIRI produces an archival digital image stack. This digital image stack is run through a supervised machine-learning-based image processing technique that quickly and accurately segments data into predefined classes. These classified data then can be loaded into three-dimensional visualization software for measurement. We share three case studies to illustrate how GIRI can address questions with a significant morphological component for which two-dimensional or small-volume three-dimensional measurements are inadequate. The analyzed metrics include: the morphologies of objects and pores in a granular material, the bulk mineralogy of polyminerallic solids, and measurements of the internal angles and symmetry of crystals.

Color in motion: Generating 3-dimensional multispectral models to study dynamic visual signals in animals

Analyzing color and pattern in the context of motion is a central and ongoing challenge in the quantification of animal coloration. Many animal signals are spatially and temporally variable, but traditional methods fail to capture this dynamism because they use stationary animals in fixed positions. To investigate dynamic visual displays and to understand the evolutionary forces that shape dynamic colorful signals, we require cross-disciplinary methods that combine measurements of color, pattern, 3-dimensional (3D) shape, and motion. Here, we outline a workflow for producing digital 3D models with objective color information from museum specimens with diffuse colors. The workflow combines multispectral imaging with photogrammetry to produce digital 3D models that contain calibrated ultraviolet (UV) and human-visible (VIS) color information and incorporate pattern and 3D shape. These “3D multispectral models” can subsequently be animated to incorporate both signaler and receiver movement and analyzed in silico using a variety of receiver-specific visual models. This approach—which can be flexibly integrated with other tools and methods—represents a key first step toward analyzing visual signals in motion. We describe several timely applications of this workflow and next steps for multispectral 3D photogrammetry and animation techniques.

Photogrammetric reconstruction of 3D carpological collection in high resolution for plants authentication and species discovery

This study provides an accurate and efficient method to reconstruct detailed and high-resolution digital 3D models of carpological materials by photogrammetric method, in which only about 100 to 150 images are required for each model reconstruction. The 3D models reflect the realistic morphology and genuine color of the carpological materials. The 3D models are scaled to represent the true size of the materials even as small as 3 mm in diameter. The interfaces are interactive, in which the 3D models can be rotated in 360° to observe the structures and be zoomed to inspect the macroscopic details. This new platform is beneficial for developing a virtual herbarium of carpological collection which is thus the most important to botanical authentication and education.

3D Visualization Processes for Recreating and Studying Organismal Form

The study of biological form is a vital goal of evolutionary biology and functional morphology. We review an emerging set of methods that allow scientists to create and study accurate 3D models of living organisms and animate those models for biomechanical and fluid dynamic analyses. The methods for creating such models include 3D photogrammetry, laser and CT scanning, and 3D software. New multi-camera devices can be used to create accurate 3D models of living animals in the wild and captivity. New websites and virtual reality/augmented reality devices now enable the visualization and sharing of these data. We provide examples of these approaches for animals ranging from large whales to lizards and show applications for several areas: Natural history collections; body condition/scaling, bioinspired robotics, computational fluids dynamics (CFD), machine learning, and education. We provide two datasets to demonstrate the efficacy of CFD and machine learning approaches and conclude with a prospectus.

Digital 3D Technologies for Humanities Research and Education: An Overview

Digital 3D modelling and visualization technologies have been widely applied to support research in the humanities since the 1980s. Since technological backgrounds, project opportunities, and methodological considerations for application are widely discussed in the literature, one of the next tasks is to validate these techniques within a wider scientific community and establish them in the culture of academic disciplines. This article resulted from a postdoctoral thesis and is intended to provide a comprehensive overview on the use of digital 3D technologies in the humanities with regards to (1) scenarios, user communities, and epistemic challenges; (2) technologies, UX design, and workflows; and (3) framework conditions as legislation, infrastructures, and teaching programs. Although the results are of relevance for 3D modelling in all humanities disciplines, the focus of our studies is on modelling of past architectural and cultural landscape objects via interpretative 3D reconstruction methods.

Morphology of migration: associations between wing shape, bill morphology and migration in kingbirds (Tyrannus)

Morphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviours also interact with diet, such that migratory animals tend to be dietary generalists, whereas sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations that selection favours improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.

Web databases of feather photographs are useful tools for avian morphometry studies

Wing area, wing loading, and aspect ratio are key variables for studies of avian comparative ecology, despite the complexity of measuring wing characteristics in living and museum specimens. The systematic databases of feather photographs available on the Internet may offer an alternative way of obtaining such morphometric data. Here, we evaluate whether measurements of scanned feathers from web photograph databases may offer reliable estimates of avian morphometry.Published data on wing area were obtained for 317 bird species and feather measurements from web photograph databases for 225 of them. A variable termed "lift generation area," a proxy for wing area, was calculated for each species on the basis of the mean length of the five distal secondary feathers and wingspan data from literature. The fit between this proposed variable and data extracted from the literature was examined by correlation, employing linear regression to explore the lack of fit among species."Lift generation area" proved to be highly informative as a proxy for wing area for the study species as a whole (R 2 > .98). Discrepancies observed between species were strongly negatively associated with the size of the original sample used to calculate wing area (p = .001) and, to a lesser extent, with bird size (p = .023), but not with aspect ratio. It was also found that the mean value of the mismatch between "lift generation area" and wing area (13.1%) among the study species as a whole was of similar magnitude to that found between sources of bibliographic wing area data for the 64 species for which two published estimates of this variable were available (15.3%).We conclude that measurements made from feather photograph databases are reliable for use in studies of avian comparative ecology, enabling the inclusion of biomechanical parameters of many more species than featured at present.

Coastal Erosion of Arctic Cultural Heritage in Danger: A Case Study from Svalbard, Norway

Strong cultural heritage management relies on a thorough evaluation of the threats faced by heritage sites, both in the present and in the future. In this study, we analysed the changes in the position of Hiorthhamn shoreline (Svalbard), which is affecting coastal cultural heritage sites, for a period of 93 years (1927–2020). Shoreline changes were mapped by using maps, ortophotos, drone images, terrestrial laser scanning (TLS), and topographic surveys. Also, TLS was used to 3D document the endangered coastal cultural heritage sites. Detailed sedimentological and morphological mapping was made in the field and from the newly acquired drone images in order to understand shoreline-landscape interaction and to depict changes occurring from 2019 to 2020. Short-term (2019–2020) and long-term (1927–2020) shoreline erosion/accretion was made with the help of the Digital Shoreline Analysis System (DSAS) and prompted a subdivision of three sectors, based on change pattern. Compared to a previous long-term analysis (1927–2019), this year’s average erosion rate analysis (expressed by the EPR parameter) for the 93-year period is −0.14 m/yr. This shift in mean development is due to a newly formed spit-bar in Sector 2. Referring strictly to Sector 1, where the protected cultural heritage objects are located, the erosion rate increased from the previous analysis of –0.76 m/yr to −0.77 m/yr. The shoreline forecast analysis highlights that half of the protected cultural heritage objects will likely disappear over the next decade and almost all the cultural heritage objects analysed in this study will disappear in roughly two decades. This shows the great danger the Arctic’s cultural heritage sites is in if no mitigation measures are undertaken by the local authorities.