Micro-computed tomography: Introducing new dimensions to taxonomy

A Cybertaxonomic Revision of the "Crocidura pergrisea" Species Complex with a Special Focus on Endemic Rocky Shrews: Crocidura armenica and Crocidura arispa (Soricidae)

The extraction of museum DNA from a unique collection of samples of the "Crocidura pergrisea" species complex, which comprises local endemics of Central and West Asia, allowed us to determine their inter- and intragroup relationships. The first step of this study was the re-evaluation of heavily damaged type specimens of C. armenica via a microcomputed-tomography-based cybertaxonomic approach (CTtax), which enabled a precise description of the species' morphology; three-dimensional models of the cybertypes were made available through the MorphoBank Repository. We developed the "AProMaDesU" pipeline on the basis of five requirements for micro-CT-based cyber-datasets in relation to mammalian collections. Our second step was a combination of several meticulous approaches to morphological investigation against a background of a cytb-based phylogeny, which helped us to make a taxonomic decision about the status of species of the "pergrisea" group, e.g., C. arispa, C. armenica, and C. serezkyensis, when the morphological results were partly incongruent with the molecular phylogeny. Nevertheless, under two assumptions, our findings preserved a separate species-level status of C. serezkyensis and C. arispa. In addition, we restored the species-level status of C. armenica. This taxonomic decision is based on our morphospace analysis, which revealed unique craniomandibular shape transformations within the rocky shrews that helped them with the transition to a new area of morphospace/trophic niches and consequently separated them from the other analyzed Crocidura groups.

Volume X-Ray Micro-Computed Tomography Analysis of the Early Cephalized Central Nervous System in a Marine Flatworm, Stylochoplana pusilla

Platyhelminthes are a phylum of simple bilaterian invertebrates with prototypic body systems. Compared with non-bilaterians such as cnidarians, the bilaterians are likely to exhibit integrated free-moving behaviors, which require a concentrated nervous system "brain" rather than the distributed nervous system of radiatans. Marine flatworms have an early cephalized 'central' nervous system compared not only with non-bilaterians but also with parasitic flatworms or freshwater planarians. In this study, we used the marine flatworm Stylochoplana pusilla as an excellent model organism in Platyhelminthes because of the early cephalized central nervous system. Here, we investigated the three-dimensional structures of the flatworm central nervous system by the use of X-ray micro-computed tomography (micro-CT) in a synchrotron radiation facility. We found that the obtained tomographic images were sufficient to discriminate some characteristic structures of the nervous system, including nerve cords around the cephalic ganglion, mushroom body-like structures, and putative optic nerves forming an optic commissure-like structure. Through the micro-CT imaging, we could obtain undistorted serial section images, permitting us to visualize precise spatial relationships of neuronal subpopulations and nerve tracts. 3-D micro-CT is very effective in the volume analysis of the nervous system at the cellular level; the methodology is straightforward and could be applied to many other non-model organisms.

An in situ digital synthesis strategy for the discovery and description of ocean life

Revolutionary advancements in underwater imaging, robotics, and genomic sequencing have reshaped marine exploration. We present and demonstrate an interdisciplinary approach that uses emerging quantitative imaging technologies, an innovative robotic encapsulation system with in situ RNA preservation and next-generation genomic sequencing to gain comprehensive biological, biophysical, and genomic data from deep-sea organisms. The synthesis of these data provides rich morphological and genetic information for species description, surpassing traditional passive observation methods and preserved specimens, particularly for gelatinous zooplankton. Our approach enhances our ability to study delicate mid-water animals, improving research in the world's oceans.

X-ray phase contrast reveals soft tissue and shell growth lines in mollusks

High-resolution 3D imaging of species with exoskeletons such as shell-bearing mollusks typically involves destructive steps. Nondestructive alternatives are desirable since samples can be rare and valuable, and destructive steps are time-consuming and may distort the tissue. Here, we show for the first time that propagation-based phase-contrast X-ray imaging can significantly increase contrast in mollusks with intact shells. By using the recently upgraded monochromator at the SPring-8 BL20B2 synchrotron beamline, we imaged six species of mollusks, showing that X-ray phase contrast enhances soft-tissue contrast. Features that are almost invisible in conventional attenuation-based micro-computed tomography (micro-CT) are clearly reproduced with phase-contrast imaging under the same scan conditions. Furthermore, this method can reveal features such as growth rings in the shell and differentiate between calcite and aragonite crystal forms. Phase-contrast imaging can thus serve as a compelling alternative when destructive methods are not an option.

Comparative diagnostic imaging in giant African land snails (Achatinidae)

Giant African land snails (GALS) have become increasingly popular, for example, as pets or in kindergartens in Europe, but little is known about their clinically relevant anatomy, diseases, or further details in diagnostic imaging. The present study focuses on the techniques and image interpretation of radiography, computed tomography, and sonography in GALS. The aim of the study is to find the most appropriate imaging tool to visualize the various organs within the mantle cavity (also known as visceral mass) in GALS. The detailed anatomy of GALS is presented with numerous figures of the different imaging techniques. The sensory organs and nervous system will not be part of the present study.

Potentialities of iodine-enhanced micro-CT imaging in the morphological study of adult Aedes (Stegomyia) aegypti (Linnaeus, 1762) mosquitoes

X-ray micro-computed tomography (CT) produces three-dimensional images of samples on a micrometer scale. This technique has several advantages, such as its nondestructive character and low measurement time, compared with other techniques. However, when applied to biological samples of soft tissue, the low attenuation and low effective contrast between structures pose difficulties in creating appropriate images for morphological studies. Diffusible iodine-based contrast-enhanced CT (DICE-CT), which uses iodine solutions to enhance contrast, is a viable alternative for addressing the aforementioned challenges. Given the variety of biological samples, an appropriate methodology must be adapted depending on the dimensions and morphological characteristics of the investigated object. A specimen that has not been morphologically studied by micro-CT and is of high sanitary importance is the adult Aedes aegypti mosquito. This study investigated the stage of iodine staining in the treatment of the A. aegypti mosquito to determine the most suitable staining time for the morphological study of this mosquito in adulthood. After determining the appropriate staining time, we discuss the potential of applying DICE-CT and methodology to mosquito studies. Seven A. aegypti females were treated using fixation steps with Bouin's solution, dehydration in a graded ethanol series, staining with iodine solution (1%), and washing in absolute ethanol. Only the staining step was different between samples. Each mosquito spent a varying amount of time (6-72 h) in the iodine solution (1%). For comparison, one of the mosquitoes was not stained. After treatment, the samples were scanned using the Bruker SkyScan 1172 micro-CT scanner. The reconstructed volumes and histograms were compared to determine the most suitable time. In addition, a quantitative analysis was performed based on a comparison of the attenuation profiles of the mosquito brains. Thereafter, the most suitable treatment process was selected, and two other samples were scanned after applying the selected process. Although fewer than 18 h was insufficient for an effective increase in attenuation and effective contrast, surpassing 24 h proved unnecessary and resulted in saturating the gray tones visualized through the histograms, leading to information loss. Therefore, a time of approximately 24 h was the most suitable staining time for studying adult A. aegypti. It was possible to isolate the organs of the digestive and reproductive systems of the mosquito stained for 24 h. Thus, micro-CT was confirmed to be an excellent technique in studies of individual structures of adult A. aegypti mosquitoes.

Micro-CT and deep learning: Modern techniques and applications in insect morphology and neuroscience

Advances in modern imaging and computer technologies have led to a steady rise in the use of micro-computed tomography (µCT) in many biological areas. In zoological research, this fast and non-destructive method for producing high-resolution, two- and three-dimensional images is increasingly being used for the functional analysis of the external and internal anatomy of animals. µCT is hereby no longer limited to the analysis of specific biological tissues in a medical or preclinical context but can be combined with a variety of contrast agents to study form and function of all kinds of tissues and species, from mammals and reptiles to fish and microscopic invertebrates. Concurrently, advances in the field of artificial intelligence, especially in deep learning, have revolutionised computer vision and facilitated the automatic, fast and ever more accurate analysis of two- and three-dimensional image datasets. Here, I want to give a brief overview of both micro-computed tomography and deep learning and present their recent applications, especially within the field of insect science. Furthermore, the combination of both approaches to investigate neural tissues and the resulting potential for the analysis of insect sensory systems, from receptor structures via neuronal pathways to the brain, are discussed.

Morphological and Tissue Characterization with 3D Reconstruction of a 350-Year-Old Austrian Ardea purpurea Glacier Mummy

Glaciers are dwindling archives, releasing animal mummies preserved in the ice for centuries due to climate changes. As preservation varies, residual soft tissues may differently expand the biological information content of such mummies. DNA studies have proven the possibility of extracting and analyzing DNA preserved in skeletal residuals and sediments for hundreds or thousands of years. Paleoradiology is the method of choice as a non-destructive tool for analyzing mummies, including micro-computed tomography (micro-CT) and magnetic resonance imaging (MRI). Together with radiocarbon dating, histo-anatomical analyses, and DNA sequencing, these techniques were employed to identify a 350-year-old Austrian Ardea purpurea glacier mummy from the Ötztal Alps. Combining these techniques proved to be a robust methodological concept for collecting inaccessible information regarding the structural organization of the mummy. The variety of methodological approaches resulted in a distinct picture of the morphological patterns of the glacier animal mummy. The BLAST search in GenBank resulted in a 100% and 98.7% match in the cytb gene sequence with two entries of the species Purple heron (Ardea purpurea; Accession number KJ941160.1 and KJ190948.1) and a 98% match with the same species for the 16 s sequence (KJ190948.1), which was confirmed by the anatomic characteristics deduced from micro-CT and MRI.

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.

Discovering marine biodiversity in the 21st century

We review the current knowledge of the biodiversity of the ocean as well as the levels of decline and threat for species and habitats. The lack of understanding of the distribution of life in the ocean is identified as a significant barrier to restoring its biodiversity and health. We explore why the science of taxonomy has failed to deliver knowledge of what species are present in the ocean, how they are distributed and how they are responding to global and regional to local anthropogenic pressures. This failure prevents nations from meeting their international commitments to conserve marine biodiversity with the results that investment in taxonomy has declined in many countries. We explore a range of new technologies and approaches for discovery of marine species and their detection and monitoring. These include: imaging methods, molecular approaches, active and passive acoustics, the use of interconnected databases and citizen science. Whilst no one method is suitable for discovering or detecting all groups of organisms many are complementary and have been combined to give a more complete picture of biodiversity in marine ecosystems. We conclude that integrated approaches represent the best way forwards for accelerating species discovery, description and biodiversity assessment. Examples of integrated taxonomic approaches are identified from terrestrial ecosystems. Such integrated taxonomic approaches require the adoption of cybertaxonomy approaches and will be boosted by new autonomous sampling platforms and development of machine-speed exchange of digital information between databases.

An earliest Triassic age for Tasmaniolimulus and comments on synchrotron tomography of Gondwanan horseshoe crabs

Constraining the timing of morphological innovations within xiphosurid evolution is central for understanding when and how such a long-lived group exploited vacant ecological niches over the majority of the Phanerozoic. To expand the knowledge on the evolution of select xiphosurid forms, we reconsider the four Australian taxa: Austrolimulus fletcheri, Dubbolimulus peetae, Tasmaniolimulus patersoni, and Victalimulus mcqueeni. In revisiting these taxa, we determine that, contrary to previous suggestion, T. patersoni arose after the Permian and the origin of over-developed genal spine structures within Austrolimulidae is exclusive to the Triassic. To increase the availability of morphological data pertaining to these unique forms, we also examined the holotypes of the four xiphosurids using synchrotron radiation X-ray tomography (SRXT). Such non-destructive, in situ imaging of palaeontological specimens can aid in the identification of novel morphological data by obviating the need for potentially extensive preparation of fossils from the surrounding rock matrix. This is particularly important for rare and/or delicate holotypes. Here, SRXT was used to emphasize A. fletcheri and T. patersoni cardiac lobe morphologies and illustrate aspects of the V. mcqueeni thoracetronic doublure, appendage impressions, and moveable spine notches. Unfortunately, the strongly compacted D. peetae precluded the identification of any internal structures, but appendage impressions were observed. The application of computational fluid dynamics to high-resolution 3D reconstructions are proposed to understand the hydrodynamic properties of divergent genal spine morphologies of austrolimulid xiphosurids.

A new millipede genus and species of the tribe Pachyiulini from the Caucasus (Diplopoda, Julida, Julidae)

A new genus and species of the millipede tribe Pachyiulini, Bellatoiulus golovatchigen. et sp. nov., is described from the Lesser Caucasus, Azerbaijan. Cybertypes of the new species are created from the physical holotype male and from a paratype female. The distribution and ecological features of the new species, and the position of the new genus within Pachyiulini are discussed.

Micro-CT image gallery visually presenting the effects of ocean warming and acidification on marine gastropod shells

Background

Digitisation of specimens (e.g. zoological, botanical) can provide access to advanced morphological and anatomical information and promote new research opportunities. The micro-CT technology may support the development of "virtual museums" or "virtual laboratories" where digital 3D imaging data are shared widely and freely. There is currently a lack of universal standards concerning the publication and curation of micro-CT datasets.

New information

The aim of the current project was to create a virtual gallery with micro-CT scans of individuals of the marine gastropod Hexaplextrunculus, which were maintained under a combination of increased temperature and low pH conditions, thus simulating future climate change scenarios. The 3D volume-rendering models created were used to visualise the structure properties of the gastropods shells. Finally, the 3D analysis performed on the micro-CT scans was used to investigate potential changes in the shell properties of the gastropods. The derived micro-CT 3D images were annotated with detailed metadata and can be interactively displayed and manipulated using online tools through the micro-CT virtual laboratory, which was developed under the LifeWatchGreece Research Infrastructure for the dissemination of virtual image galleries collection supporting the principles of FAIR data.

Micro-CT protocols for scanning and 3D analysis of Hexaplextrunculus during its different life stages

Micro-computed tomography (micro-CT) is a high-resolution 3D-imaging technique which is now increasingly applied in biological studies focusing on taxonomy and functional morphology. The creation of virtual representations of specimens can increase availability of otherwise underexploited and inaccessible samples. The 3D model dataset can be also further processed through volume rendering and morphometric analysis. The success of micro-CT as a visualisation technique depends on several methodological manipulations, including the use of contrast enhancing staining agents, filters, scanning mediums, containers, exposure time and frame averaging. The aim of this study was to standardise a series of micro-CT scanning and 3D analysis protocols for a marine gastropod species, Hexaplextrunculus. The analytical protocols have followed all the developmental stages of this gastropod, from egg capsules and embryos to juveniles and adults.

Micro-CT for Biological and Biomedical Studies: A Comparison of Imaging Techniques

Several imaging techniques are used in biological and biomedical studies. Micro-computed tomography (micro-CT) is a non-destructive imaging technique that allows the rapid digitisation of internal and external structures of a sample in three dimensions and with great resolution. In this review, the strengths and weaknesses of some common imaging techniques applied in biological and biomedical fields, such as optical microscopy, confocal laser scanning microscopy, and scanning electron microscopy, are presented and compared with the micro-CT technique through five use cases. Finally, the ability of micro-CT to create non-destructively 3D anatomical and morphological data in sub-micron resolution and the necessity to develop complementary methods with other imaging techniques, in order to overcome limitations caused by each technique, is emphasised.

Underground Down Under: Skull anatomy of the southern blind snake Anilios australis Gray, 1845 (Typhlopidae: Serpentes: Squamata)

The cranial anatomy of blindsnakes has been markedly understudied, with the small size and relative rarity of encountering these subterranean reptiles being significant limiting factors. In this article, we re-visit the skull anatomy of the Australian southern blind snake Anilios australis Gray, 1845 using microCT data, and produce the first complete atlas for the cranial anatomy of a representative of this speciose typhlopid genus. The skull is formed by 18 paired and four unpaired elements. We here produce a bone-by-bone description of each element as well as an inner ear endocast for each of two specimens differing in skull size. This approach has revealed the presence of a highly perforated dorsal plate on the septomaxilla-a structure convergent with the cribriform plate of the mammalian ethmoid bone-and a feature previously unknown for typhlopid snakes. This detailed anatomical study will facilitate ongoing taxonomic and systematic studies in the genus Anilios as well as provide comparative data for future studies on blindsnake anatomy more broadly.

Taxonomic description and phylogenetic placement of two new species of Spalangiopelta (Hymenoptera: Pteromalidae: Ceinae) from Eocene Baltic amber

Spalangiopelta is a small genus of chalcid wasps that has received little attention despite the widespread distribution of its extant species. The fossil record of the genus is restricted to a single species from Miocene Dominican amber. We describe two new fossil species, Spalangiopelta darlingi sp. n. and Spalangiopelta semialba sp. n. from Baltic amber. The species can be placed within the extant genus Spalangiopelta based on the distinctly raised hind margin of the mesopleuron. 3D models reconstructed from µCT data were utilized to assist in the descriptions. Furthermore, we provide a key for the females of all currently known Spalangiopelta species. The phylogenetic placement of the fossils within the genus is analyzed using parsimony analysis based on morphological characters. Phylogenetic and functional relevance of two wing characters, admarginal setae and the hyaline break, are discussed. The newly described Baltic amber fossils significantly extend the minimum age of Spalangiopelta to the Upper Eocene.

A new species group of Strumigenys (Hymenoptera, Formicidae) from Ecuador, with a description of its mandible morphology

Strumigenys is one of the most diverse ant genera in the world and arguably the most morphologically diverse, exhibiting an exceptional range of mandible shape and function. A new species, Strumigenysayerstheysp. nov., discovered in the Chocó region of Ecuador is described. With two morphological characters, this species is shown to be a morphologically unique outlier among Strumigenys globally, having predominately smooth and shining cuticle surface sculpturing and long trap-jaw mandibles. Using µCT scans, we produced 3D images of the worker ant and static images to examine and compare mandible articular morphologies with most morphologically similar members of the mandibularis species group. Cuticular, pilosity, and articular mandible morphological differences supports placing the new species in its own new species group.

Holistic description of new deep sea megafauna (Cephalopoda: Cirrata) using a minimally invasive approach

BACKGROUND

In zoology, species descriptions conventionally rely on invasive morphological techniques, frequently leading to damage of the specimens and thus only a partial understanding of their structural complexity. More recently, non-destructive imaging techniques have successfully been used to describe smaller fauna, but this approach has so far not been applied to identify or describe larger animal species. Here, we present a combination of entirely non-invasive as well as minimally invasive methods that permit taxonomic descriptions of large zoological specimens in a more comprehensive manner.

RESULTS

Using the single available representative of an allegedly novel species of deep-sea cephalopod (Mollusca: Cephalopoda), digital photography, standardized external measurements, high-field magnetic resonance imaging, micro-computed tomography, and DNA barcoding were combined to gather all morphological and molecular characters relevant for a full species description. The results show that this specimen belongs to the cirrate octopod (Octopoda: Cirrata) genus Grimpoteuthis Robson, 1932. Based on the number of suckers, position of web nodules, cirrus length, presence of a radula, and various shell characters, the specimen is designated as the holotype of a new species of dumbo octopus, G. imperator sp. nov. The digital nature of the acquired data permits a seamless online deposition of raw as well as derived morphological and molecular datasets in publicly accessible repositories.

CONCLUSIONS

Using high-resolution, non-invasive imaging systems intended for the analysis of larger biological objects, all external as well as internal morphological character states relevant for the identification of a new megafaunal species were obtained. Potentially harmful effects on this unique deep-sea cephalopod specimen were avoided by scanning the fixed animal without admixture of a contrast agent. Additional support for the taxonomic placement of the new dumbo octopus species was obtained through DNA barcoding, further underlining the importance of combining morphological and molecular datasets for a holistic description of zoological specimens.

Integrative anatomical study of the branched annelid Ramisyllis multicaudata (Annelida, Syllidae)

The sponge-dwelling Syllidae Ramisyllis multicaudata and Syllis ramosa are the only annelid species for which a branched body with one head and multiple posterior ends is known. In these species, the head is located deep within the sponge, and the branches extend through the canal system of their host. The morphology of these creatures has captivated annelid biologists since they were first discovered in the late XIXth century, and their external characteristics have been well documented. However, how their branched bodies fit within their symbiotic host sponges and how branches translate into internal anatomy has not been documented before. These features are crucially relevant for understanding the body of these animals, and therefore, the aim of this study was to investigate these aspects. In order to assess these questions, live observation, as wells as histology, immunohistochemistry, micro-computed tomography, and transmission electron microscopy techniques were used on specimens of R. multicaudata. By using these techniques, we show that the complex body of R. multicaudata specimens extends greatly through the canal system of their host sponges. We demonstrate that iterative external bifurcation of the body is accompanied by the bifurcation of the longitudinal organ systems that are characteristic of annelids. Additionally, we also highlight that the bifurcation process leaves an unmistakable fingerprint in the form of newly-described "muscle bridges." These structures theoretically allow one to distinguish original and derived branches at each bifurcation. Last, we characterize some of the internal anatomical features of the stolons (reproductive units) of R. multicaudata, particularly their nervous system. Here, we provide the first study of the internal anatomy of a branched annelid. This information is not only crucial to deepen our understanding of these animals and their biology, but it will also be key to inform future studies that try to explain how this morphology evolved.

Cellular and molecular profiles of anterior nervous system regeneration in Diopatra claparedii Grube, 1878 (Annelida, Polychaeta)

The polychaete Diopatra claparedii Grube, 1878 is among those organisms successfully carrying out full body regeneration, including the whole nervous system. Thus, D. claparedii potentially can be regarded for the nervous system regeneration (NSR) study. However, data on the property of its nervous system and the NSR profile are still lacking. In this study, we investigated the morphology of D. claparedii anterior nervous system (ANS) and examined the cellular and molecular profiles on its early anterior NSR. The nervous system of D. claparedii consists of a symmetry brain with nerves branching off, circumpharyngeal connectives that connect the brain and nerve cord as well as obvious segmental ganglia. Moreover, we identified changes in the cellular condition of the ganglionic cells in the regenerating tissue, such as the accumulation of lysosomes and lipofuscins, elongated mitochondria and multiple nucleoli. Furthermore, mRNA of tissues at two regenerating stages, as well as intact tissue (non-regenerating), were sequenced with Illumina sequencer. We identified from these tissues 37,248 sequences, 18 differential expressed proteins of which upregulated were involved in NSR with noelin-like isoform X2 turned up to be the highest being expressed. Our results highlight the cellular and molecular changes during early phase of NSR, thus providing essential insights on regeneration within Annelida and understanding the neurodegenerative diseases.

Enhancing CT imaging: A safe protocol to stain and de-stain rare fetal museum specimens using diffusible iodine-based staining (diceCT)

Computed tomography (CT) scanning is being increasingly employed in the study of natural history, particularly to investigate the internal anatomy of unique specimens in museum collections. Different techniques to enhance the contrast between tissues have been developed to improve the quality of the scans while preserving the integrity of these rare specimens. Diffusible iodine-based contrast enhanced computed tomography (diceCT) was found to be particularly effective and reversible for staining tissues in formalin preserved specimens. While it can also be effectively employed to stain ethanol-preserved specimens of small size, the reversibility of this process and the applicability to large-bodied animals has never been thoroughly tested. Here, we describe a novel diceCT protocol developed to stain and de-stain ethanol-preserved prenatal specimens of baleen whales (Mysticeti, Cetacea). These large (10-90 cm in length only considering early fetal stages) specimens present unique challenges as they are rare in collections and irreplaceable, therefore it is imperative to not damage them with the staining process. Before trying this protocol on baleen whales' specimens, we conducted a pilot study on commercially available fetal pigs using the same parameters. This allowed us to optimize the staining time to obtain the best results in CT scanning and to test first-hand the effect of de-staining on ethanol-based specimens. External coloration of the specimens is also a concern with iodine-staining, as stained specimens assume a bright red color that needs to be removed from both internal and external tissues before they can be stored. To test the reversibility of the stain in ethanol-preserved specimens with fur, we also conducted a small experiment using commercially acquired domestic mice. After these trials were successful, we applied the staining and de-staining protocol to multiple fetal specimens of mysticetes up to 90 cm in length, both ethanol- and formalin-preserved. Specimens were soaked in a solution of 1% pure iodine in 70% ethanol for 1-28 days, according to their size. After scanning, specimens are soaked in a solution of 3% sodium thiosulfate in 70% ethanol that is able to completely wash out the iodine from the tissues in a shorter time frame, between a few hours and 14 days. The same concentrations were used for formalin-preserved specimens, but DI water was used as solvent instead of ethanol. The staining technique proved particularly useful to enhance the contrast difference between cartilage, mineralized bone, teeth, and the surrounding soft tissues even when the specimens where scanned in medical-grade CT scans. The specimens did not suffer any visible damage or shrinkage due to the procedure, and in both the fetal samples and in the mice the color of the stain was completely removed by the de-staining process. We conclude therefore that this protocol can be safely applied to a variety of ethanol-preserved museum specimens to enhance the quality of the CT scanning and highlight internal morphological features without recurring to dissection or other irreversible procedures. We also provide tips to best apply this protocol, from how to mix the solutions to how to minimize the staining time.

Psolidium bathygalego nom. nov. (Echinodermata, Holothuroidea) from bathyal bottoms of Galicia (NW Iberian Peninsula)

It is proposed to name the Atlantic holothuria Psolidium complanatum Cherbonnier, 1969, whose denomination is already occupied by Psolidium complanatum (Semper, 1867) from the Philippines, as Psolidium bathygalego nom. nov. 843 specimens of Psolidium bathygalego nom. nov., collected between 417 and 1191 m deep in the NW and W of Galicia and in the Galicia Bank, were studied. A detailed description of the external and internal anatomy of Psolidium bathygalego nom. nov. is made by studying the ossicles and the skeletal structure by means of scanning electron microscopy (SEM) as well as the introvert, calcareous ring, retractor muscles, water-vascular system, digestive system, respiratory trees, and reproductive system by means of micro-computed tomography (micro-CT). The habitat, feeding system, and geographical distribution of Psolidium bathygalego nom. nov. are also described.

Exploring the macrostructural anatomy of dendrochirotid sea cucumber's (Echinodermata) calcareous rings under micro-computed tomography and its bearing on phylogeny

Despite descending from heavily calcified ancestors, the holothuroid skeleton is fully internal and composed of microscopic ossicles and a ring of plates bound by connective tissue, the calcareous ring. The calcareous ring exhibits a complex and poorly understood morphology; as a result, establishing unambiguous homology statements about its macrostructure has been challenging and phylogenetic studies have had to simplify this important structure. Here, we provide the first broad comparative study of Dendrochirotida calcareous rings using micro-computed tomography (μCT). A detailed description of the three-dimensional macrostructure of the calcareous ring of 10 sea cucumber species, including rare and type specimens, is presented. The structures observed were highly variable at the subfamily level, especially at the point of tissue attachment. The relationship between the calcareous ring and its associated organs, and their functional morphology are discussed. To aid future phylogenetic studies, we listed 22 characters and performed a preliminary cladistic analysis. The topology obtained supports the idea that the simple, cucumariid ring is ancestral to the mosaic-like phyllophorid ring; however, it did not support the monophyly of the cucumariids. It also did not support the family Sclerodactylidae, which was described based on the ring morphology. Differently from the dermal ossicles, which are highly homoplastic, the general homoplasy index of the calcareous ring characters was relatively low. This result highlights the importance of this structure for phylogenetic inference. Unfortunately, time since collection, rough collection methods and fixation can damage the skeleton, and the calcareous ring is often overlooked in taxonomic descriptions. The data presented here will improve our understanding of holothuroid relationships and facilitate studies on holothuroid functional morphology and biomechanics.

Repositories for Taxonomic Data: Where We Are and What is Missing

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000-20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term-ideally perpetual-data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach-linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated $ \le $2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000-40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.].

Unravelling taxonomic ambiguity of the Mastacembelidae in the Mekong Delta (Vietnam) through DNA barcoding and morphological approaches

Morphological-based species identification can be problematic for a comparative worldwide survey if taxonomic keys are limited and inconsistent, as illustrated in the family Mastacembelidae. This study combined DNA barcoding and morphological methods to test species identification of Mastacembelidae in the Mekong Delta with emphasis on taxonomic ambiguity of the precise identification of the fish locally known as chach bong. Fish specimens were collected from fishermen in different regions of the delta. Five presumed species within two genera were recorded. Samples were morphologically measured for morphometric and meristic traits. Representative samples of each species were sequenced at the cytochrome c oxidase subunit I (COI) gene. The number of dorsal fin spines and general morphological appearance are distinguishable among the five presumed species. However, morphometric measurements overlapped between Macrognathus semiocellatus and Macrognathus siamensis. K2P distances based on COI sequences among species were high, ranging from 12.4% to 18.7%. All individuals were separated into monophyletic groups of species, clustered into Mastacembelus and two Macrognathus lineages. Chach bong should be recognized as Mastacembelus favus and not Mastacembelus armatus as previously classified. No Mastacembelus armatus was recorded in the Mekong Delta. GenBank sequences of Mastacembelus armatus formed a sister relationship to Mastacembelus favus although both have the same range of number of dorsal fin spines and similar reticulated patterns on the body. Misidentification between these two species has been widely recorded in international databases of species taxonomy and DNA barcodes. Nonetheless, their genetic distance (12.4%) is higher than conspecific distances of samples from other regions, indicating the two species can be differentiated by DNA barcoding.

Contrast-enhanced micro-CT to assess dental pulp tissue debridement in root canals of extracted teeth: a series of cascading experiments towards method validation

AIM

To validate a new method for the evaluation of pulp tissue debridement in the root canals of extracted teeth using an impregnation protocol involving potassium triiodide, a radiocontrast solution known as Lugol's, combined with micro-computed tomographic (micro-CT) imaging.

METHODOLOGY

The impact of NaOCl on the radiopacity of Lugol's solution was assessed using a two-fold dilution series of Lugol in distilled water and 5.25% NaOCl, which were then pipetted into transparent dishes and radiographed. To verify the influence of Lugol on the proteolytic effect of NaOCl, a dissolution test was performed using fresh bovine meat. Ten slices did not undergo any tissue processing, whilst twenty slices were fixed in formaldehyde for 24 h. After that, 10 of them were immersed in Lugol for another 24 h. Then, all specimens were placed in NaOCl and the time required for a complete tissue dissolution was recorded. For the last experiments (histological validation and micro-CT assessment), 8 extracted mandibular premolars with formerly vital pulps were immersed in buffered formalin, scanned in a micro-CT device, accessed, immersed in Lugol for 7 days and scanned again. Then, the root canals of 5 teeth were prepared and scanned, and the volume of remaining pulp tissue identified and quantified, whilst 3 teeth were histologically processed. The same specimens were subjected to histological assessment, and the images of the histologic sections were registered with the corresponding micro-CT images to verify whether the pulp tissue in the histological sections matched its counterpart in the Lugol-impregnated tissues identified in the micro-CT slices.

RESULTS

There was no discernible effect on radiopacity when NaOCl was mixed with Lugol's solution. Tissue processing did not affect the time required for the complete dissolution of fresh bovine meat. Histological evaluation revealed a correlation between micro-CT and histological images confirming the identification of Lugol-impregnated pulp tissue in micro-CT images.

CONCLUSIONS

The radiocontrast Lugol's solution was unaffected by NaOCl and did not interfere with its soft tissue dissolution capability. The impregnation protocol using Lugol's solution allowed the visualization of pulp tissue on the micro-CT images and the identification of pulp remnants after chemical-mechanical canal procedures.

High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

High-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

Odontomachus davidsoni sp. nov. (Hymenoptera, Formicidae), a new conspicuous trap-jaw ant from Ecuador

One of the largest species in its genus, Odontomachusdavidsoni Hoenle, Lattke & Donoso, sp. nov. is described from workers and queens collected at lowland forests in the Chocó-Darién bioregion in coastal Ecuador. The workers are characterized by their uniform red coloration, their large size (16–18 mm body length), and their frontal head striation that reaches the occipital margin. DNA barcodes (COI) and high resolution 2D images of the type material are provided, as well as an updated key for the Neotropical species of Odontomachus. In addition, a three-dimensional digital model of the worker holotype and a paratype queen scanned with DISC3D based on photogrammetry is presented, for the first time in a species description. Findings of large and conspicuous new species are uncommon around the world and suggest that these Ecuadorian rainforests may conceal many more natural treasures that deserve conservation.

Bimodal Whole-Mount Imaging of Tendon Using Confocal Microscopy and X-ray Micro-Computed Tomography

Background

Three-dimensional imaging modalities for optically dense connective tissues such as tendons are limited and typically have a single imaging methodological endpoint. Here, we have developed a bimodal procedure utilising fluorescence-based confocal microscopy and x-ray micro-computed tomography for the imaging of adult tendons to visualise and analyse extracellular sub-structure and cellular composition in small and large animal species.

Results

Using fluorescent immunolabelling and optical clearing, we visualised the expression of the novel cross-species marker of tendon basement membrane, laminin-α4 in 3D throughout whole rat Achilles tendons and equine superficial digital flexor tendon 5 mm segments. This revealed a complex network of laminin-α4 within the tendon core that predominantly localises to the interfascicular matrix compartment. Furthermore, we implemented a chemical drying process capable of creating contrast densities enabling visualisation and quantification of both fascicular and interfascicular matrix volume and thickness by x-ray micro-computed tomography. We also demonstrated that both modalities can be combined using reverse clarification of fluorescently labelled tissues prior to chemical drying to enable bimodal imaging of a single sample.

Conclusions

Whole-mount imaging of tendon allowed us to identify the presence of an extensive network of laminin-α4 within tendon, the complexity of which cannot be appreciated using traditional 2D imaging techniques. Creating contrast for x-ray micro-computed tomography imaging of tendon using chemical drying is not only simple and rapid, but also markedly improves on previously published methods. Combining these methods provides the ability to gain spatio-temporal information and quantify tendon substructures to elucidate the relationship between morphology and function.

An Integrative Approach Using Phylogenomics and High-Resolution X-Ray Computed Tomography for Species Delimitation in Cryptic Taxa

Morphologically cryptic taxa have proved to be a long-standing challenge for taxonomists. Lineages that show strong genomic structuring across the landscape but are phenotypically similar pose a conundrum, with traditional morphological analyses of these cryptic lineages struggling to keep up with species delimitation advances. Micro X-ray computed tomography (CT) combined with geometric morphometric analyses provides a promising avenue for identification of morphologically cryptic taxa, given its ability to detect subtle differences in anatomical structures. However, this approach has yet to be used in combination with genomic data in a comparative analytical framework to distinguish cryptic taxa. We present an integrative approach incorporating genomic and geometric morphometric evidence to assess the species delimitation of grassland earless dragons (Tympanocryptis spp.) in north-eastern Australia. Using mitochondrial and nuclear genes (ND2 and RAG1, respectively), along with $>$8500 SNPs (nuclear single nucleotide polymorphisms), we assess the evolutionary independence of target lineages and several closely related species. We then integrate phylogenomic data with osteological cranial variation between lineages using landmark-based analyses of three-dimensional CT models. High levels of genomic differentiation between the three target lineages were uncovered, also supported by significant osteological differences. By incorporating multiple lines of evidence, we provide strong support for three undescribed cryptic lineages of Tympanocryptis in north-eastern Australia that warrant taxonomic review. Our approach demonstrates the successful application of CT with integrative taxonomic approaches for cryptic species delimitation, which is broadly applicable across vertebrates containing morphologically similar yet genetically distinct lineages. Additionally, we provide a review of recent integrative taxonomic approaches for cryptic species delimitation and an assessment of how our approach can value-add to taxonomic research.

X-ray microcomputed tomography applied to the taxonomic study of rare material: redescriptions of seven of Schirch's Brazilian species of land planarians (Geoplanidae, Platyhelminthes)

In 2016, the type-material of ten of the 15 Brazilian land planarians (Platyhelminthes, Tricladida, Geoplanidae) described by Schirch (1929) was discovered deposited in the Museu Nacional do Rio de Janeiro (MNRJ). Schirch only described the external morphology of these species, all originally placed in the genus Geoplana. By the 1930s and 1950s Geoplanaitatiayana, G.plana, and G.rezendei underwent taxonomic revision based on the study of non-type specimens. The remaining 12 species also underwent a taxonomic revision but only based on the literature. Current names of these species are Geoplanagoettei, Pseudogeoplanaarpi, Ps.blaseri, Ps.bonita, Ps.bresslaui, Ps.cardosi, Ps.doederleini, Ps.lumbricoides, Ps.obscura, Ps.riedeli, Ps.theresopolitana, and Ps.wetzeli. The species Geoplanamaximiliani sensu Schirch (1929) was renamed as Ps.schirchi Ogren & Kawakatsu, 1990.

The present study reports a taxonomic revision of seven of Schirch’s species using type material, namely Obamaitatiayana, Pasiphaplana, Pseudogeoplanaarpi, Ps.bresslaui, Ps.doederleini, Ps.schirchi and Ps.wetzeli. Additional specimens of some of these species were also examined. Morphological data from histological preparations and from virtual sections were obtained through a non-destructive technique of X-ray computed microtomography (µCT). This approach resulted in the preservation of the entire body of at least one type-specimen of each species, and the holotype of Ps.bresslaui. Conspecificity of O.itatiayana and P.plana was confirmed, as previously reported in the literature. It is also proposed that Ps.bresslaui belongs to the genus Paraba, while the other species should remain in Pseudogeoplana, since type-specimens are either immature, poorly preserved or simply lost.

Comparison of structure and composition of a fossil Champsosaurus vertebra with modern Crocodylidae vertebrae: A multi-instrumental approach

Information on the adaptation of bone structures during evolution is rare since histological data are limited. Micro- and nano-computed tomography of a fossilized vertebra from Champsosaurus sp., which has an estimated age of 70-73 million years, revealed lower porosity and higher bone density compared to modern Crocodylidae vertebrae. Mid-infrared reflectance and energy dispersive X-ray mapping excluded a petrification process, and demonstrated a typical carbonate apatite distribution, confirming histology in light- and electron microscopy of the preserved vertebra. As a consequence of this evolutionary process, the two vertebrae of modern Crocodylidae show reduced overall stiffness in the finite element analysis simulation compared to the fossilized Champsosaurus sp. vertebra, with predominant stiffness along the longitudinal z-axes.

Eurytrema coelomaticum: updated morphology of adult worms using advanced microscopy experiments

Eurytrema coelomaticum is a digenean flatworm of ruminants that is the causative agent of eurytrematosis, a disease of veterinary health concern. Although modern techniques of morphological analysis have provided new insights about the morphology and anatomy of parasitic helminths, most studies on E. coelomaticum adults are based on conventional light microscopy. In the present study, a combined approach using brightfield, fluorescence, confocal and scanning electron microscopies (SEMs), together with the cryofracture technique, have updated morphological data on E. coelomaticum recovered from cattle in Rio de Janeiro State, Brazil. Light microscopy confirmed the presence of several structures present in the current description, such as suckers, pharynx, oesophagus, intestinal bifurcation and the cirrus-sac. Fluorescence stereomicroscopy revealed for the first time the cubic crystal protein inclusions in the forebody, which were further detailed by confocal and SEMs. Confocal microscopy provided detailed information of the muscular architecture associated with the attachment structures (suckers), digestive system (pharynx and oesophagus), egg-forming complex (ovary, Mehlis' gland and Laurer's canal) and male reproductive system, which are similar to those found in other digenean flukes. SEM images of cryofractured parasites showed mucus and developing eggs within uterine loops. It was demonstrated that the combination of advanced tools generated complementary information, confirming the importance of experimental morphology in parasitology. Therefore, the knowledge of the adult structural organization of E. coelomaticum was improved and this work has contributed to propose new morphological criteria to evaluate the effects of antiparasitic drugs on flukes of medical and veterinary importance.

Micro-CT screening of old shell collections helps to understand the distribution of viviparity in the highly diversified clausiliid clade of land snails

Current zoological research may benefit in many ways from the study of old collections of shells. These collections may provide materials for the verification of broad zoogeographical and ecological hypotheses on the reproduction of molluscs, as they include records from many areas where sampling is currently impossible or very difficult due to political circumstances. In the present paper we present data on viviparous and embryo-retention reproductive modes in clausiliid land snails (subfamily Phaedusinae) acquired from specimens collected since the nineteenth century in the Pontic, Hyrcanian, and East and Southeast Asian regions. X-ray imaging (micro-CT) enabled relatively quick screening of more than 1,000 individuals classified within 141 taxa, among which we discovered 205 shells containing embryos or eggs. Gravid individuals were found to belong to 55 species, representing, for some of these species, the first indication of brooding reproductive strategy.

X-Ray Microscopy of the Larval Crustacean Brain

Micro-computed X-ray tomography (μCT) coupled with visualization techniques such as three-dimensional reconstruction of internal morphological structures has opened up new pathways for analyzing the anatomy of nervous systems in intact specimens. The possibility for combining μCT with other techniques is one of the major advantages of μCT scanning, and the technical development of higher resolutions in lab-based μCT-scanners allows for investigating the anatomy of specimens in the sub-milimeter range. The European shore crab Carcinus maenas features a larval development over four zoeal and one megalopal stage with body lengths ranging from 500 μm to 2000 μm. The developing nervous system in the larvae of C. maenas is organized into a central brain which is connected via esophageal connectives with a ventral nerve chord and segmental ganglia. Since soft tissues such as the nervous tissues feature low contrasts compared to other tissues such as muscles or cuticularized body parts, the interpretation in μCT scans is challenging and needs some practice. The protocol described here is also applicable for larger specimens of a variety of species and spans over 2-3 days resulting in an image stack ready for postprocessing and visualization.

Advances in Contrast Agents for Contrast-Enhanced Magnetic Resonance Imaging

INTRODUCTION

Magnetic resonance imaging (MRI) is a well-established medical invention in modern medical technology diagnosis. It is a nondestructive, versatile, and sensitive technique with a high spatial resolution for medical diagnosis. However, MRI has some limitations in differentiating certain tissues, particularly tiny blood vessels, pathological to healthy tissues, specific tumors, and inflammatory conditions such as arthritis, atherosclerosis, and multiple sclerosis. The contrast agent (CA) assisted imaging is the best possible solution to resolve the limitations of MRI.

METHOD

The literature review was carried out using the keywords, "MRI, T1&T2 relaxation, MRI CAs, delivery and adverse effects, classification of CAs." The tools used for the literature search were PubMed, Scopus, and Google Scholar.

RESULT AND DISCUSSION

The literature findings focus on MRI technique, limitations, and possible solutions. Primarily, the review focuses on the mechanism of CAs in image formation with detailed explanations of T1 and T2 relaxations, the mechanism of the MRI-CA image formations. This review presents the adverse effects of CA as well as available marketed formulations and recent patents to extent complete information about the MRI-CA.

CONCLUSION

MRI generates detailed visual information of various tissues with high resolution and contrast. The proton present in the biological fluid plays a crucial role in MR image formation, and it is unable to distinguish pathological conditions in many cases. The CAs are the best solution to resolve the limitation by interacting with native protons. The present review discusses the mechanism of CAs in contrast enhancement and its broad classification with the latest literature. Furthermore, the article presents information about CA biodistribution and adverse effects. The review concludes with an appropriate solution for adverse effects and presents the future prospective for researchers to develop advanced formulations.

The utility of micro-computed tomography for the non-destructive study of eye microstructure in snails

Molluscan eyes exhibit an enormous range of morphological variation, ranging from tiny pigment-cup eyes in limpets, compound eyes in ark clams and pinhole eyes in Nautilus, through to concave mirror eyes in scallops and the large camera-type eyes of the more derived cephalopods. Here we assess the potential of non-destructive micro-computed tomography (µ-CT) for investigating the anatomy of molluscan eyes in three species of the family Solariellidae, a group of small, deep-sea gastropods. We compare our results directly with those from traditional histological methods applied to the same specimens, and show not only that eye microstructure can be visualised in sufficient detail for meaningful comparison even in very small animals, but also that μ-CT can provide additional insight into gross neuroanatomy without damaging rare and precious specimens. Data from μ-CT scans also show that neurological innervation of eyes is reduced in dark-adapted snails when compared with the innervation of cephalic tentacles, which are involved in mechanoreception and possibly chemoreception. Molecular tests also show that the use of µ-CT and phosphotungstic acid stain do not prevent successful downstream DNA extraction, PCR amplification or sequencing. The use of µ-CT methods is therefore highly recommended for the investigation of difficult-to-collect or unique specimens.

Estudio microtomográfico de la anatomía de Laubieriopsis cabiochi (Amoureux, 1982) (Annelida, Fauveliopsidae)

La Microtomografía Computarizada (micro-CT o μCT) es una técnica de estudio microestructural, no destructiva, que permite estudiar la anatomía interna y externa de muestras biológicas, y realizar su reconstrucción a través de un modelo virtual en tres dimensiones. En los últimos años esta técnica está aportando avances significativos en el conocimiento anatómico de diversos invertebrados marinos. En este trabajo se estudia la anatomía externa e interna de Laubieriopsis cabiochi (Amoureux, 1982) (Annelida, Fauveliopsidae) y paralelamente se valora la calidad de las imágenes de μCT frente a las obtenidas en estudios previos mediante métodos histológicos clásicos.

Taxonomy of Arabian Temnothorax Mayr (Formicidae: Myrmicinae) with description of a new species enhanced by x-ray microtomography

Temnothorax elmenshawyi sp. n., a new ant species from the Asir Mountains of the southwestern region of the Kingdom of Saudi Arabia, is described based on the worker caste. The new species is a member of the T. exilis species group and is distinguished from the other species included in this group by the impressed metanotal groove, the short, acute and broadly-based propodeal spines, the finely punctate posterior half of cephalic surface, and absence of a median clypeal carina. Despite extensive collecting by the authors at the type locality, only two specimens are available for description, suggesting that this species may be rare and likely endemic to the Asir Mountains. The species description is complemented by still images of volume renderings of a 3D model and a 3D rotation video of the holotype based on x-ray microtomography (micro-CT), allowing remote in-depth examination of the specimen. The virtual micro-CT data is provided as cybertype dataset and freely available online https://doi.org/10.5061/dryad.4gg39k6 , as well as 3D surface model (Sketchfab.com, https://skfb.ly/6HYRz). An updated identification key to the Arabian species is presented.

An integrative approach to the anatomy of Syllis gracilis Grube, 1840 (Annelida) using micro-computed X-ray tomography

BACKGROUND

The overall anatomy of the genus Syllis (Annelida: Syllidae) has been largely studied; however, an integrative approach considering different anatomical techniques has never been considered. Here, we use micro-computed X-ray tomography (micro-CT) to examine the internal anatomy of Syllis gracilis Grube, 1840, along with other widely available techniques.

METHODS

We studied the anatomy of the marine annelid S. gracilis through an integrative approach, including micro-CT along with stereo and light compound microscopy (STM, LCM), scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM) and histological sectioning (HIS). In this manner, we evaluated the applicability of micro-CT for the examination of annelid anatomy by testing whether the images obtained make it possible to visualize the main body structures, in comparison with other current techniques, of the various elements of its internal anatomy.

RESULTS

Overall external and internal body elements are clearly shown by the integrative use of all techniques, thus overcoming the limitations of each when studied separately.Any given method shows disparate results, depending on the body part considered. For instance, micro-CT provided good images of the external anatomy, including relevant characters such as the shape, length and number of articles of dorsal parapodial cirri. However, it is especially useful for the examination of internal anatomy, thus allowing for 3D visualization of the natural spatial arrangement of the different organs. The features best visualized are those of higher tissue density (i.e., body musculature, anterior parts of the digestive tract), particularly in 3D images of unstained specimens, whereas less electrodense tissues (i.e., the peritoneal lining of septa and nervous system) are less clearly visualized. The use of iodine stain with micro-CT has shown advantages against non-staining for the adequate observation of delicate elements of low density, such as the segmental organs, the connective between the ganglia, the ventral nerve cord and segmental nerves.

DISCUSSION

Main external anatomical elements of S. gracilis are well shown with micro-CT, but images show lesser optical resolution and contrast when compared to micrographs provided by SEM and CLSM, especially for fine structural features of chaetae. Comparison of micro-CT and HIS images revealed the utility and reliability of the former to show the presence, shape and spatial disposition of most internal body organs; the resolution of micro-CT images at a cellular level is, however, much lower than that of HIS, which makes both techniques complementary.

Psychology, not technology, is our biggest challenge to open digital morphology data

The past two decades have seen a revolution in digital imaging techniques for capturing gross morphology, offering an unprecedented volume of data for biological research. Despite the rapid increase in scientific publications incorporating those images, the underlying datasets remain largely inaccessible. As the technical barriers to data sharing continue to fall, we face a more intimate, and perhaps more complicated, obstacle to open data – the one in our minds.

MicroCT imaging applied to description of a new species of Pagurus Fabricius, 1775 (Crustacea: Decapoda: Anomura: Paguridae), with selection of three-dimensional type data

A new species of hermit crab, Pagurus fraserorum n. sp. (family Paguridae) is described from rocky subtidal reefs off KwaZulu-Natal, South Africa, and illustrated using both conventional drawings and colour photographs, and via three-dimensional (3D) X-ray micro-computed tomography (μCT). Because of the limitation μCT has in detecting very fine and soft structures, a novel approach of manually drawing setation and spinulation onto the two-dimensional images of the 3D visualizations was used to illustrate the pereopods. In addition, an interactive figure and rotation movie clips in the supplement section complement the species description, and the 3D raw data of the 3D type data are downloadable from the Gigascience Database repository. The new species is the sixth species of Pagurus Fabricius, 1775 reported from South Africa and is closely allied to the Indo-Pacific P. boriaustraliensis Morgen, 1990 and P. pitagsaleei McLaughlin, 2002, from which it differs by its shorter ocular peduncles, by the armature of the carpus of the right cheliped, and also in colouration. This study presents the first description of a hermit crab in which a majority of taxonomic details are illustrated through 3D volume-rendered illustrations. In addition, colour photographs and COI molecular barcodes are provided, and the latter compared to COI sequences of specimens from Western Australia previously identified as P. boriaustraliensis and of specimens of P. pitagsaleei from Taiwan, as well as to three additional South African members of the genus. The South African taxon was confirmed to be genetically distinct from all species tested.

Structure of the Ambrosia Beetle (Coleoptera: Curculionidae) Mycangia Revealed Through Micro-Computed Tomography

Ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) rely on a symbiosis with fungi for their nutrition. Symbiotic fungi are preserved and transported in specialized storage structures called mycangia. Although pivotal in the symbiosis, mycangia have been notoriously difficult to study, given their minute size and membranous structure. We compared the application of novel visualization methods for the study of mycangia, namely micro-computed tomography (micro-CT) and laser ablation tomography (LATscan) with traditional paraffin sectioning. Micro-CT scanning has shown the greatest promise in new organ discovery, while sectioning remains the only method with sufficient resolution for cellular visualization. All three common types of mycangia (oral, mesonotal, and pronotal) were successfully visualized and presented for different species of ambrosia beetles: Ambrosiodmus minor (Stebbing) 1909, Euplatypus compositus (Say) 1823, Premnobius cavipennis Eichhoff 1878, Scolytoplatypus raja Blandford 1893, Xylosandrus crassiusculus (Motschulsky) 1866 and X. amputatus (Blandford) 1894. A reconstruction of the mycangium and the surrounding musculature in X. amputatus is also presented. The advantages of micro-CT compared to the previously commonly used microtome sectioning include the easy visualization and recording of three-dimensional structures, their position in reference to other internal structures, the ability to distinguish natural aberrations from technical artifacts, and the unprecedented visualizations of the anatomic context of mycangia enabled by the integrated software.

Three-Dimensional Portable Document Format (3D PDF) in Clinical Communication and Biomedical Sciences: Systematic Review of Applications, Tools, and Protocols

Background

The Portable Document Format (PDF) is the standard file format for the communication of biomedical information via the internet and for electronic scholarly publishing. Although PDF allows for the embedding of three-dimensional (3D) objects and although this technology has great potential for the communication of such data, it is not broadly used by the scientific community or by clinicians.

Objective

The objective of this review was to provide an overview of existing publications that apply 3D PDF technology and the protocols and tools for the creation of model files and 3D PDFs for scholarly purposes to demonstrate the possibilities and the ways to use this technology.

Methods

A systematic literature review was performed using PubMed and Google Scholar. Articles searched for were in English, peer-reviewed with biomedical reference, published since 2005 in a journal or presented at a conference or scientific meeting. Ineligible articles were removed after screening. The found literature was categorized into articles that (1) applied 3D PDF for visualization, (2) showed ways to use 3D PDF, and (3) provided tools or protocols for the creation of 3D PDFs or necessary models. Finally, the latter category was analyzed in detail to provide an overview of the state of the art.

Results

The search retrieved a total of 902 items. Screening identified 200 in-scope publications, 13 covering the use of 3D PDF for medical purposes. Only one article described a clinical routine use case; all others were pure research articles. The disciplines that were covered beside medicine were many. In most cases, either animal or human anatomies were visualized. A method, protocol, software, library, or other tool for the creation of 3D PDFs or model files was described in 19 articles. Most of these tools required advanced programming skills and/or the installation of further software packages. Only one software application presented an all-in-one solution with a graphical user interface.

Conclusions

The use of 3D PDF for visualization purposes in clinical communication and in biomedical publications is still not in common use, although both the necessary technique and suitable tools are available, and there are many arguments in favor of this technique. The potential of 3D PDF usage should be disseminated in the clinical and biomedical community. Furthermore, easy-to-use, standalone, and free-of-charge software tools for the creation of 3D PDFs should be developed.

X-ray computed tomography and its potential in ecological research: A review of studies and optimization of specimen preparation

Imaging techniques are a cornerstone of contemporary biology. Over the last decades, advances in microscale imaging techniques have allowed fascinating new insights into cell and tissue morphology and internal anatomy of organisms across kingdoms. However, most studies so far provided snapshots of given reference taxa, describing organs and tissues under "idealized" conditions. Surprisingly, there is an almost complete lack of studies investigating how an organism's internal morphology changes in response to environmental drivers. Consequently, ecology as a scientific discipline has so far almost neglected the possibilities arising from modern microscale imaging techniques. Here, we provide an overview of recent developments of X-ray computed tomography as an affordable, simple method of high spatial resolution, allowing insights into three-dimensional anatomy both in vivo and ex vivo. We review ecological studies using this technique to investigate the three-dimensional internal structure of organisms. In addition, we provide practical comparisons between different preparation techniques for maximum contrast and tissue differentiation. In particular, we consider the novel modality of phase contrast by self-interference of the X-ray wave behind an object (i.e., phase contrast by free space propagation). Using the cricket Acheta domesticus (L.) as model organism, we found that the combination of FAE fixative and iodine staining provided the best results across different tissues. The drying technique also affected contrast and prevented artifacts in specific cases. Overall, we found that for the interests of ecological studies, X-ray computed tomography is useful when the tissue or structure of interest has sufficient contrast that allows for an automatic or semiautomatic segmentation. In particular, we show that reconstruction schemes which exploit phase contrast can yield enhanced image quality. Combined with suitable specimen preparation and automated analysis, X-ray CT can therefore become a promising quantitative 3D imaging technique to study organisms' responses to environmental drivers, in both ecology and evolution.

Evaluation of standard imaging techniques and volumetric preservation of nervous tissue in genetically identical offspring of the crayfish Procambarus fallax cf. virginalis (Marmorkrebs)

In the field of comparative neuroanatomy, a meaningful interspecific comparison demands quantitative data referring to method-specific artifacts. For evaluating the potential of state-of-the-art imaging techniques in arthropod neuroanatomy, micro-computed X-ray microscopy (μCT) and two different approaches using confocal laser-scanning microscopy (cLSM) were applied to obtain volumetric data of the brain and selected neuropils in Procambarus fallax forma virginalis (Crustacea, Malacostraca, Decapoda). The marbled crayfish P. fallax cf. virginalis features a parthogenetic reproduction generating genetically identical offspring from unfertilized eggs. Therefore, the studied organism provides ideal conditions for the comparative analysis of neuroanatomical imaging techniques and the effect of preceding sample preparations of nervous tissue. We found that wet scanning of whole animals conducted with μCT turned out to be the least disruptive method. However, in an additional experiment it was discovered that fixation in Bouin’s solution, required for μCT scans, resulted in an average tissue shrinkage of 24% compared to freshly dissected and unfixed brains. The complete sample preparation using fixation in half-strength Karnovsky’s solution of dissected brains led to an additional volume decrease of 12.5%, whereas the preparation using zinc-formaldehyde as fixative resulted in a shrinkage of 5% in comparison to the volumes obtained by μCT. By minimizing individual variability, at least for aquatic arthropods, this pioneer study aims for the inference of method-based conversion factors in the future, providing a valuable tool for reducing quantitative neuroanatomical data already published to a common denominator. However, volumetric deviations could be shown for all experimental protocols due to methodological noise and/or phenotypic plasticity among genetically identical individuals. MicroCT using undried tissue is an appropriate non-disruptive technique for allometry of arthropod brains since spatial organ relationships are conserved and tissue shrinkage is minimized. Collecting tissue-based shrinkage factors according to specific sample preparations might allow a better comparability of volumetric data from the literature, even if another technique was applied.