A comprehensive and user-friendly framework for 3D-data visualisation in invertebrates and other organisms

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.

Putting a new spin on insect jumping performance using 3D modeling and computer simulations of spotted lanternfly nymphs

How animals jump and land on diverse surfaces is ecologically important and relevant to bioinspired robotics. Here, we describe the jumping biomechanics of the planthopper Lycorma delicatula (spotted lanternfly), an invasive insect in the USA that jumps frequently for dispersal, locomotion and predator evasion. High-speed video was used to analyze jumping by spotted lanternfly nymphs from take-off to impact on compliant surfaces. These insects used rapid hindleg extensions to achieve high take-off speeds (2.7-3.4 m s-1) and accelerations (800-1000 m s-2), with mid-air trajectories consistent with ballistic motion without drag forces or steering. Despite rotating rapidly (5-45 Hz) about time-varying axes of rotation, they landed successfully in 58.9% of trials. They also attained the most successful impact orientation significantly more often than predicted by chance, consistent with their using attitude control. Notably, these insects were able to land successfully when impacting surfaces at all angles, pointing to the importance of collisional recovery behaviors. To further understand their rotational dynamics, we created realistic 3D rendered models of spotted lanternflies and used them to compute their mechanical properties during jumping. Computer simulations based on these models and drag torques estimated from fits to tracked data successfully predicted several features of the measured rotational kinematics. This analysis showed that the rotational inertia of spotted lanternfly nymphs is predominantly due to their legs, enabling them to use posture changes as well as drag torque to control their angular velocity, and hence their orientation, thereby facilitating predominately successful landings when jumping.

Evolution of reproductive structures for in-flight mating in thynnine wasps (Hymenoptera: Thynnidae: Thynninae)

Thynnine wasps have an unusual mating system that involves concurrent in-flight copulation and nuptial feeding of wingless females by alate males. Consequently, thynnine genitalia play a multifunctional role and have likely been subject to various different selective pressures for both reproductive success and food provisioning. Here, we present a new molecular phylogeny for the Australian Thynninae and use 3D-geometric morphometrics and comparative methods to investigate the morphological evolution of select genital structures across the group. We found significant morphological integration between all male and female structures analysed, which is likely influenced by sexual selection, but also reproductive isolation requirements and mechanical constraints. The morphology of the primary male and female coupling structures was correlated with female body size, and female genitalia exhibited strong negative size allometry. Those male and female coupling structures have evolved at similar evolutionary rates, whereas female structures appear to have evolved a higher degree of morphological novelty over time. We conclude that the unique reproductive strategies of thynnine wasps have resulted in complex evolutionary patterns in their genital morphology, which has likely played a central role in the extensive diversification of the subfamily across Australasia and South America. Our study reinforces the need to treat composite characters such as genitalia by their component parts, and to consider the roles of both male and female reproductive structures in evolutionary studies.

Radionuclide, magnetic resonance and computed tomography imaging in European round back slugs (Arionidae) and leopard slugs (Limacidae)

Other than in animal models of human disease, little functional imaging has been performed in most of the animal world. The aim of this study was to explore the functional anatomy of the European round back slug (Arionidae) and leopard slug (Limacidae) and to establish an imaging protocol for comparative species study. Radionuclide images with single photon emission computed tomography (SPECT) and positron emission tomography (PET) were obtained after injections of standard clinical radiopharmaceuticals ^99mtechnetium dicarboxypropane diphosphonate (bone scintigraphy), ^99mtechnetium mercaptoacetyltriglycine (kidney function), ^99mtechnetium diethylenetriaminepentaacetic acid (kidney function), ^99mtechnetium pertechnetate (mediated by the sodium-iodide symporter), ^99mtechnetium sestamibi (cardiac scintigraphy) or ¹⁸F-fluoro-deoxyglucose (glucose metabolism) in combination with magnetic resonance imaging (MRI) and computed tomography (CT) for uptake anatomic definition. Images were compared with anatomic drawings for the Arionidae species. Additionally, organ uptake data was determined for a description of slug functional anatomy in comparison to human tracer biodistribution patterns identifying the heart, the open circulatory anatomy, calcified shell remnant, renal structure (nephridium), liver (digestive gland) and intestine. The results show the detailed functional anatomy of Arionidae and Limacidae, and describe an in vivo whole-body imaging procedure for invertebrate species.

Intraspecific variation in the Cambrian: new observations on the morphology of the Chengjiang euarthropod Sinoburius lunaris

Background

The Chengjiang biota from southwest China (518-million-years old, early Cambrian) has yielded nearly 300 species, of which more than 80 species represent early chelicerates, crustaceans and relatives. The application of µCT-techniques combined with 3D software (e.g., Drishti), has been shown to be a powerful tool in revealing and analyzing 3D features of the Chengjiang euarthropods. In order to address several open questions that remained from previous studies on the morphology of the xandarellid euarthropod Sinoburius lunaris, we reinvestigated the µCT data with Amira to obtain a different approach of visualization and to generate new volume-rendered models. Furthermore, we used Blender to design 3D models showing aspects of intraspecific variation.

Results

New findings are: (1) antennulae consist of additional proximal articles that have not been detected before; (2) compared to other appendages, the second post-antennular appendage has a unique shape, and its endopod is comprised of only five articles (instead of seven); (3) the pygidium bears four pairs of appendages which are observed in all specimens. On the other hand, differences between specimens also have been detected. These include the presence/absence of diplotergites resulting in different numbers of post-antennular appendages and tergites and different distances between the tip of the hypostome and the anterior margin of the head shield.

Conclusions

Those new observations reveal intraspecific variation among Chengjiang euarthropods not observed before and encourage considerations about possible sexual dimorphic pairs or ontogenetic stages. Sinoburius lunaris is a variable species with respect to its morphological characters, cautioning that taxon-specific variabilities need to be considered when exploring new species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01854-1.

Three-dimensional segmentation of computed tomography data using Drishti Paint: new tools and developments

Computed tomography (CT) has become very widely used in scientific and medical research and industry for its non-destructive and high-resolution means of detecting internal structure. Three-dimensional segmentation of computed tomography data sheds light on internal features of target objects. Three-dimensional segmentation of CT data is supported by various well-established software programs, but the powerful functionalities and capabilities of open-source software have not been fully revealed. Here, we present a new release of the open-source volume exploration, rendering and three-dimensional segmentation software, Drishti v. 2.7. We introduce a new tool for thresholding volume data (i.e. gradient thresholding) and a protocol for performing three-dimensional segmentation using the 3D Freeform Painter tool. These new tools and workflow enable more accurate and precise digital reconstruction, three-dimensional modelling and three-dimensional printing results. We use scan data of a fossil fish as a case study, but our procedure is widely applicable in biological, medical and industrial research.

Tools of the trade: MicroCT reveals native structure and functional morphology of organs that drive caterpillar-ant interactions

Caterpillars of many lycaenid butterflies are tended by ants that offer protection from predators and parasitoids. Specialized structures such as glands, ciliary organs and chitinous ornamentation in caterpillars play key roles in the underlying tactile, acoustic, and chemical communication between caterpillars and ants. Although the ecological, evolutionary, and behavioural aspects of these interactions are well studied, the mechanisms (i.e., the functional morphology) that drive the specialized interactive organs are poorly characterized. We used advanced X-ray microtomography (MicroCT) to delineate internal, native morphology of specialized larval dew patches, nectar glands, and tactile ciliary organs that mediate interactions between Crematogaster ants and caterpillars of the obligate myrmecophilous Apharitis lilacinus butterfly. Our non-destructive MicroCT analysis provided novel 3-D insights into the native structure and positions of these specialized organs in unmatched detail. This analysis also suggested a functional relationship between organ structures and surrounding muscles and nervation that operate the glands and tactile organs, including a ‘lasso bag’ control mechanism for dew patches and muscle control for other organs. This provided a holistic understanding of the organs that drive very close caterpillar–ant interactions. Our MicroCT analysis opens a door for similar structural and functional analysis of adaptive insect morphology.

A comprehensive and user-friendly framework for 3D-data visualisation in invertebrates and other organisms

Methods for 3D‐imaging of biological samples are experiencing unprecedented development, with tools such as X‐ray micro‐computed tomography (μCT) becoming more accessible to biologists. These techniques are inherently suited to small subjects and can simultaneously image both external and internal morphology, thus offering considerable benefits for invertebrate research. However, methods for visualising 3D‐data are trailing behind the development of tools for generating such data. Our aim in this article is to make the processing, visualisation and presentation of 3D‐data easier, thereby encouraging more researchers to utilise 3D‐imaging. Here, we present a comprehensive workflow for manipulating and visualising 3D‐data, including basic and advanced options for producing images, videos and interactive 3D‐PDFs, from both volume and surface‐mesh renderings. We discuss the importance of visualisation for quantitative analysis of invertebrate morphology from 3D‐data, and provide example figures illustrating the different options for generating 3D‐figures for publication. As more biology journals adopt 3D‐PDFs as a standard option, research on microscopic invertebrates and other organisms can be presented in high‐resolution 3D‐figures, enhancing the way we communicate science.

An interactive and intuitive visualisation method for X-ray computed tomography data of biological samples in 3D Portable Document Format

3D imaging approaches based on X-ray microcomputed tomography (microCT) have become increasingly accessible with advancements in methods, instruments and expertise. The synergy of material and life sciences has impacted biomedical research by proposing new tools for investigation. However, data sharing remains challenging as microCT files are usually in the range of gigabytes and require specific and expensive software for rendering and interpretation. Here, we provide an advanced method for visualisation and interpretation of microCT data with small file formats, readable on all operating systems, using freely available Portable Document Format (PDF) software. Our method is based on the conversion of volumetric data into interactive 3D PDF, allowing rotation, movement, magnification and setting modifications of objects, thus providing an intuitive approach to analyse structures in a 3D context. We describe the complete pipeline from data acquisition, data processing and compression, to 3D PDF formatting on an example of craniofacial anatomical morphology in the mouse embryo. Our procedure is widely applicable in biological research and can be used as a framework to analyse volumetric data from any research field relying on 3D rendering and CT-biomedical imaging.

Description of a new species of Membranobalanus (Crustacea, Cirripedia) from southern Australia

A new species of sponge-inhabiting barnacle, Membranobalanusporphyrophilussp. nov., is described herein. This species can be distinguished from all other congeners by a combination of characters, in particular by the shapes of the tergum and scutum and the armament of the cirri. COI sequence data from the type specimens have been lodged with GenBank and a morphological key to the species of Membranobalanus is provided to aid future research. The host of the new species is the southern Australian endemic demosponge Spheciospongiapurpurea. The new species of barnacle is thought to be host species specific.

Visualization of insect metamorphosis

Metamorphosis and, in particular, holometaboly, the development of organisms through a series of discrete stages (egg, larva, pupa, adult) that hardly resemble one another but are finely adapted to specific roles in the life cycle of the organism, has fascinated and mystified humans throughout history. However, it can be difficult to visualize the dramatic changes that occur during holometaboly without destructive sampling, traditionally through histology. However, advances in imaging technologies developed mainly for medical sciences have been applied to studies of insect metamorphosis over the past couple of decades. These include micro-computed tomography, magnetic resonance imaging and optical coherence tomography. A major advantage of these techniques is that they are rapid and non-destructive, enabling virtual dissection of an organism in any plane by anyone who has access to the image files and the necessary software. They can also be applied in some cases to visualize metamorphosis in vivo, including the periods of most rapid and dramatic morphological change. This review focusses on visualizing the intra-puparial holometabolous metamorphosis of cyclorraphous flies (Diptera), including the primary model organism for all genetic investigations, Drosophila melanogaster, and the blow flies of medical, veterinary and forensic importance, but also discusses similar studies on other insect orders. This article is part of the theme issue 'The evolution of complete metamorphosis'.

The evolution of female genitalia

Female genitalia have been largely neglected in studies of genital evolution, perhaps due to the long-standing belief that they are relatively invariable and therefore taxonomically and evolutionarily uninformative in comparison with male genitalia. Contemporary studies of genital evolution have begun to dispute this view, and to demonstrate that female genitalia can be highly diverse and covary with the genitalia of males. Here, we examine evidence for three mechanisms of genital evolution in females: species isolating 'lock-and-key' evolution, cryptic female choice and sexual conflict. Lock-and-key genital evolution has been thought to be relatively unimportant; however, we present cases that show how species isolation may well play a role in the evolution of female genitalia. Much support for female genital evolution via sexual conflict comes from studies of both invertebrate and vertebrate species; however, the effects of sexual conflict can be difficult to distinguish from models of cryptic female choice that focus on putative benefits of choice for females. We offer potential solutions to alleviate this issue. Finally, we offer directions for future studies in order to expand and refine our knowledge surrounding female genital evolution.