High-resolution 3D Reconstruction Research Articles

MICOS Complex Loss Governs Age-Associated Murine Mitochondrial Architecture and Metabolism in the Liver, While Sam50 Dictates Diet Changes.

The liver, the largest internal organ and a metabolic hub, undergoes significant declines due to aging, affecting mitochondrial function and increasing the risk of systemic liver diseases. How the mitochondrial three-dimensional (3D) structure changes in the liver across aging, and the biological mechanisms regulating such changes confers remain unclear. In this study, we employed Serial Block Face-Scanning Electron Microscopy (SBF-SEM) to achieve high-resolution 3D reconstructions of murine liver mitochondria to observe diverse phenotypes and structural alterations that occur with age, marked by a reduction in size and complexity. We also show concomitant metabolomic and lipidomic changes in aged samples. Aged human samples reflected altered disease risk. To find potential regulators of this change, we examined the Mitochondrial Contact Site and Cristae Organizing System (MICOS) complex, which plays a crucial role in maintaining mitochondrial architecture. We observe that the MICOS complex is lost during aging, but not Sam50. Sam50 is a component of the sorting and assembly machinery (SAM) complex that acts in tandem with the MICOS complex to modulate cristae morphology. In murine models subjected to a high-fat diet, there is a marked depletion of the mitochondrial protein SAM50. This reduction in Sam50 expression may heighten the susceptibility to liver disease, as our human biobank studies corroborate that Sam50 plays a genetically regulated role in the predisposition to multiple liver diseases. We further show that changes in mitochondrial calcium dysregulation and oxidative stress accompany the disruption of the MICOS complex. Together, we establish that a decrease in mitochondrial complexity and dysregulated metabolism occur with murine liver aging. While these changes are partially be regulated by age-related loss of the MICOS complex, the confluence of a murine high-fat diet can also cause loss of Sam50, which contributes to liver diseases. In summary, our study reveals potential regulators that affect age-related changes in mitochondrial structure and metabolism, which can be targeted in future therapeutic techniques.

Automated Camera Pose Generation for High-Resolution 3D Reconstruction of Bridges by Unmanned Aerial Vehicles

This work explores the possibility of automating the aerial survey of bridges to generate high-resolution images necessary for digital damage inspection. High-quality unmanned aerial vehicle (UAV) based 3D reconstruction of bridges is an important step towards autonomous infrastructure inspection. However, the calculation of optimal camera poses remains challenging due to the complex structure of bridges and is therefore often conducted manually. This process is time-consuming and can lead to quality losses. Research in this field to automate this process is yet sparse and often requires high informative models of the bridge as the base for calculations, which are not given widely. Therefore, this paper proposes an automated camera pose calculation method solely based on an easily accessible polygon mesh of the bridge. For safe operation, point cloud data of the environment are used for automated ground detection and obstacle avoidance including vegetation. First, an initial set of camera poses is generated based on a voxelized mesh created in respect to the quality requirements for 3D reconstruction using defined camera specification. Thereafter, camera poses not fulfilling safety distances are removed and specific camera poses are added to increase local coverage quality. Evaluations of three bridges show that for diverse bridge types, near-complete coverage was achieved. Due to the low computational effort of the voxel approach, the runtime was kept to a minimum, even for large bridges. The subsequent algorithm is able to find alternative camera poses even in areas where the optimal pose could not be placed due to obstacles.

New Insights into Boxer's Knuckle Injury of the Little Finger.

The original description of boxer's knuckle injury of the fifth ray mentions that the injury occurs between the extensor digitorum communis (EDC) and the extensor digiti minimi (EDM). Subsequent reports claim similar findings. Anatomical studies show that the EDC of the fifth ray is absent in most patients, while the EDM is generally composed of two slips. We present a modification of the current description of boxer's knuckle injury of the little finger based on the correlation between advanced preoperative 3D imaging and intraoperative findings. Five patients were investigated preoperatively using high-resolution ultrasound and 3D tendon reconstruction-based MR arthrography. Surgical exploration identified the lesion site relative to the EDM and EDC. All patients had two slips of the EDM and no EDC to the fifth ray. The injury appeared as a longitudinal tear of the EDM between its two slips. The mean gap was 7.8 mm (range 4.5-10 mm) on the pathological side vs. 1.3 mm (range 1-2 mm) on the healthy contralateral side. We believe that previous descriptions of boxer's knuckle of the fifth ray are inaccurate. High-resolution ultrasound and 3D reconstructions based on MR arthrography are reliable diagnostic tools allowing to locate the injury with precision.

B4GALT1-Dependent Glycosylation Is Essential to Bone Marrow Reconstitution Following Chemotherapeutic Injury

The bone marrow (BM) comprises a three-dimensional (3D) network of branching sinusoids surrounding hematopoietic cells, embedded in an extracellular matrix (ECM) rich in glycans vital for cell maintenance and function. While the interaction between megakaryocytes (MKs) and the components of the environment for BM recovery post-injury becomes more apparent, the role of glycan-dependent thrombopoiesis and nascent platelets in BM maintenance and reconstitution is underexplored. We have found that β-1,4-galactosyltransferase 1 (β4galt1) deficiency results in dysplastic MKs, disrupted proplatelet release, and severe thrombocytopenia. KEGG analysis of SLAM marker sorted hematopoietic stem and progenitor cells (HSPC) bulk RNAseq data, showed downregulation of ECM-receptor interaction, focal adhesion, gap junction, and proteoglycans in cancer pathways in β4galt1 -/- HSPCs compared to controls. We hypothesized that β4galt1-dependent glycosylation regulates the BM microenvironment at steady state and post-injury. To test this, we conducted a study examining the effects of a single dose of 5-fluorouracil (5-FU) treatment (150 µg/g) on BM MKs, c-kit + progenitors, vasculature, ECM, and platelet count in both control and β4GalT1-deficient (B4 -/-) mice. We analyzed femur BM sections using immunofluorescence, targeting the vasculature marker laminin, progenitor marker c-kit, and ECM markers perlecan and fibrinogen, and MK marker GPIbα (CD42b) and CD41. Image processing with Imaris software and MATLAB facilitated cell count, spatial distribution, and 3D reconstruction assessments of the BM. An automated hemoanalyzer quantified platelet counts from days 1-10 post-treatment. Post-5-FU treatment, control mice exhibited a 50% decrease in reticulated and total platelet counts from day 3, persisting until day 8. On day 10, platelet counts increased to 150% above average. As BM cellularity diminished, a marrow sinusoidal cavity emerged at the bone's center, reaching maximum size on day 3 post-injury (mean size = 2.10 ± 0.14 µm 2; p=0.013), contracting from day 4 (mean size = 1.35 ± 0.14 µm 2; p=0.19), and restoring its size by day 8. GPIbα + MKs and c-kit + cell counts decreased by 50% 3 days following the injury while colocalization of c-kit + GPIbα + expressing cells increased preferentially localizing at the sinusoidal cavity, hinting at their role in BM recovery after injury. At day 5 post-injury, c-kit + cellcounts increased but reduced again on day 10, coinciding with the rise of MK number. 3D imaging post-5-FU treatment revealed a preferential localization of GPIbα + MKs and c-kit + cells in the center of the bone by day 10, adjacent to the previously injured area. High-resolution 3D reconstruction revealed that the sinusoidal cavity was filled with ECM components, including perlecan and fibrinogen, and platelets, as determined using GPIbα staining, on day 5 post-injury. Platelets were not released into circulation until the 8th day of reconstitution of BM, suggesting that although platelets are produced by BM MKs and distributed within the sinusoidal cavity, they do not immediately enter circulation. Depleting platelets using a platelet specific antibody before administering 5-FU slowed reconstitution of the BM sinusoidal cavity. In contrast to control mice, B4 -/- mice showed a reduction in platelet count and a notable accumulation of highly dysplastic MKs clusters around the sinusoidal cavity (MK/mm 3= 3598 vs. MK/mm 3=2748) at day 5 post-5FU. Moreover, SLAM marker defined long-term HSCs showed that MK-biased (CD41 + and CD41 +/ GPIbα +) populations notably increased in B4 -/- mice compared to controls (p=0.0043), indicating heightened emergency hematopoiesis in the absence of β4galt1. While the control BM sinusoidal cavity almost returned to normal size at day 8, the B4 -/- BM displayed a lack of organized vasculature, increased sinusoidal cavity size and a heightened expression of GPIbα + dysplastic and clustered MKs, particularly near the sinusoidal cavity. The findings emphasize the crucial role of β4galt1-dependent glycosylation in platelet production and distribution, fundamental for blood clotting and wound healing, during BM reconstitution after injury. Furthermore, the identification of the sinusoidal cavity as a reservoir of ECM and platelets, continuously remodeled during BM recovery, adds unexpected insights to our understanding of the BM reconstitution processes.

Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias.

Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.

Baited reconstruction with 2D template matching for high-resolution structure determination in vitro and in vivo without template bias

Previously we showed that 2D template matching (2DTM) can be used to localize macromolecular complexes in images recorded by cryogenic electron microscopy (cryo-EM) with high precision, even in the presence of noise and cellular background (Lucas et al., 2021; Lucas et al., 2022). Here, we show that once localized, these particles may be averaged together to generate high-resolution 3D reconstructions. However, regions included in the template may suffer from template bias, leading to inflated resolution estimates and making the interpretation of high-resolution features unreliable. We evaluate conditions that minimize template bias while retaining the benefits of high-precision localization, and we show that molecular features not present in the template can be reconstructed at high resolution from targets found by 2DTM, extending prior work at low-resolution. Moreover, we present a quantitative metric for template bias to aid the interpretation of 3D reconstructions calculated with particles localized using high-resolution templates and fine angular sampling.

Main channel width effects on overtopping-induced non-cohesive fluvial dike breaching

Laboratory experiments were conducted on the breaching of homogeneous non-cohesive sandy fluvial dikes induced by flow overtopping. Tests were conducted using a main channel, an erodible lateral dike and a floodplain. The main channel width and Froude number prior to overtopping were systematically varied. Breach discharge was deduced from water level measurements and mass conservation. High-resolution 3D reconstructions of the evolving breach geometry were obtained using a non-intrusive laser profilometry technique. The main channel width and Froude number show significant influence on the breach expansion and hydrograph. Breach hydrographs are divided into three types, depending on the Froude number and a non-dimensional main channel width. An adapted fluvial dike breaching model based on the concept of “effective breach width” is proposed. Using the laboratory data, the computed breach discharge is found extremely satisfactory, although the breach downstream expansion is not accurately reproduced by the model.

Mesoscale-driven dispersion of early life stages of European eel

The larvae of the European eel travel an extensive distance of approximately 5,000 km from the spawning area in the Sargasso Sea to the European coasts. We here study the larval drift with focus on the effects of mesoscale processes, analyzing data from a targeted survey and modeling possible drift trajectories. The survey covered the initial distribution of larvae in the Subtropical Convergence Zone (STCZ), which is characterized by complex patterns of oceanic fronts and mesoscale eddies. During March–April 2014, sampling was carried out along north–south transects. Hydrography was described using vertical CTD casts and UCTD profiles, and larval distributions assessed from hauls of a large ring net. Patterns in water mass distribution and particle dispersion dynamics were analyzed by reconstruction and diagnosis of mesoscale dynamics, combining satellite observations and Argo profiles. Lagrangian drift trajectories of eel larvae were subsequently simulated starting from a data-driven high-resolution 3D reconstruction of the modeled flow. We found the area of larval distribution delimited by frontal zones, defined by the combined effects of marked longitudinal salinity gradients and large-scale zonal temperature variations. Modeled patterns of eel larvae dispersion were predominantly influenced by the current shear and eddy strain, and while the direction was mainly westward, a significant dispersal was also observed in northeastward directions. Such almost isotropic transport of European eels is supported by historical data on larval size distribution, and results challenge common interpretations of eel larval drift, which propose an initial westward advection of the entire population to the Gulf Stream along the offshore edge of the Antilles current.

One-stage 3D profile-based pavement crack detection and quantification

To improve the robustness and efficiency of pavement crack inspection tasks, a one-stage pavement crack detection and quantification method is proposed to directly extract crack geometry from 3D pavement profile. A low-cost stereo imaging system is implemented for high-resolution 3D reconstruction. Based on the generated 3D profile, an algorithm that integrates crack detection and quantification is developed to obtain the crack map, length, width, and depth simultaneously. The results show that the proposed method is robust to surrounding noises and has no demand for prior data. Compared with deep learning-based crack detection methods, the mean IoU of the proposed method is 6.23% higher than that of state-of-the-art methods. The proposed method outperforms existing methods in terms of crack length and width measurement. Moreover, the proposed method automatically measures crack depth with a correlation coefficient R2 of 0.9679 against the manual measurement.

Evaluation of Anal Sphincter with High Resolution Anorectal Manometry and 3D Reconstruction in Patients with Anorectal Malformation

Background: Patients with anorectal malformation (ARM) need long-term follow-up, in order to evaluate fecal continence; the main predictors of longer-term success are the type of ARM, associated anomalies and sacral integrity. Three-Dimensional High Resolution Anorectal Manometry (3D-HRAM) gives detailed information on pressure on the anal complex profile. Our objective was to analyze anal sphincter activity in ARM patients with 3D-HRAM establishing the correlation between manometric and clinical data. Methods: Forty ARM patients were submitted to 3D-HRAM: manometric, anatomical and clinical scores were correlated with each other and with the bowel management response (BM). Results: A positive correlation between all scores and types of ARM was found: in high ARM and in patients with spinal anomalies (regardless to ARM type) lower scores were reported and even after BM they did not achieve good continence. Conclusions: 3D-HRAM gives detailed data on the functional activity of the anal sphincter complex. Our study revealed a correlation between manometric parameters and clinical outcomes, confirming spinal malformations and ARM type as the most important prognostic risk factors for a bad outcome. Specific sphincteric defects can also be explored with manometry, allowing for tailored bowel management strategies.

A COMPARATIVE NEURAL RADIANCE FIELD (NERF) 3D ANALYSIS OF CAMERA POSES FROM HOLOLENS TRAJECTORIES AND STRUCTURE FROM MOTION

Abstract. Neural Radiance Fields (NeRFs) are trained using a set of camera poses and associated images as input to estimate density and color values for each position. The position-dependent density learning is of particular interest for photogrammetry, enabling 3D reconstruction by querying and filtering the NeRF coordinate system based on the object density. While traditional methods like Structure from Motion are commonly used for camera pose calculation in pre-processing for NeRFs, the HoloLens offers an interesting interface for extracting the required input data directly. We present a workflow for high-resolution 3D reconstructions almost directly from HoloLens data using NeRFs. Thereby, different investigations are considered: Internal camera poses from the HoloLens trajectory via a server application, and external camera poses from Structure from Motion, both with an enhanced variant applied through pose refinement. Results show that the internal camera poses lead to NeRF convergence with a PSNR of 25 dB with a simple rotation around the x-axis and enable a 3D reconstruction. Pose refinement enables comparable quality compared to external camera poses, resulting in improved training process with a PSNR of 27 dB and a better 3D reconstruction. Overall, NeRF reconstructions outperform the conventional photogrammetric dense reconstruction using Multi-View Stereo in terms of completeness and level of detail.

Visuomotor interactions in the mouse forebrain mediated by extrastriate cortico-cortical pathways.

The mammalian visual system can be broadly divided into two functional processing pathways: a dorsal stream supporting visually and spatially guided actions, and a ventral stream enabling object recognition. In rodents, the majority of visual signaling in the dorsal stream is transmitted to frontal motor cortices via extrastriate visual areas surrounding V1, but exactly where and to what extent V1 feeds into motor-projecting visual regions is not well known. We employed a dual labeling strategy in male and female mice in which efferent projections from V1 were labeled anterogradely, and motor-projecting neurons in higher visual areas were labeled with retrogradely traveling adeno-associated virus (rAAV-retro) injected in M2. We characterized the labeling in both flattened and coronal sections of dorsal cortex and made high-resolution 3D reconstructions to count putative synaptic contacts in different extrastriate areas. The most pronounced colocalization V1 output and M2 input occurred in extrastriate areas AM, PM, RL and AL. Neurons in both superficial and deep layers in each project to M2, but high resolution volumetric reconstructions indicated that the majority of putative synaptic contacts from V1 onto M2-projecting neurons occurred in layer 2/3. These findings support the existence of a dorsal processing stream in the mouse visual system, where visual signals reach motor cortex largely via feedforward projections in anteriorly and medially located extrastriate areas.

DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images

Single-particle cryo-electron microscopy (cryo-EM) is a technique for biomolecular structure reconstruction from vitrified samples containing many copies of a biomolecular complex (known as single particles) at random unknown 3D orientations and positions. Cryo-EM allows reconstructing multiple conformations of the complexes from images of the same sample, which usually requires many rounds of 2D and 3D classifications to disentangle and interpret the combined conformational, orientational, and translational heterogeneity. The elucidation of different conformations is the key to understand molecular mechanisms behind the biological functions of the complexes and the key to novel drug discovery. Continuous conformational heterogeneity, due to gradual conformational transitions giving raise to many intermediate conformational states of the complexes, is both an obstacle for high-resolution 3D reconstruction of the conformational states and an opportunity to obtain information about multiple coexisting conformational states at once. HEMNMA method, specifically developed for analyzing continuous conformational heterogeneity in cryo-EM, determines the conformation, orientation, and position of the complex in each single particle image by image analysis using normal modes (the motion directions simulated for a given atomic structure or EM map), which in turn allows determining the full conformational space of the complex but at the price of high computational cost. In this article, we present a new method, referred to as DeepHEMNMA, which speeds up HEMNMA by combining it with a residual neural network (ResNet) based deep learning approach. The performance of DeepHEMNMA is shown using synthetic and experimental single particle images.

How innovations in methodology offer new prospects for volume electron microscopy

Detailed knowledge of biological structure has been key in understanding biology at several levels of organisation, from organs to cells and proteins. Volume electron microscopy (volume EM) provides high resolution 3D structural information about tissues on the nanometre scale. However, the throughput rate of conventional electron microscopes has limited the volume size and number of samples that can be imaged. Recent improvements in methodology are currently driving a revolution in volume EM, making possible the structural imaging of whole organs and small organisms. In turn, these recent developments in image acquisition have created or stressed bottlenecks in other parts of the pipeline, like sample preparation, image analysis and data management. While the progress in image analysis is stunning due to the advent of automatic segmentation and server‐based annotation tools, several challenges remain. Here we discuss recent trends in volume EM, emerging methods for increasing throughput and implications for sample preparation, image analysis and data management.

Recent Technical Advances in Sample Preparation for Single-Particle Cryo-EM.

Cryo-sample preparation is a vital step in the process of obtaining high-resolution structures of macromolecules by using the single-particle cryo–electron microscopy (cryo-EM) method; however, cryo-sample preparation is commonly hampered by high uncertainty and low reproducibility. Specifically, the existence of air-water interfaces during the sample vitrification process could cause protein denaturation and aggregation, complex disassembly, adoption of preferred orientations, and other serious problems affecting the protein particles, thereby making it challenging to pursue high-resolution 3D reconstruction. Therefore, sample preparation has emerged as a critical research topic, and several new methods for application at various preparation stages have been proposed to overcome the aforementioned hurdles. Here, we summarize the methods developed for enhancing the quality of cryo-samples at distinct stages of sample preparation, and we offer insights for developing future strategies based on diverse viewpoints. We anticipate that cryo-sample preparation will no longer be a limiting step in the single-particle cryo-EM field as increasing numbers of methods are developed in the near future, which will ultimately benefit the entire research community.

Modeling the biomechanics of the conventional aqueous outflow pathway microstructure in the human eye

Background and objectiveIntraocular pressure (IOP) is determined by aqueous humor outflow resistance, which is a function of the combined resistance of Schlemm's canal (SC) endothelium and the trabecular meshwork (TM) and their interactions in the juxtacanalicular connective tissue (JCT) region. Aqueous outflow in the conventional outflow pathway results in pressure gradient across the TM, JCT, and SC inner wall, and induces mechanical stresses and strains that influence the geometry and homeostasis of the outflow system. The outflow resistance is affected by alteration in tissues’ geometry, so there is potential for active, two-way, fluid-structure interaction (FSI) coupling between the aqueous humor (fluid) and the TM, JCT, and SC inner wall (structure). However, our understanding of the biomechanical interactions of the aqueous humor with the outflow connective tissues and its contribution to the outflow resistance regulation is incomplete. MethodsIn this study, a microstructural finite element (FE) model of a human eye TM, JCT, and SC inner wall was constructed from a segmented, high-resolution histologic 3D reconstruction of the human outflow system. Three different elastic moduli (0.004, 0.128, and 51.5 MPa based on prior reports) were assigned to the TM/JCT complex while the elastic modulus of the SC inner wall was kept constant at 0.00748 MPa. The hydraulic conductivity was programmed separately for the TM, JCT, and SC inner wall using a custom subroutine. Cable elements were embedded into the TM and JCT extracellular matrix to represent the directional stiffness imparted by anisotropic collagen fibril orientation. The resultant stresses and strains in the outflow system were calculated using fluid-structure interaction method. ResultsThe higher TM/JCT stiffness resulted in larger stresses, but smaller strains in the outflow connective tissues, and resulted in a 4- and 5-fold larger pressure drop across the SC inner wall, respectively, compared to the most compliant model. Funneling through µm-sized SC endothelial pores was evident in the models at lower tissue stiffness, but aqueous flow was more turbulent in models with higher TM/JCT stiffness. ConclusionsThe mechanical properties of the outflow tissues play a crucial role in the hydrodynamics of the aqueous humor in the conventional outflow system.

Fluorescently Labeled Gadolinium Ferrate/Trigadolinium Pentairon(III) Oxide Nanoparticles: Synthesis, Characterization, In Vivo Biodistribution, and Application for Visualization of Myocardial Ischemia-Reperfusion Injury.

Various gadolinium compounds have been proposed as contrasting agents for magnetic resonance imaging (MRI). In this study, we suggested a new synthesis method of gadolinium ferrate/trigadolinium pentairon(III) oxide nanoparticles (GF/TPO NPs). The specific surface area of gadolinium ferrate (GdFeO3) and trigadolinium pentairon(III) oxide (Gd3Fe5O12) nanoparticles was equal to 42 and 66 m2/g, respectively. The X-ray diffraction analysis confirmed that the synthesized substances were GdFeO3 and Gd3Fe5O12. The gadolinium content in the samples was close to the theoretically calculated value. The free gadolinium content was negligible. Biodistribution of the GF/TPO NPs was studied in rats by fluorescent imaging and Fe2+/Fe3+ quantification demonstrating predominant accumulation in such organs as lung, kidney, and liver. We showed in the in vivo rat model of myocardial ischemia–reperfusion injury that GF/TPO NPs are able to target the area of myocardial infarction as evidenced by the significantly greater level of fluorescence. In perspective, the use of fluorescently labeled GF/TPO NPs in multimodal imaging may provide basis for high-resolution 3D reconstruction of the infarcted heart, thereby serving as unique theranostic platform.

Efficacy of High-Resolution Preoperative 3D Reconstructions for Lesion Localization in Oncological Colorectal Surgery-First Pilot Study.

When planning an operation, surgeons usually rely on traditional 2D imaging. Moreover, colon neoplastic lesions are not always easy to locate macroscopically, even during surgery. A 3D virtual model may allow surgeons to localize lesions with more precision and to better visualize the anatomy. In this study, we primary analyzed and discussed the clinical impact of using such 3D models in colorectal surgery. This is a monocentric prospective observational pilot study that includes 14 consecutive patients who presented colorectal lesions with indication for surgical therapy. A staging computed tomography (CT)/magnetic resonance imaging (MRI) scan and a colonoscopy were performed on each patient. The information gained from them was provided to obtain a 3D rendering. The 2D images were shown to the surgeon performing the operation, while the 3D reconstructions were shown to a second surgeon. Both of them had to locate the lesion and describe which procedure they would have performed; we then compared their answers with one another and with the intraoperative and histopathological findings. The lesion localizations based on the 3D models were accurate in 100% of cases, in contrast to conventional 2D CT scans, which could not detect the lesion in two patients (in these cases, lesion localization was based on colonoscopy). The 3D model reconstruction allowed an excellent concordance correlation between the estimated and the actual location of the lesion, allowing the surgeon to correctly plan the procedure with excellent results. Larger clinical studies are certainly required.

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.

Polyomavirus Localized with Deep Learning Methods

This case study shows how to apply a deep learning algorithm to detect specific particles in transmission electron microscopy images. The main difficulty consists in the confusing background where a mix of artifacts introduced by the negative staining method coexist with biological debris, and low contrast inherent to the acquisition process of the samples. Considering that a high-resolution 3D reconstruction of virus particles or other macromolecular structures needs thousands of particles, the recent advances in deep-learning methods makes the reach of a comfortable number of particles attainable with a high level of confidence. Deep learning algorithms based on convolutional neural networks can overcome the major issues after a train and validation stage, and subsequently process thousands of similar images in a short amount of time, with a few seconds required for each image, localizing all the particles of interest with very few mistakes, or missed particles. We applied one of such algorithms to a dataset of polyomavirus images containing about 390 particles and evaluate its performance against human curation, verifying that 88.9% of the dataset were processed with zero false positive detections.