Herbivorous fish feeding dynamics and energy expenditure on a coral reef: Insights from stereo-video and AI-driven 3D tracking.

Unveiling the intricate relationships between animal movement ecology, feeding behavior, and internal energy budgeting is crucial for a comprehensive understanding of ecosystem functioning, especially on coral reefs under significant anthropogenic stress. Here, herbivorous fishes play a vital role as mediators between algae growth and coral recruitment. Our research examines the feeding preferences, bite rates, inter-bite distances, and foraging energy expenditure of the Brown surgeonfish (Acanthurus nigrofuscus) and the Yellowtail tang (Zebrasoma xanthurum) within the fish community on a Red Sea coral reef. To this end, we used advanced methods such as remote underwater stereo-video, AI-driven object recognition, species classification, and 3D tracking. Despite their comparatively low biomass, the two surgeonfish species significantly influence grazing pressure on the studied coral reef. A. nigrofuscus exhibits specialized feeding preferences and Z. xanthurum a more generalist approach, highlighting niche differentiation and their importance in maintaining reef ecosystem balance. Despite these differences in their foraging strategies, on a population level, both species achieve a similar level of energy efficiency. This study highlights the transformative potential of cutting-edge technologies in revealing the functional feeding traits and energy utilization of keystone species. It facilitates the detailed mapping of energy seascapes, guiding targeted conservation efforts to enhance ecosystem health and biodiversity.

Evaluation of breast skin and tissue stiffness using a non-invasive aspiration device and impact of clinical predictors.

A personalized 3D breast model could present a real benefit for preoperative discussion with patients, surgical planning, and guidance. Breast tissue biomechanical properties have been poorly studied in vivo, although they are important for breast deformation simulation. The main objective of our study was to determine breast skin thickness and breast skin and adipose/fibroglandular tissue stiffness. The secondary objective was to assess clinical predictors of elasticity and thickness: age, smoking status, body mass index, contraception, pregnancies, breastfeeding, menopausal status, history of radiotherapy or breast surgery. Participants were included at the Montpellier University Breast Surgery Department from March to May 2022. Breast skin thickness was measured by ultrasonography, breast skin and adipose/fibroglandular tissue stiffnesses were determined with a VLASTIC non-invasive aspiration device at three different sites (breast segments I-III). Multivariable linear models were used to assess clinical predictors of elasticity and thickness. In this cohort of 196 women, the mean breast skin and adipose/fibroglandular tissue stiffness values were 39 and 3 kPa, respectively. The mean breast skin thickness was 1.83 mm. Only menopausal status was significantly correlated with breast skin thickness and adipose/fibroglandular tissue stiffness. The next step will be to implement these stiffness and thickness values in a biomechanical breast model and to evaluate its capacity to predict breast tissue deformations.

Micro-CT and high-field MRI for studying very early post-mortem human fetal anatomy at 8 weeks of gestation.

OBJECTIVE: This study involved very early post-mortem (PM) examination of human fetal anatomy at 8 weeks of gestation (WG) using whole-body multimodal micro-imaging: micro-CT and high-field MRI (HF-MRI). We discuss the potential place of this imaging in early first-trimester virtual autopsy. METHODS: We performed micro-CT after different contrast-bath protocols including diffusible iodine-based contrast-enhanced (dice) and HF-MRI with a 9.4 T machine with qualitative and quantitative evaluation and obtained histological sections. RESULTS: Nine fetuses were included: the crown-rump length was 10-24 mm and corresponded to 7 and 9 WG according to the Robinson formula. The Carnegie stages were 17-21. Dice micro-CT and HF-MRI presented high signal to noise ratio, >5, according to the Rose criterion, and for allowed anatomical phenotyping in these specimens. Imaging did not alter the histology, allowing immunostaining and pathological examination. CONCLUSION: PM non-destructive whole-body multimodal micro-imaging: dice micro-CT and HF-MRI allows for PM human fetal anatomy study as early as 8 WG. It paves the way to virtual autopsy in the very early first trimester. Obtaining a precision phenotype, even regarding miscarriage products, allows a reverse phenotyping to select variants of interest in genome-wide analysis, offering potential genetic counseling for bereaved parents.

Combinatorial Maps, a New Framework to Model Agroforestry Systems.

Agroforestry systems are complex due to the diverse interactions between their elements, and they develop over several decades. Existing numerical models focus either on the structure or on the functions of agroforestry systems. However, both of these aspects are necessary, as function influences structure and vice versa. Here, we present a representation of agroforestry systems based on combinatorial maps (which are a type of multidimensional graphs), that allows conceptualizing the structure-function relationship at the agroecosystem scale. We show that such a model can represent the structure of agroforestry systems at multiple scales and its evolution through time. We propose an implementation of this framework, coded in Python, which is available on GitHub. In the future, this framework could be coupled with knowledge based or with biophysical simulation models to predict the production of ecosystem services. The code can also be integrated into visualization tools. Combinatorial maps seem promising to provide a unifying and generic description of agroforestry systems, including their structure, functions, and dynamics, with the possibility to translate to and from other representations.

Dynamic three-dimensional virtual environment to improve learning of anatomical structures.

Increasing number of medical students and limited availability of cadavers have led to a reduction in anatomy teaching through human cadaveric dissection. These changes triggered the emergence of innovative teaching and learning strategies in order to maximize students learning of anatomy. An alternative approach to traditional dissection was presented in an effort to improve content delivery and student satisfaction. The objective of this study is to acquire three-dimensional (3D) anatomical data using structured-light surface scanning to create a dynamic four-dimensional (4D) dissection tool of four regions: neck, male inguinal and femoral areas, female perineum, and brachial plexus. At each dissection step, identified anatomical structures were scanned using a 3D surface scanner (Artec Spider™). Resulting 3D color meshes were overlaid to create a 4D (3D+time) environment. An educational interface was created for neck dissection. Its implementation in the visualization platform allowed 4D virtual dissection by navigating from surface to deep layers and vice versa. A group of 28 second-year medical students and 17 first-year surgery residents completed a satisfaction survey. A majority of medical students (96.4%) and 100% of surgery residents said that they would recommend this tool to their colleagues. According to surgery residents, the main elements of this virtual tool were the realistic high-quality of 3D acquisitions and possibility to focus on each anatomical structure. As for medical students, major elements were the interactivity and entertainment aspect, precision, and accuracy of anatomical structures. This approach proves that innovative solutions to anatomy education can be found to help to maintain critical content and student satisfaction in anatomy curriculum.

Shape-changing chains for morphometric analysis of 2D and 3D, open or closed outlines.

Morphometrics is a multivariate technique for shape analysis widely employed in biological, medical, and paleoanthropological applications. Commonly used morphometric methods require analyzing a huge amount of variables for problems involving a large number of specimens or complex shapes. Moreover, the analysis results are sometimes difficult to interpret and assess. This paper presents a methodology to synthesize a shape-changing chain for 2D or 3D curve fitting and to employ the chain parameters in stepwise discriminant analysis (DA). The shape-changing chain is comprised of three types of segments, including rigid segments that have fixed length and shape, scalable segments with a fixed shape, and extendible segments with constant curvature and torsion. Three examples are presented, including 2D mandible profiles of fossil hominin, 2D leaf outlines, and 3D suture curves on infant skulls. The results demonstrate that the shape-changing chain has several advantages over common morphometric methods. Specifically, it can be applied to a wide range of 2D or 3D profiles, including open or closed curves, and smooth or serrated curves. Additionally, the segmentation of profiles is a flexible and automatic protocol that can consider both biological and geometric features, the number of variables obtained from the fitting results for statistical analysis is modest, and the chain parameters that characterize the profiles can have physical meaning.

Feasibility of Cochlea High-frequency Ultrasound and Microcomputed Tomography Registration for Cochlear Computer-assisted Surgery: A Testbed.

INTRODUCTION: There remains no standard imaging method that allows computer-assisted surgery of the cochlea in real time. However, recent evidence suggests that high-frequency ultrasound (HFUS) could permit real-time visualization of cochlear architecture. Registration with an imaging modality that suffers neither attenuation nor conical deformation could reveal useful anatomical landmarks to surgeons. Our study aimed to address the feasibility of an automated three-dimensional (3D) HFUS/microCT registration, and to evaluate the identification of cochlear structures using 2D/3D HFUS and microCT. METHODS: MicroCT, and 2D/3D 40 MHz US in B-mode were performed on ex vivo guinea pig cochlea. An automatic rigid registration algorithm was applied to segmented 3D images. This automatic registration was then compared to a reference method using manual annotated landmarks placed by two senior otologists. Inter- and intrarater reliabilities were evaluated using intraclass correlation coefficient (ICC) and the mean registration error was calculated. RESULTS: 3D HFUS/microCT automatic registration was successful. Excellent levels of concordance were achieved with regards intra-rater reliability for both raters with micro-CT and US images (ICC ranging from 0.98 to 1, p < 0.001) and with regards inter-rater reliability (ICC ranging from 0.99 to 1, p < 0.001). The mean HFUS/microCT automated RE for both observers was 0.17 ±â€Š0.03 mm [0.10-0.25]. Identification of the basilar membrane, modiolus, scala tympani, and scala vestibuli was possible with 2D/3D HFUS and micro-CT. CONCLUSIONS: HFUS/microCT image registration is feasible. 2D/3D HFUS and microCT allow the visualization of cochlear structures. Many potential clinical applications are conceivable.

Are endocasts reliable proxies for brains? A 3D quantitative comparison of the extant human brain and endocast.

Endocasts (i.e., replicas of the inner surface of the bony braincase) constitute a critical proxy for qualifying and quantifying variations in brain shape and organization in extinct taxa. In the absence of brain tissues preserved in the fossil record, endocasts provide the only direct evidence of brain evolution. However, debates on whether or not information inferred from the study of endocasts reflects brain shape and organization have polarized discussions in paleoneurology since the earliest descriptions of cerebral imprints in fossil hominin crania. By means of imaging techniques (i.e., MRIs and CT scans) and 3D modelling methods (i.e., surface-based comparisons), we collected consistent morphological (i.e., shape) and structural (i.e., sulci) information on the variation patterns between the brain and the endocast based on a sample of extant human individuals (N = 5) from the 3D clinical image database of the Steve Biko Academic Hospital in Pretoria (South Africa) and the Hôpitaux Universitaires Pitié Salpêtrière in Paris (France). Surfaces of the brain and endocast of the same individual were segmented from the 3D MRIs and CT images, respectively. Sulcal imprints were automatically detected. We performed a deformation-based shape analysis to compare both the shape and the sulcal pattern of the brain and the endocast. We demonstrated that there is close correspondence in terms of morphology and organization between the brain and the corresponding endocast with the exception of the superior region. By comparatively quantifying the shape and organization of the brain and endocast, this work represents an important reference for paleoneurological studies.

HFUS Imaging of the Cochlea: A Feasibility Study for Anatomical Identification by Registration with MicroCT.

Cochlear implantation consists in electrically stimulating the auditory nerve by inserting an electrode array inside the cochlea, a bony structure of the inner ear. In the absence of any visual feedback, the insertion results in many cases of damages of the internal structures. This paper presents a feasibility study on intraoperative imaging and identification of cochlear structures with high-frequency ultrasound (HFUS). 6 ex-vivo guinea pig cochleae were subjected to both US and microcomputed tomography (µCT) we respectively referred as intraoperative and preoperative modalities. For each sample, registration based on simulating US from the scanner was performed to allow a precise matching between the visible structures. According to two otologists, the procedure led to a target registration error of 0.32 mm ± 0.05. Thanks to referring to a better preoperative anatomical representation, we were able to intraoperatively identify the modiolus, both scalae vestibuli and tympani and deduce the location of the basilar membrane, all of which is of great interest for cochlear implantation. Our main objective is to extend this procedure to the human case and thus provide a new tool for inner ear surgery.

Author Correction: A new method to control error rates in automated species identification with deep learning algorithms.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A new method to control error rates in automated species identification with deep learning algorithms.

Processing data from surveys using photos or videos remains a major bottleneck in ecology. Deep Learning Algorithms (DLAs) have been increasingly used to automatically identify organisms on images. However, despite recent advances, it remains difficult to control the error rate of such methods. Here, we proposed a new framework to control the error rate of DLAs. More precisely, for each species, a confidence threshold was automatically computed using a training dataset independent from the one used to train the DLAs. These species-specific thresholds were then used to post-process the outputs of the DLAs, assigning classification scores to each class for a given image including a new class called "unsure". We applied this framework to a study case identifying 20 fish species from 13,232 underwater images on coral reefs. The overall rate of species misclassification decreased from 22% with the raw DLAs to 2.98% after post-processing using the thresholds defined to minimize the risk of misclassification. This new framework has the potential to unclog the bottleneck of information extraction from massive digital data while ensuring a high level of accuracy in biodiversity assessment.

Automatic extraction of the 3D symmetry line of back surface: application on scoliotic adolescents.

We propose a new method to extract automatically the symmetry line of the 3D back surface of patients affected by scoliosis. Our method is based on the detection of local symmetry planes computed on thick layers of the back. Results have been obtained on a sample of 112 scoliotic adolescents and we compare the symmetry line obtained by our method with a reference line defined by clinicians. We also study the influence of the scoliosis severity and of the Body Mass Index on the results.

The endocranial shape of Australopithecus africanus: surface analysis of the endocasts of Sts 5 and Sts 60.

Assessment of global endocranial morphology and regional neuroanatomical changes in early hominins is critical for the reconstruction of evolutionary trajectories of cerebral regions in the human lineage. Early evidence of cortical reorganization in specific local areas (e.g. visual cortex, inferior frontal gyrus) is perceptible in the non-human South African hominin fossil record. However, to date, little information is available regarding potential global changes in the early hominin brain. The introduction of non-invasive imaging techniques opens up new perspectives for the study of hominin brain evolution. In this context, our primary aim in this study is to explore the organization of the Australopithecus africanus endocasts, and highlight the nature and extent of the differences distinguishing A. africanus from the extant hominids at both local and global scales. By means of X-ray-based imaging techniques, we investigate two A. africanus specimens from Sterkfontein Member 4, catalogued as Sts 5 and Sts 60, respectively a complete cranium and a partial cranial endocast. Endocrania were virtually reconstructed and compared by using a landmark-free registration method based on smooth and invertible surface deformation. Both local and global information provided by our deformation-based approach are used to perform statistical analyses and topological mapping of inter-specific variation. Statistical analyses indicate that the endocranial shape of Sts 5 and Sts 60 approximates the Pan condition. Furthermore, our study reveals substantial differences with respect to the extant human condition, particularly in the parietal regions. Compared with Pan, the endocranial shape of the fossil specimens differs in the anterior part of the frontal gyri.

Geometric and mechanical evaluation of 3D-printing materials for skull base anatomical education and endoscopic surgery simulation - A first step to create reliable customized simulators.

INTRODUCTION: Endoscopic skull base surgery allows minimal invasive therapy through the nostrils to treat infectious or tumorous diseases. Surgical and anatomical education in this field is limited by the lack of validated training models in terms of geometric and mechanical accuracy. We choose to evaluate several consumer-grade materials to create a patient-specific 3D-printed skull base model for anatomical learning and surgical training. METHODS: Four 3D-printed consumer-grade materials were compared to human cadaver bone: calcium sulfate hemihydrate (named Multicolor), polyamide, resin and polycarbonate. We compared the geometric accuracy, forces required to break thin walls of materials and forces required during drilling. RESULTS: All materials had an acceptable global geometric accuracy (from 0.083mm to 0.203mm of global error). Local accuracy was better in polycarbonate (0.09mm) and polyamide (0.15mm) than in Multicolor (0.90mm) and resin (0.86mm). Resin and polyamide thin walls were not broken at 200N. Forces needed to break Multicolor thin walls were 1.6-3.5 times higher than in bone. For polycarbonate, forces applied were 1.6-2.5 times higher. Polycarbonate had a mode of fracture similar to the cadaver bone. Forces applied on materials during drilling followed a normal distribution except for the polyamide which was melted. Energy spent during drilling was respectively 1.6 and 2.6 times higher on bone than on PC and Multicolor. CONCLUSION: Polycarbonate is a good substitute of human cadaver bone for skull base surgery simulation. Thanks to short lead times and reasonable production costs, patient-specific 3D printed models can be used in clinical practice for pre-operative training, improving patient safety.

Method to evaluate the noise of 3D intra-oral scanner.

In dentistry, 3D intra-oral scanners are gaining increasing popularity essentially for the production of dental prostheses. However, there is no normalized procedure to evaluate their basic performance and enable comparisons among intra-oral scanners. The noise value highlights the trueness of a 3D intra-oral scanner and its capacity to plan prosthesis with efficient clinical precision. The aim of the present study is to develop a reproducible methodology for determining the noise of an intra-oral scanner. To this aim, and as a reference, an ultra-flat and ultra-smooth alumina wafer is used as a blank test. The roughness is calculated using an AFM (atomic force microscope) and interferometric microscope measurements to validate this ultra-flat characteristic. Then, two intra-oral scanners (Carestream CS3500 and Trios 3Shape) are used. The wafer is imaged by the two intra-oral scanners with three different angles and two different directions, 10 times for each parameter, given a total of 50 3D-meshes per intra-oral scanner. RMS (root mean square), representing the noise, is evaluated and compared for each angle/direction and each intra-oral scanner, for the whole mesh, and then in a central ROI (region of interest). In this study, we obtained RMS values ranging between 5.29 and 12.58 micrometers. No statistically significant differences were found between the mean RMS of the two intra-oral scanners, but significant differences in angulation and orientations were found between different 3D intra-oral scanners. This study shows that the evaluation of RMS can be an indicator of the value of the noise, which can be easily assessed by applying the present methodology.

Cerebrospinal fluid volume does not have etiological role in the incidence of positional skull deformities.

BACKGROUND: Positional skull deformities (PSD) are becoming a daily health concern for craniofacial surgeons. Several reports have indicated that cerebrospinal fluid (CSF) space increases on computed tomography (CT) scans of infants suffering from PSD, suggesting a potential causal link. Here, we describe a semi-automatic method to estimate total brain and CSF volumes quantitatively. We tested the potential correlation between total CSF volume and the occurrence of PSD. METHODS: A single-center retrospective study was carried out using 79 CT scans of PSD and 60 CT scans of control subjects. The endocranium was segmented automatically using a three-dimensional deformable surface model, and the brain was segmented using a semi-automatic threshold-based method. Total CSF volume was estimated based on the difference between endocranial and brain volumes. RESULTS: Automatic segmentation of the endocranium was possible in 75 CT scans. Semi-automatic brain and CSF volume evaluations were performed in 40 CT scans of infants with PSD (18 = occipital plagiocephaly, 11 = fronto-occipital plagiocephaly, and 11 = posterior brachycephaly) and in six control CT scans. Endocranial and total CSF volumes were not significantly different between patients with PSD and controls. The occipital plagiocephaly group had an enlarged brain volume compared with that in patients in the other groups. CONCLUSIONS: Total CSF volume did not change in infants with PSD, and the results do not support a role for volume changes in CSF in the etiology of PSD. Macrocephaly in patients with occipital plagiocephaly may be a specific etiological factor compared with that in other PSDs.