Laplace-Beltrami Refined Shape Regression Applied to Neck Reconstruction for Craniosynostosis Patients

This contribution is part of a project concerning the creation of an artificial dataset comprising 3D head scans of craniosynostosis patients for a deep-learning-based classification. To conform to real data, both head and neck are required in the 3D scans. However, during patient recording, the neck is often covered by medical staff. Simply pasting an arbitrary neck leaves large gaps in the 3D mesh. We therefore use a publicly available statistical shape model (SSM) for neck reconstruction. However, most SSMs of the head are constructed using healthy subjects, so the full head reconstruction loses the craniosynostosis-specific head shape. We propose a method to recover the neck while keeping the pathological head shape intact. We propose a Laplace- Beltrami-based refinement step to deform the posterior mean shape of the full head model towards the pathological head. The artificial neck is created using the publicly available Liverpool-York-Model. We apply our method to construct artificial necks for head scans of 50 scaphocephaly patients. Our method reduces mean vertex correspondence error by approximately 1.3 mm compared to the ordinary posterior mean shape, preserves the pathological head shape, and creates a continuous transition between neck and head. The presented method showed good results for reconstructing a plausible neck to craniosynostosis patients. Easily generalized it might also be applicable to other pathological shapes.

On the fuzziness of circulation types derived from the application of obliquely rotated principal component analysis to a T-mode climatic field

This study examined the separability of circulation types (CTs) classified from the application of principal component analysis (PCA) to the T-mode matrix (variable is time series and observation is grid points) of a climatic field that explains atmospheric circulation; in addition to the uncertainty introduced on (i) the probability of occurrence, (ii) the mean shape of the CTs, (iii) the trend in the annual frequency of occurrence, (iv) the frequency distribution of the CTs, by using varying threshold values within the range of 0.2–0.35 to assign days to a given CT. The study region is Africa, south of the equator. Some large clusters were classified with most days in the analysis period assigned to them; these classes are interpreted as the dominant states of the atmosphere and generally, their existence results in the poor separability of the CTs since their features overlap with other CTs. Qualitatively, the choice of the threshold values within the defined range has little or no influence on the overall structure of the probability of occurrence of the CTs, the mean shape of the CTs, and the year-to-year variations in the annual occurrence of the CTs. However, it significantly impacts the frequency distribution of the CTs and the statistical significance of the trend in the annual occurrence of the CTs. Stringent threshold values within the defined range might benefit studies that aim to isolate days when specific CTs are most expressed and analyze their mechanism using composite maps, without focus on the frequency distribution and annual occurrence of the CTs. Overall, for the study region, lower threshold values within the defined range might be recommended since relatively, they do not tend to further constrain the probability of group membership, and equally seem to reveal the mechanisms that might be consistent when a given CT occurred regardless of the strength of its signal at a given time.

Analysis of the Habitat Fragmentation of Ecosystems in Belize Using Landscape Metrics

Landscape metrics have been of game changing importance in the analysis of ecosystems’ composition and landscape cohesion. With the increasing urban and agricultural expansion, the natural flora and fauna of many highly diverse areas have been degraded. Fragmentation of ecosystems and habitats have stressed the biodiversity of Belize. To understand the dynamics of this change, a study was conducted using three moderately separate years of ecosystem landscape data. The metrics used for the analysis were area-weighted mean shape index (AWMSI), mean shape index (MSI), edge density (ED), mean patch size (MPS), number of patches (NUMP), and class area (CA). These metrics were produced for the years 2001, 2011, and 2017. The classes of agricultural use, lowland savannas, mangroves and littoral forests, urban, and wetlands were the subjects for analysis. Using the GIS extension Patch Analyst, parametric runs were performed. From these results, a one-way ANOVA test of the NUMP, Tukey HSD test, and Scheffé Multiple Comparison test were performed. The results indicate that there has been significant habitat fragmentation, especially from the years 2001 to 2011. Agricultural areas increased by 19.37% in just 10 years, with the NUMP of some habitats increasing by 284%. The results also show fluctuation in ED and a decrease in overall MPS, all indicating high fragmentation. These changes have been mostly induced due to the expansion of agricultural activities and urbanization, especially in the northern parts of Belize. It is imperative that additional policies be implemented to deter the effects of habitat fragmentation upon the existing ecosystems of Belize and elsewhere.

When the presence of a vateritic otolith has morphological effect on its aragonitic partner: trans-lateral compensation induces bias in microecological patterns in one-side-only vateritic otolith

In many teleost species, aragonite is the normal form of calcium carbonate in sagittal otoliths. In the case of one-side-only (OSO) vateritic otoliths (abnormal crystalline structure), morphological investigations are systematically conducted on the other side. The implicit assumption is that the morphological information on the aragonitic side remains unaffected by the presence of vaterite on the other side. However, the extent to which this assumption is met has never been explored. Applying geometric morphometrics on experimentally maintained brown trout (Salmo trutta) revealed incongruent variational patterns and mean shape differences between OSO and two-sided aragonitic otoliths, possibly due to trans-lateral compensation to preserve their auditory function. More specifically, fully aragonitic pairs of otoliths are more prone to exhibit microecological variations compared with OSO vateritic pairs. Simulation emphasizes the relative robustness of both micro- and macroecological effects until a high proportion of OSO vateritic otoliths is used. Given that otolith shape analysis provides a useful basis for stock separation, care should be taken when interpreting otolith shape in the presence of vateritic otoliths.

A Registration and Deep Learning Approach to Automated Landmark Detection for Geometric Morphometrics

ABSTRACTGeometric morphometrics is the statistical analysis of landmark-based shape variation and its covariation with other variables. Over the past two decades, the gold standard of landmark data acquisition has been manual detection by a single observer. This approach has proven accurate and reliable in small-scale investigations. However, big data initiatives are increasingly common in biology and morphometrics. This requires fast, automated, and standardized data collection. Image registration, or the spatial alignment of images, is a fundamental technique in automatic image analysis that is well-poised for such purposes. Yet, in the few studies that have explored the utility of registration-based landmarks for geometric morphometrics, relatively high or catastrophic labelling errors around anatomical extrema are common. Such errors can result in misleading representations of the mean shape, an underestimation of biological signal, and altered variance-covariance patterns.We combine image registration with a deep and domain-specific neural network to automate and optimize anatomical landmark detection for geometric morphometrics. Using micro-computed tomography images of genetically and morphologically variable mouse skulls, we test our landmarking approach under a variety of registration conditions, including different non-linear deformation frameworks (small vs. large) and atlas strategies (single vs. multi).Compared to landmarks derived from conventional image registration workflows, our optimized landmark data show significant reductions in error at problematic locations (up to 0.63 mm), a 36.4% reduction in average landmark coordinate error, and up to a 45.1% reduction in total landmark distribution error. We achieve significant improvements in estimates of the sample mean shape and variance-covariance structure.For biological imaging datasets and morphometric research questions, our method can eliminate the time and subjectivity of manual landmark detection whilst retaining the biological integrity of these expert annotations.

The occasional perils of reflection (across the midline; in geometric morphometrics)

Manually collecting landmark data on a large biological sample takes a long time. Several options exist to speed data collection, though each strategy introduces problems or raises concerns of its own. For bilaterally symmetric structures (e.g., crania), some recent papers recommend limiting landmark collection to one side and the midline, then “mirror-reflecting” landmarks across the midline to produce an approximation of the true bilateral configuration. However, where the midline is narrow relative to the bilateral anatomy, net midline landmark deviations from the mid-sagittal axis or plane will distort the mirror-reflected configuration. Here, I test whether this is a substantive concern at the scale of real biology. To do so, I simulate small amounts of mediolateral error on the mean shape from a sample of human mandibles (n = 178), then compare the distribution of simulated forms to variation in the data. I also test how faithfully mirror-reflected configurations replicate bilateral shape and size relationships. In both analyses, midline deviations from symmetry create striking distortions. I go on to show that incorporating a small number of landmarks from the opposite side of the mandible produces far more accurate estimates of bilateral shape than does mirror reflection. Mirror reflection is clearly inappropriate for these data and is likely suspect in all cases of narrow midline morphology.