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Standard methods for modeling anaerobic digestion processes assume homogeneous conditions inside the tank and thus suffer from the negligence of hydrodynamics. In this work, we present the software toolbox Coupled Hydrodynamics and Anaerobic Digestion (CHAD), a novel parallelized solver that is capable of utilizing CFD results as the basis for Anaerobic digestion model No.1 (ADMno1) simulations. CHAD uses a particle-based Lagrangian CFD solver i.e., DualSPHysics (DSPH) as input and provides for a parallelized, C++ code implementation of the standard ADMno1. This paper demonstrates a conceptual and numerical verification of the toolbox and outlines the future pathway to enhance the approach., Comment: conference paper

Optical coherence tomography angiography (OCTA) is a non-invasive imaging modality that can acquire high-resolution volumes of the retinal vasculature and aid the diagnosis of ocular, neurological and cardiac diseases. Segmenting the visible blood vessels is a common first step when extracting quantitative biomarkers from these images. Classical segmentation algorithms based on thresholding are strongly affected by image artifacts and limited signal-to-noise ratio. The use of modern, deep learning-based segmentation methods has been inhibited by a lack of large datasets with detailed annotations of the blood vessels. To address this issue, recent work has employed transfer learning, where a segmentation network is trained on synthetic OCTA images and is then applied to real data. However, the previously proposed simulations fail to faithfully model the retinal vasculature and do not provide effective domain adaptation. Because of this, current methods are unable to fully segment the retinal vasculature, in particular the smallest capillaries. In this work, we present a lightweight simulation of the retinal vascular network based on space colonization for faster and more realistic OCTA synthesis. We then introduce three contrast adaptation pipelines to decrease the domain gap between real and artificial images. We demonstrate the superior segmentation performance of our approach in extensive quantitative and qualitative experiments on three public datasets that compare our method to traditional computer vision algorithms and supervised training using human annotations. Finally, we make our entire pipeline publicly available, including the source code, pretrained models, and a large dataset of synthetic OCTA images., Comment: Currently under review

Accurate segmentation of connective soft tissues is still a challenging task, which hinders the generation of corresponding geometric models for biomechanical computations. Alternatively, one could predict ligament insertion sites and then approximate the shapes, based on anatomical knowledge and morphological studies. Here, we describe a corresponding integrated framework for the automatic modelling of human musculoskeletal ligaments. We combine statistical shape modelling with geometric algorithms to automatically identify insertion sites, based on which geometric surface and volume meshes are created. For demonstrating a clinical use case, the framework has been applied to generate models of the interosseous membrane in the forearm. For the adoption to the forearm anatomy, ligament insertion sites in the statistical model were defined according to anatomical predictions following an approach proposed in prior work. For evaluation we compared the generated sites, as well as the ligament shapes, to data obtained from a cadaveric study, involving five forearms with a total of 15 ligaments. Our framework permitted the creation of 3D models approximating ligaments' shapes with good fidelity. However, we found that the statistical model trained with the state-of-the-art prediction of the insertion sites was not always reliable. Using that model, average mean square errors as well as Hausdorff distances of the meshes increased by more than one order of magnitude, as compared to employing the known insertion locations of the cadaveric study. Using the latter an average mean square error of 0.59 mm and an average Hausdorff distance of less than 7 mm resulted, for the complete set of ligaments. In conclusion, the presented approach for generating ligament shapes from insertion points appears to be feasible but the detection of the insertion sites with a SSM is too inaccurate., Comment: 16 pages, 8 figures