TY - CHAP A1 - Hoffmann, René A1 - Zachow, Stefan T1 - Non-invasive approach to shed new light on the buoyancy business of chambered cephalopods (Mollusca) T2 - Proc. of the Intl. Assoc. for Mathematical Geosciences, Salzburg Y1 - 2011 U6 - https://doi.org/10.5242/iamg.2011.0163 SP - 1 EP - 11 ER - TY - JOUR A1 - Rybak, Jürgen A1 - Kuß, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Lienhard, Matthias A1 - Singer, Jochen A1 - Neubert, Kerstin A1 - Menzel, Randolf T1 - The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System JF - Front. Syst. Neurosci. Y1 - 2010 U6 - https://doi.org/10.3389/fnsys.2010.00030 VL - 4 IS - 30 ER - TY - JOUR A1 - Galloway, Francis A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Worsley, Peter A1 - Zachow, Stefan A1 - Nair, Prasanth A1 - Taylor, Mark T1 - A large scale finite element study of a cementless osseointegrated tibial tray JF - Journal of Biomechanics Y1 - 2013 U6 - https://doi.org//10.1016/j.jbiomech.2013.04.021 VL - 46 IS - 11 SP - 1900 EP - 1906 ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Zöckler, Maja A1 - Haberl, Ernst T1 - Computergestützte Planung zur chirurgischen Korrektur von frühkindlichen Schädelfehlbildungen (Craniosynostosen) JF - Face 02/09, Int. Mag. of Orofacial Esthetics, Oemus Journale Leipzig Y1 - 2009 SP - 48 EP - 53 ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Pumberger, Matthias A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Influence of pelvic tilt on functional acetabular orientation JF - Technology and Health Care Y1 - 2016 U6 - https://doi.org/10.3233/THC-161281 VL - 25 IS - 3 SP - 557 EP - 565 PB - IOS Press ER - TY - JOUR A1 - Lemanis, Robert A1 - Korn, Dieter A1 - Zachow, Stefan A1 - Rybacki, Erik A1 - Hoffmann, René T1 - The Evolution and Development of Cephalopod Chambers and Their Shape JF - PLOS ONE N2 - The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0151404 VL - 11 IS - 3 ER - TY - JOUR A1 - Dunlop, Jason A1 - Apanaskevich, Dmitry A1 - Lehmann, Jens A1 - Hoffmann, Rene A1 - Fusseis, Florian A1 - Ehlke, Moritz A1 - Zachow, Stefan A1 - Xiao, Xianghui T1 - Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus JF - BMC Evolutionary Biology N2 - Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases. Y1 - 2016 U6 - https://doi.org/10.1186/s12862-016-0777-y VL - 16 IS - 1 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse Data JF - arXiv N2 - The reconstruction of an object's shape or surface from a set of 3D points is a common topic in materials and life sciences, computationally handled in computer graphics. Such points usually stem from optical or tactile 3D coordinate measuring equipment. Surface reconstruction also appears in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or the alignment of intra-operative navigation and preoperative planning data. In contrast to mere 3D point clouds, medical imaging yields contextual information on the 3D point data that can be used to adopt prior information on the shape that is to be reconstructed from the measurements. In this work we propose to use a statistical shape model (SSM) as a prior for surface reconstruction. The prior knowledge is represented by a point distribution model (PDM) that is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we reformulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given measurements are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are oriented according to the surface normals at the PDM points, a surface-based tting is accomplished. By estimating the parameters of the GMM in a maximum a posteriori manner, the reconstruction of the surface from the given measurements is achieved. Extensive experiments suggest that our proposed approach leads to superior surface reconstructions compared to Iterative Closest Point (ICP) methods. Y1 - 2016 SP - 1602.08425v1 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Hoffmann, René T1 - Comparative cephalopod shell strength and the role of septum morphology on stress distribution JF - PeerJ N2 - The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio used to characterize septal morphology in the septal strength index and in calculations of tensile strength of nacre are likely insufficient. A better understanding of the material properties of cephalopod nacre may allow the estimation of maximum depth limits of shelled cephalopods through finite element analysis. Y1 - 2016 U6 - https://doi.org/10.7717/peerj.2434 VL - 4 SP - e2434 ER - TY - JOUR A1 - Brüning, Jan A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Numerical Analysis of Nasal Breathing - A Pilot Study JF - Facial Plastic Surgery N2 - Background: Currently, there is no fully sufficient way to differentiate between symptomatic and normal nasal breathing. Using the nose’s total resistance is disputed as a valid means to objectify nasal airflow, and the need for a more comprehensive diagnostic method is increasing. This work’s aim was to test a novel approach considering intranasal wall shear stress as well as static pressure maps obtained by computational fluid dynamics (CFD). Methods: X-ray computed tomography (CT) scan data of six symptom-free subjects and seven symptomatic patients were used. Patient-specific geometries of the nasal cavity were segmented from these data sets. Inspiratory and expiratory steady airflow simulations were performed using CFD. Calculated static pressures and wall shear stresses (WSS) were mapped onto a common template of the nasal septum, allowing for comparison of these parameters between the two patient groups. Results: Significant differences in wall shear stress distributions during the inspiratory phase could be identified between the two groups, whereas no differences were found for the expiratory phase. It is assumed that one essential feature of normal nasal breathing probably consists in distinctively different intranasal flow fields for inspiration and expiration. This is in accordance with previous investigations. Conclusion: The proposed method seems to be a promising tool for developing a new kind of patient-specific assessment of nasal breathing. However, more studies and a greater case number of data with an expanded focus, would be ideal. Y1 - 2017 U6 - https://doi.org/doi:10.1055/s-0037-1603789 VL - 33 IS - 4 SP - 388 EP - 395 ER - TY - GEN A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. From that we identify the most crucial parameters to measure or estimate, and obtain a local uncertainty quantifcation for the ToD. T3 - ZIB-Report - 17-18 KW - forensic medicine KW - determination of time of death KW - heat transfer equation KW - sensitivity i.r.t. thermal parameters KW - sensitivity i.r.t. geometric resolution Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63818 SN - 1438-0064 ER - TY - CHAP A1 - Baum, Daniel A1 - Mahlow, Kristin A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Müller, Johannes A1 - Hege, Hans-Christian T1 - The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis) T2 - Abstract in DigitalSpecimen 2014 N2 - Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term ‘surface-based morphometrics’. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called ‘surface paths’, might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique. Y1 - 2014 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Wilson, Dave A1 - Anglin, Carolyn A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data N2 - In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients’ distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated. T3 - ZIB-Report - 17-71 KW - Knee Arthroplasty KW - Sparse Geometry Reconstruction KW - Statistical Shape Models Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66052 SN - 1438-0064 ER - TY - GEN A1 - Joachimsky, Robert A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung früher Gonarthrose N2 - Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein häufiges Krankheitsbild unter älteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder geschädigter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfläche erhöhen und so der teilweise oder vollständige Gelenkersatz hinausgezögert oder vermieden werden. In dieser Arbeit präsentieren wir eine Planungssoftware für die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgewählt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. Für jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern Rückmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterstützt somit als Entscheidungshilfe die behandelnden Ärzte bei der patientenspezifischen Spacerauswahl. T3 - ZIB-Report - 17-72 KW - Osteoarthrose KW - Kniegelenk KW - Medizinische Planung KW - Visualisierung Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66064 SN - 1438-0064 ER - TY - JOUR A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death JF - Heat and Mass Transfer N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. Y1 - 2018 U6 - https://doi.org/10.1007/s00231-018-2324-4 VL - 54 IS - 9 SP - 2815 EP - 2826 PB - Springer ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds JF - Medical Image Analysis N2 - The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. Y1 - 2017 UR - http://www.sciencedirect.com/science/article/pii/S1361841517300233 U6 - https://doi.org/10.1016/j.media.2017.02.005 VL - 38 SP - 77 EP - 89 ER - TY - JOUR A1 - Lube, Juliane A1 - Flack, Natasha A1 - Cotofana, Sebastian A1 - Özkurtul, Orkun A1 - Woodley, Stephanie A1 - Zachow, Stefan A1 - Hammer, Niels T1 - Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature JF - Surgical and Radiologic Anatomy N2 - Purpose: Morphological data pertaining to the pelvis and lower extremity muscles are increasingly being used in biomechanical modeling to compare healthy and pathological conditions. Very few data sets exist that encompass all of the muscles of the lower limb, allowing for comparisons between regions. The aims of this study were to (a) provide physiological cross-sectional area (PCSA) data for the pelvic, thigh, and leg muscles in young, healthy participants, using magnetic resonance imaging (MRI), and (b) to compare these data with summarized PCSAs obtained from the literature. Materials and Methods: Six young and healthy volunteers participated and were scanned using 3 T MRI. PCSAs were calculated from volumetric segmentations obtained bilaterally of 28 muscles/muscle groups of the pelvis, thigh, and leg. These data were compared to published, summarized PCSA data derived from cadaveric, computed tomography, MRI and ultrasound studies. Results: The PCSA of the pelvis, thigh, and leg muscles tended to be 20–130% larger in males than in females, except for the gemelli which were 34% smaller in males, and semitendinosus and triceps surae which did not differ (<20% different). The dominant and the non-dominant sides showed similar and minutely different PCSA with less than 18% difference between sides. Comparison to other studies revealed wide ranges within, and large differences between, the cadaveric and imaging PCSA data. Comparison of the PCSA of this study and published literature revealed major differences in the iliopsoas, gluteus minimus, tensor fasciae latae, gemelli, obturator internus, biceps femoris, quadriceps femoris, and the deep leg flexor muscles. Conclusions: These volume-derived PCSAs of the pelvic and lower limb muscles alongside the data synthesised from the literature may serve as a basis for comparative and biomechanical studies of the living and healthy young, and enable calculation of muscle forces. Comparison of the literature revealed large variations in PCSA from each of the different investigative modalities, hampering omparability between studies. Sample size, age, post-mortem changes of muscle tone, chemical fixation of cadaveric tissues, and the underlying physics of the imaging techniques may potentially influence PCSA calculations. Y1 - 2017 U6 - https://doi.org/10.1007/s00276-016-1807-6 VL - 39 IS - 8 SP - 849 EP - 857 ER - TY - CHAP A1 - Mukhopadhyay, Anirban A1 - Morillo, Oscar A1 - Zachow, Stefan A1 - Lamecker, Hans T1 - Robust and Accurate Appearance Models Based on Joint Dictionary Learning Data from the Osteoarthritis Initiative T2 - Lecture Notes in Computer Science, Patch-Based Techniques in Medical Imaging. Patch-MI 2016 N2 - Deformable model-based approaches to 3D image segmentation have been shown to be highly successful. Such methodology requires an appearance model that drives the deformation of a geometric model to the image data. Appearance models are usually either created heuristically or through supervised learning. Heuristic methods have been shown to work effectively in many applications but are hard to transfer from one application (imaging modality/anatomical structure) to another. On the contrary, supervised learning approaches can learn patterns from a collection of annotated training data. In this work, we show that the supervised joint dictionary learning technique is capable of overcoming the traditional drawbacks of the heuristic approaches. Our evaluation based on two different applications (liver/CT and knee/MR) reveals that our approach generates appearance models, which can be used effectively and efficiently in a deformable model-based segmentation framework. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-47118-1_4 VL - 9993 SP - 25 EP - 33 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Szengel, Angelika A1 - Zachow, Stefan T1 - Addressing multi-label imbalance problem of Surgical Tool Detection using CNN JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: A fully automated surgical tool detection framework is proposed for endoscopic video streams. State-of-the-art surgical tool detection methods rely on supervised one-vs-all or multi-class classification techniques, completely ignoring the co-occurrence relationship of the tools and the associated class imbalance. Methods: In this paper, we formulate tool detection as a multi-label classification task where tool co-occurrences are treated as separate classes. In addition, imbalance on tool co-occurrences is analyzed and stratification techniques are employed to address the imbalance during Convolutional Neural Network (CNN) training. Moreover, temporal smoothing is introduced as an online post-processing step to enhance run time prediction. Results: Quantitative analysis is performed on the M2CAI16 tool detection dataset to highlight the importance of stratification, temporal smoothing and the overall framework for tool detection. Conclusion: The analysis on tool imbalance, backed by the empirical results indicates the need and superiority of the proposed framework over state-of-the-art techniques. Y1 - 2017 UR - https://link.springer.com/article/10.1007/s11548-017-1565-x U6 - https://doi.org/10.1007/s11548-017-1565-x N1 - Selected for final oral presentation VL - 12 IS - 6 SP - 1013 EP - 1020 PB - Springer ER - TY - JOUR A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Erdmann, Bodo A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Heinrich, Andreas A1 - Güttler, Felix Victor A1 - Teichgräber, Ulf A1 - Mall, Gita T1 - Automatic CT-based finite element model generation for temperature-based death time estimation: feasibility study and sensitivity analysis JF - International Journal of Legal Medicine N2 - Temperature based death time estimation is based either on simple phenomenological models of corpse cooling or on detailed physical heat transfer models. The latter are much more complex, but allow a higher accuracy of death time estimation as in principle all relevant cooling mechanisms can be taken into account. Here, a complete work flow for finite element based cooling simulation models is presented. The following steps are demonstrated on CT-phantoms: • CT-scan • Segmentation of the CT images for thermodynamically relevant features of individual geometries • Conversion of the segmentation result into a Finite Element (FE) simulation model • Computation of the model cooling curve • Calculation of the cooling time For the first time in FE-based cooling time estimation the steps from the CT image over segmentation to FE model generation are semi-automatically performed. The cooling time calculation results are compared to cooling measurements performed on the phantoms under controlled conditions. In this context, the method is validated using different CTphantoms. Some of the CT phantoms thermodynamic material parameters had to be experimentally determined via independent experiments. Moreover the impact of geometry and material parameter uncertainties on the estimated cooling time is investigated by a sensitivity analysis. KW - temperature based death time estimation KW - finite element method KW - CT segmentation KW - sensitivity analysis Y1 - 2017 U6 - https://doi.org/doi:10.1007/s00414-016-1523-0 VL - 131 IS - 3 SP - 699 EP - 712 ER - TY - JOUR A1 - Zachow, Stefan T1 - Computational Planning in Facial Surgery JF - Facial Plastic Surgery N2 - This article reflects the research of the last two decades in computational planning for cranio-maxillofacial surgery. Model-guided and computer-assisted surgery planning has tremendously developed due to ever increasing computational capabilities. Simulators for education, planning, and training of surgery are often compared with flight simulators, where maneuvers are also trained to reduce a possible risk of failure. Meanwhile, digital patient models can be derived from medical image data with astonishing accuracy and thus can serve for model surgery to derive a surgical template model that represents the envisaged result. Computerized surgical planning approaches, however, are often still explorative, meaning that a surgeon tries to find a therapeutic concept based on his or her expertise using computational tools that are mimicking real procedures. Future perspectives of an improved computerized planning may be that surgical objectives will be generated algorithmically by employing mathematical modeling, simulation, and optimization techniques. Planning systems thus act as intelligent decision support systems. However, surgeons can still use the existing tools to vary the proposed approach, but they mainly focus on how to transfer objectives into reality. Such a development may result in a paradigm shift for future surgery planning. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564717 VL - 31 IS - 5 SP - 446 EP - 462 ER - TY - GEN A1 - Lamas-Rodríguez, Julián A1 - Ehlke, Moritz A1 - Hoffmann, René A1 - Zachow, Stefan T1 - GPU-accelerated denoising of large tomographic data sets with low SNR BT - Application for non-invasive analysis of paleontological data N2 - Enhancements in tomographic imaging techniques facilitate non-destructive methods for visualizing fossil structures. However, to penetrate dense materials such as sediments or pyrites, image acquisition is typically performed with high beam energy and very sensitive image intensifiers, leading to artifacts and noise in the acquired data. The analysis of delicate fossil structures requires the images to be captured in maximum resolution, resulting in large data sets of several giga bytes (GB) in size. Since the structural information of interest is often almost in the same spatial range as artifacts and noise, image processing and segmentation algorithms have to cope with a very low signal-to-noise ratio (SNR). Within this report we present a study on the performance of a collection of denoising algorithms applied to a very noisy fossil dataset. The study shows that a non-local means (NLM) filter, in case it is properly configured, is able to remove a considerable amount of noise while preserving most of the structural information of interest. Based on the results of this study, we developed a software tool within ZIBAmira that denoises large tomographic datasets using an adaptive, GPU-accelerated NLM filter. With the help of our implementation a user can interactively configure the filter's parameters and thus its effectiveness with respect to the data of interest, while the filtering response is instantly visualized for a preselected region of interest (ROI). Our implementation efficiently denoises even large fossil datasets in a reasonable amount of time. T3 - ZIB-Report - 15-14 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56339 SN - 1438-0064 ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Pelvic tilt compensates for increased acetabular anteversion JF - International Orthopaedics N2 - Pelvic tilt determines functional orientation of the acetabulum. In this study, we investigated the interaction of pelvic tilt and functional acetabular anteversion (AA) in supine position. Y1 - 2015 U6 - https://doi.org/10.1007/s00264-015-2949-6 VL - 40 IS - 8 SP - 1571 EP - 1575 ER - TY - CHAP A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Statistical Shape Modeling of Musculoskeletal Structures and Its Applications T2 - Computational Radiology for Orthopaedic Interventions N2 - Statistical shape models (SSM) describe the shape variability contained in a given population. They are able to describe large populations of complex shapes with few degrees of freedom. This makes them a useful tool for a variety of tasks that arise in computer-aided madicine. In this chapter we are going to explain the basic methodology of SSMs and present a variety of examples, where SSMs have been successfully applied. Y1 - 2016 SN - 978-3-319-23481-6 U6 - https://doi.org/10.1007/978-3-319-23482-3 VL - 23 SP - 1 EP - 23 PB - Springer ER - TY - JOUR A1 - Zachow, Stefan A1 - Heppt, Werner T1 - The Facial Profile JF - Facial Plastic Surgery N2 - Facial appearance in our societies is often associated with notions of attractiveness, juvenileness, beauty, success, and so forth. Hence, the role of facial plastic surgery is highly interrelated to a patient's desire to feature many of these positively connoted attributes, which of course, are subject of different cultural perceptions or social trends. To judge about somebody's facial appearance, appropriate quantitative measures as well as methods to obtain and compare individual facial features are required. This special issue on facial profile is intended to provide an overview on how facial characteristics are surgically managed in an interdisciplinary way based on experience, instrumentation, and modern technology to obtain an aesthetic facial appearance with harmonious facial proportions. The facial profile will be discussed within the context of facial aesthetics. Latest concepts for capturing facial morphology in high speed and impressive detail are presented for quantitative analysis of even subtle changes, aging effects, or facial expressions. In addition, the perception of facial profiles is evaluated based on eye tracking technology. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1566132 VL - 31 IS - 5 SP - 419 EP - 420 ER - TY - CHAP A1 - Ramm, Heiko A1 - Victoria Morillo, Oscar Salvador A1 - Todt, Ingo A1 - Schirmacher, Hartmut A1 - Ernst, Arneborg A1 - Zachow, Stefan A1 - Lamecker, Hans ED - Freysinger, Wolfgang T1 - Visual Support for Positioning Hearing Implants T2 - Proceedings of the 12th annual meeting of the CURAC society Y1 - 2013 SP - 116 EP - 120 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Heller, Markus O. A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Omnidirectional Displacements for Deformable Surfaces JF - Medical Image Analysis Y1 - 2013 U6 - https://doi.org/10.1016/j.media.2012.11.006 VL - 17 IS - 4 SP - 429 EP - 441 PB - Elsevier ER - TY - JOUR A1 - Lamas-Rodríguez, Julián A1 - Heras, Dora Blanco A1 - Argüello, Francisco A1 - Kainmüller, Dagmar A1 - Zachow, Stefan A1 - Bóo, Montserrat T1 - GPU-accelerated level-set segmentation JF - Journal of Real-Time Image Processing Y1 - 2013 UR - http://dx.doi.org/10.1007/s11554-013-0378-6 U6 - https://doi.org/10.1007/s11554-013-0378-6 SN - 1861-8200 SP - 1 EP - 15 PB - Springer Berlin Heidelberg ER - TY - JOUR A1 - Hoffmann, René A1 - Schultz, Julia A. A1 - Schellhorn, Rico A1 - Rybacki, Erik A1 - Keupp, Helmut A1 - Gerden, S. R. A1 - Lemanis, Robert A1 - Zachow, Stefan T1 - Non-invasive imaging methods applied to neo- and paleontological cephalopod research JF - Biogeosciences N2 - Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied. Y1 - 2014 U6 - https://doi.org/10.5194/bg-11-2721-2014 N1 - To access the corresponding discussion paper go to www.biogeosciences-discuss.net/10/18803/2013/ - Biogeosciences Discuss., 10, 18803-18851, 2013 VL - 11 IS - 10 SP - 2721 EP - 2739 ER - TY - CHAP A1 - von Berg, Jens A1 - Dworzak, Jalda A1 - Klinder, Tobias A1 - Manke, Dirk A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Lorenz, Cristian T1 - Temporal Subtraction of Chest Radiographs Compensating Pose Differences T2 - SPIE Medical Imaging Y1 - 2011 ER - TY - CHAP A1 - Bindernagel, Matthias A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - An Articulated Statistical Shape Model of the Human Knee T2 - Bildverarbeitung für die Medizin 2011 Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-19335-4_14 SP - 59 EP - 63 PB - Springer ER - TY - CHAP A1 - Kahnt, Max A1 - Galloway, Francis A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Taylor, Mark A1 - Zachow, Stefan T1 - Robust and Intuitive Meshing of Bone-Implant Compounds T2 - CURAC Y1 - 2011 SP - 71 EP - 74 CY - Magdeburg ER - TY - GEN A1 - SK, Saevarsson A1 - GB, Sharma A1 - S, Montgomery A1 - KCT, Ho A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - C, Anglin T1 - Kinematic Comparison Between Gender Specific and Traditional Femoral Implants T2 - Proceedings of the 11th Alberta Biomedical Engineering (BME) Conference (Poster) Y1 - 2011 SP - 80 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - Mehr Mathematik wagen in der Medizin T2 - acatech diskutiert, Produktionsfaktor Mathematik - Wie Mathematik Technik und Wirtschaft bewegt Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-89435-3 SP - 435 EP - 459 PB - Springer ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Coupling Deformable Models for Multi-object Segmentation T2 - Proc. Int. Symp. on Computational Models for Biomedical Simulation (ISBMS) Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-70521-5_8 SP - 69 EP - 78 ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heller, Markus O. A1 - Hege, Hans-Christian T1 - Multi-Object Segmentation with Coupled Deformable Models T2 - Proc. Medical Image Understanding and Analysis Y1 - 2008 SP - 34 EP - 38 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Kuss, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Menzel, Randolf A1 - Rybak, Juergen T1 - Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models T2 - Proc. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain Y1 - 2008 U6 - https://doi.org/10.3389/conf.neuro.11.2008.01.064 ER - TY - CHAP A1 - Dworzak, Jalda A1 - Lamecker, Hans A1 - von Berg, Jens A1 - Klinder, Tobias A1 - Lorenz, Cristian A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Towards model-based 3-D reconstruction of the human rib cage from radiographs T2 - Proc. 7. Jahrestagung der Deutschen Gesellschaft für Computer-Roboterassistierte Chirurgie (CURAC) Y1 - 2008 SP - 193 EP - 196 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Heller, Markus O. A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model T2 - Eurographics Workshop on Visual Computing for Biomedicine (VCBM) Y1 - 2008 SP - 93 EP - 100 CY - Delft, Netherlands ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - More Mathematics into Medicine! T2 - Production Factor Mathematics Y1 - 2010 UR - http://www.springer.com/mathematics/book/978-3-642-11247-8 SP - 357 EP - 378 PB - Springer ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Bindernagel, Matthias A1 - Malinowski, Jana A1 - Zachow, Stefan ED - v. Ginneken, B. T1 - Model-based Auto-Segmentation of Knee Bones and Cartilage in MRI Data T2 - Proc. MICCAI Workshop Medical Image Analysis for the Clinic Y1 - 2010 SP - 215 EP - 223 ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric shape and intensity models for accurate simulation of X-ray images T2 - Eurographics Workshop on Visual Computing for Biomedicine (NVIDIA best poster award) Y1 - 2012 ER - TY - JOUR A1 - Ramm, Heiko A1 - Kahnt, Max A1 - Zachow, Stefan T1 - Patientenspezifische Simulationsmodelle für die funktionelle Analyse von künstlichem Gelenkersatz JF - Computer Aided Medical Engineering (CaMe) Y1 - 2012 VL - 3 IS - 2 SP - 30 EP - 36 ER - TY - CHAP A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan ED - Levine, Joshua A. ED - Paulsen, Rasmus R. ED - Zhang, Yongjie T1 - Feature-Preserving, Multi-Material Mesh Generation using Hierarchical Oracles T2 - Proc. MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed) Y1 - 2012 VL - 7599 SP - 101 EP - 111 ER - TY - CHAP A1 - Ramm, Heiko A1 - Zachow, Stefan ED - Niederlag, Wolfgang ED - Lemke, Heinz ED - Peitgen, Heinz-Otto ED - Lehrach, Hans T1 - Computergestützte Planung für die individuelle Implantatversorgung T2 - Health Academy Y1 - 2012 VL - 16 SP - 145 EP - 158 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan T1 - Multi-object segmentation of head bones JF - MIDAS Journal Y1 - 2009 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - A System for Unsupervised Extraction of Orthopaedic Parameters from CT Data T2 - GI Workshop Softwareassistenten - Computerunterstützung für die medizinische Diagnose und Therapieplanung Y1 - 2009 SP - 1328 EP - 1337 CY - Lübeck, Germany ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zinser, Max A1 - Zachow, Stefan ED - Yang, Guang-Zhong ED - J. Hawkes, David ED - Rueckert, Daniel ED - Noble, J. Alison ED - J. Taylor, Chris T1 - Automatic Extraction of Mandibular Nerve and Bone from Cone-Beam CT Data T2 - Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2009 SP - 76 EP - 83 CY - London, UK ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - An Articulated Statistical Shape Model for Accurate Hip Joint Segmentation T2 - EBMC 2009. Int. Conf. of the IEEE Eng. in Med. and Biol. Society (EMBC) Y1 - 2009 SP - 6345 EP - 6351 CY - Minneapolis, USA ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Heller, Markus O. A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Automatic Extraction of Anatomical Landmarks from Medical Image Data: An Evaluation of Different Methods T2 - Proc. of IEEE Int. Symposium on Biomedical Imaging (ISBI) Y1 - 2009 SP - 538 EP - 541 CY - Boston, MA, USA ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Multi-object Segmentation with Coupled Deformable Models JF - Annals of the British Machine Vision Association (BMVA) Y1 - 2009 VL - 5 SP - 1 EP - 10 ER - TY - JOUR A1 - Zachow, Stefan A1 - Muigg, Philipp A1 - Hildebrandt, Thomas A1 - Doleisch, Helmut A1 - Hege, Hans-Christian T1 - Visual Exploration of Nasal Airflow JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2009 U6 - https://doi.org/10.1109/TVCG.2009.198 VL - 15 IS - 8 SP - 1407 EP - 1414 ER - TY - JOUR A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Computergestützte Planung in der kraniofazialen Chirurgie JF - Face 01/08, Int. Mag. of Orofacial Esthetics Y1 - 2008 SP - 43 EP - 49 PB - Oemus Journale Leipzig ER - TY - CHAP A1 - Zilske, Michael A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Adaptive Remeshing of Non-Manifold Surfaces T2 - Eurographics 2008 Annex to the Conf. Proc. Y1 - 2008 SP - 207 EP - 211 ER - TY - CHAP A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Segmentation of Bony Structures with Ligament Attachment Sites T2 - Bildverarbeitung für die Medizin 2008 Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-78640-5_42 SP - 207 EP - 211 PB - Springer ER - TY - CHAP A1 - Neugebauer, Mathias A1 - Janiga, Gabor A1 - Zachow, Stefan A1 - Krischek, Özlem A1 - Preim, Bernhard ED - Hauser, Helwig T1 - Generierung qualitativ hochwertiger Modelle für die Simulation von Blutfluss in zerebralen Aneurysmen T2 - Proc. of Simulation and Visualization 2008 Y1 - 2008 SP - 221 EP - 235 ER - TY - CHAP A1 - Dornheim, Jana A1 - Born, Silvia A1 - Zachow, Stefan A1 - Gessat, Michael A1 - Wellein, Daniela A1 - Strauß, Gero A1 - Preim, Bernhard A1 - Bartz, Dirk ED - Hauser, Helwig T1 - Bildanalyse, Visualisierung und Modellerstellung für die Implantatplanung im Mittelohr T2 - Proc. of Simulation and Visualization 2008 Y1 - 2008 SP - 139 EP - 154 ER - TY - JOUR A1 - Steinmann, Alexander A1 - Bartsch, Peter A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Breathing Easily: Simulation of airflow in human noses can become a useful rhinosurgery planning tool JF - ANSYS Advantage Y1 - 2008 VL - Vol. II, No. 1 SP - 30 EP - 31 ER - TY - JOUR A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Deuflhard, Peter T1 - Craniofacial Surgery Planning Based on Virtual Patient Models JF - it - Information Technology Y1 - 2010 U6 - https://doi.org/10.1524/itit.2010.0600 VL - 52 IS - 5 SP - 258 EP - 263 PB - Oldenbourg Verlagsgruppe ER - TY - CHAP A1 - Zachow, Stefan A1 - Hahn, Horst A1 - Lange, Thomas ED - Schlag, Peter ED - Eulenstein, Sebastian ED - Lange, Thomas T1 - Computerassistierte Chirugieplanung T2 - Computerassistierte Chirurgie Y1 - 2010 SP - 119 EP - 149 PB - Elsevier ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan A1 - Hege, Hans-Christian ED - Navab, Tianzi ED - P. W. Pluim, Josien ED - Viergever, Max T1 - Improving Deformable Surface Meshes through Omni-directional Displacements and MRFs T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15705-9_28 VL - 6361 SP - 227 EP - 234 PB - Springer ER - TY - CHAP A1 - Zachow, Stefan A1 - Kubiack, Kim A1 - Malinowski, Jana A1 - Lamecker, Hans A1 - Essig, Harald A1 - Gellrich, Nils-Claudius T1 - Modellgestützte chirurgische Rekonstruktion komplexer Mittelgesichtsfrakturen T2 - Proc. BMT, Biomed Tech 2010 Y1 - 2010 VL - 55 (Suppl 1) SP - 107 EP - 108 PB - Walter de Gruyter-Verlag ER - TY - CHAP A1 - Lamecker, Hans A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Zachow, Stefan T1 - Automatische 3D Rekonstruktion des Unterkiefers und der Mandibulärnerven auf Basis dentaler Bildgebung T2 - Proc. BMT, Biomed Tech Y1 - 2010 VL - 55 (Suppl. 1) SP - 35 EP - 36 PB - Walter de Gruyter-Verlag ER - TY - JOUR A1 - Dworzak, Jalda A1 - Lamecker, Hans A1 - von Berg, Jens A1 - Klinder, Tobias A1 - Lorenz, Cristian A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - 3D Reconstruction of the Human Rib Cage from 2D Projection Images using a Statistical Shape Model JF - Int. J. Comput. Assist. Radiol. Surg. Y1 - 2010 U6 - https://doi.org/10.1007/s11548-009-0390-2 SN - 1861-6410 VL - 5 IS - 2 SP - 111 EP - 124 PB - Springer ER - TY - GEN A1 - Kamer, Lukas A1 - Noser, Hansrudi A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Wittmers, Antonia A1 - Kaup, Thomas A1 - Schramm, Alexander A1 - Hammer, Beat T1 - Three-dimensional statistical shape analysis - A useful tool for developing a new type of orbital implant? Y1 - 2006 SP - 20 EP - 21 PB - AO Development Institute, New Products Brochure 2/06 ER - TY - JOUR A1 - Heppt, Werner A1 - Hildebrandt, Thomas A1 - Steinmann, Alexander A1 - Zachow, Stefan T1 - Aesthetic and Function in Rhinoplasty JF - Springer Journal Y1 - 2007 VL - 264 (Suppl 1), RL 126 SP - 307 ER - TY - CHAP A1 - Zachow, Stefan A1 - Zilske, Michael A1 - Hege, Hans-Christian T1 - 3D Reconstruction of Individual Anatomy from Medical Image Data: Segmentation and Geometry Processing T2 - 25. ANSYS Conference & CADFEM Users’ Meeting Y1 - 2007 CY - Dresden ER - TY - JOUR A1 - Gessat, Michael A1 - Zachow, Stefan A1 - Burgert, Oliver A1 - Lemke, Heinz T1 - Geometric Meshes in Medical Applications - Steps towards a specification of Geometric Models in DICOM JF - Int. J. of Computer Assisted Radiology and Surgery (CARS) Y1 - 2007 U6 - https://doi.org/10.1007/s11548-007-0112-6 SP - 440 EP - 442 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Heppt, Werner T1 - Innovation in der Funktionell-Ästhetischen Nasenchirurgie: Rhino-CFD JF - Face, Int. Mag. of Orofacial Esthetics Y1 - 2007 SP - 20 EP - 23 PB - Oemus Journale Leipzig ER - TY - JOUR A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Hildebrandt, Thomas A1 - Heppt, Werner T1 - Understanding nasal airflow via CFD simulation and visualization JF - Proc. Computer Aided Surgery around the Head Y1 - 2007 SP - 173 EP - 176 ER - TY - JOUR A1 - Lamecker, Hans A1 - Kamer, Lukas A1 - Wittmers, Antonia A1 - Zachow, Stefan A1 - Kaup, Thomas A1 - Schramm, Alexander A1 - Noser, Hansrudi A1 - Hammer, Beat T1 - A method for the three-dimensional statistical shape analysis of the bony orbit JF - Proc. Computer Aided Surgery around the Head Y1 - 2007 SP - 94 EP - 97 ER - TY - CHAP A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Reconstruction of mandibular dysplasia using a statistical 3D shape model T2 - Proc. Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/10.1016/j.ics.2005.03.339 SP - 1238 EP - 1243 CY - Berlin, Germany ER - TY - CHAP A1 - Nkenke, Emeka A1 - Häusler, Gerd A1 - Neukam, Friedrich A1 - Zachow, Stefan T1 - Streak artifact correction of CT data by optical 3D imaging in the simulation of orthognathic surgery T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/doi:10.1016/j.ics.2005.03.278 CY - Berlin Germany ER - TY - CHAP A1 - Nkenke, Emeka A1 - Zachow, Stefan A1 - Häusler, Gerd T1 - Fusion von optischen 3D- und CT-Daten des Gebisses zur Metallartefaktkorrektur vor computerassistierter Planung MKG-chirurgischer Eingriffe T2 - Symposium der Arbeitsgemeinschaf für Kieferchirurgie Y1 - 2005 CY - Bad Homburg v.d.H ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Haberl, Hannes A1 - Stiller, Michael T1 - Medical applications for statistical shape models JF - Computer Aided Surgery around the Head, Fortschritt-Berichte VDI - Biotechnik/Medizintechnik Y1 - 2005 VL - 17 (258) SP - 61 ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Wittmers, Antonia A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Automatic segmentation of mandibles in low-dose CT-data JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 VL - 1(1) SP - 393 EP - 395 ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Zöckler, Maja T1 - Surgical treatment of craniosynostosis based on a statistical 3D-shape model JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 U6 - https://doi.org/10.1007/s11548-006-0024-x VL - 1(1) SP - 253 EP - 254 ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Computer assisted planning in cranio-maxillofacial surgery JF - Journal of Computing and Information Technology Y1 - 2006 VL - 14(1) SP - 53 EP - 64 ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Is the course of the mandibular nerve deducible from the shape of the mandible? JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 415 EP - 417 PB - Springer ER - TY - JOUR A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Hildebrandt, Thomas A1 - Weber, Rainer A1 - Heppt, Werner T1 - CFD simulation of nasal airflow: Towards treatment planning for functional rhinosurgery JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 165 EP - 167 PB - Springer ER - TY - CHAP A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Shandiz, Mohsen Akbari A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Towards Robust Measurement Of Pelvic Parameters From AP Radiographs Using Articulated 3D Models T2 - Computer Assisted Radiology and Surgery (CARS) N2 - Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph. KW - Articulated Models, Statistical Shape And Intensity Models, 2D/3D Anatomy Reconstruction, Pelvic Parameters Measurement, Total Hip Arthroplasty Y1 - 2015 ER - TY - GEN A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Shandiz, Mohsen Akbari A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Towards Robust Measurement of Pelvic Parameters from AP Radiographs using Articulated 3D Models N2 - Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph. T3 - ZIB-Report - 15-11 KW - Articulated Models, Statistical Shape And Intensity Models, 2D/3D Anatomy Reconstruction, Pelvic Parameters Measurement, Total Hip Arthroplasty Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53707 SN - 1438-0064 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Fusseis, Florian A1 - Hoffmann, René T1 - A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells JF - Paleobiology N2 - The chambered shell of modern cephalopods functions as a buoyancy apparatus, allowing the animal to enter the water column without expending a large amount of energy to overcome its own weight. Indeed, the chambered shell is largely considered a key adaptation that allowed the earliest cephalopods to leave the ocean floor and enter the water column. It has been argued by some, however, that the iconic chambered shell of Paleozoic and Mesozoic ammonoids did not provide a sufficiently buoyant force to compensate for the weight of the entire animal, thus restricting ammonoids to a largely benthic lifestyle reminiscent of some octopods. Here we develop a technique using high-resolution computed tomography to quantify the buoyant properties of chambered shells without reducing the shell to ideal spirals or eliminating inherent biological variability by using mathematical models that characterize past work in this area. This technique has been tested on Nautilus pompilius and is now extended to the extant deep-sea squid Spirula spirula and the Jurassic ammonite Cadoceras sp. hatchling. Cadoceras is found to have possessed near-neutral to positive buoyancy if hatched when the shell possessed between three and five chambers. However, we show that the animal could also overcome degrees of negative buoyancy through swimming, similar to the paralarvae of modern squids. These calculations challenge past inferences of benthic life habits based solely on calculations of negative buoyancy. The calculated buoyancy of Cadoceras supports the possibility of planktonic dispersal of ammonite hatchlings. This information is essential to understanding ammonoid ecology as well as biotic interactions and has implications for the interpretation of geochemical data gained from the isotopic analysis of the shell. Y1 - 2015 U6 - https://doi.org/10.1017/pab.2014.17 VL - 41 IS - 2 SP - 313 EP - 329 PB - Cambridge University Press CY - Cambridge ER - TY - CHAP A1 - Tack, Alexander A1 - Zachow, Stefan T1 - Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative T2 - IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019) N2 - Volumetry of cartilage of the knee is needed for knee osteoarthritis (KOA) assessment. It is typically performed manually in a tedious and subjective process. We developed a method for an automated, segmentation-based quantification of cartilage volume by employing 3D Convolutional Neural Networks (CNNs). CNNs were trained in a supervised manner using magnetic resonance imaging data and cartilage volumetry readings performed by clinical experts for 1378 subjects provided by the Osteoarthritis Initiative. It was shown that 3D CNNs are able to achieve volume measures comparable to the magnitude of variation between expert readings and the real in vivo situation. In the future, accurate automated cartilage volumetry might support both, diagnosis of KOA as well as longitudinal analysis of KOA progression. Y1 - 2019 U6 - https://doi.org/10.1109/ISBI.2019.8759201 SP - 40 EP - 43 ER - TY - CHAP A1 - Neumann, Mario A1 - Hellwich, Olaf A1 - Zachow, Stefan T1 - Localization and Classification of Teeth in Cone Beam CT using Convolutional Neural Networks T2 - Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC) N2 - In dentistry, software-based medical image analysis and visualization provide efficient and accurate diagnostic and therapy planning capabilities. We present an approach for the automatic recognition of tooth types and positions in digital volume tomography (DVT). By using deep learning techniques in combination with dimensionality reduction through non-planar reformatting of the jaw anatomy, DVT data can be efficiently processed and teeth reliably recognized and classified, even in the presence of imaging artefacts, missing or dislocated teeth. We evaluated our approach, which is based on 2D Convolutional Neural Networks (CNNs), on 118 manually annotated cases of clinical DVT datasets. Our proposed method correctly classifies teeth with an accuracy of 94% within a limit of 2mm distance to ground truth labels. Y1 - 2019 SN - 978-3-00-063717-9 SP - 182 EP - 188 ER - TY - CHAP A1 - Joachimsky, Robert A1 - Ma, Lihong A1 - Icking, Christian A1 - Zachow, Stefan T1 - A Collision-Aware Articulated Statistical Shape Model of the Human Spine T2 - Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC) N2 - Statistical Shape Models (SSMs) are a proven means for model-based 3D anatomy reconstruction from medical image data. In orthopaedics and biomechanics, SSMs are increasingly employed to individualize measurement data or to create individualized anatomical models to which implants can be adapted to or functional tests can be performed on. For modeling and analysis of articulated structures, so called articulated SSMs (aSSMs) have been developed. However, a missing feature of aSSMs is the consideration of collisions in the course of individual fitting and articulation. The aim of our work was to develop aSSMs that handle collisions between components correctly. That way it becomes possible to adjust shape and articulation in view of a physically and geometrically plausible individualization. To be able to apply collision-aware aSSMs in simulation and optimisation, our approach is based on an e� cient collision detection method employing Graphics Processing Units (GPUs). Y1 - 2019 SP - 58 EP - 64 ER - TY - JOUR A1 - Krämer, Martin A1 - Maggioni, Marta A1 - Brisson, Nicholas A1 - Zachow, Stefan A1 - Teichgräber, Ulf A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - T1 and T2* mapping of the human quadriceps and patellar tendons using ultra-short echo-time (UTE) imaging and bivariate relaxation parameter-based volumetric visualization JF - Magnetic Resonance Imaging N2 - Quantification of magnetic resonance (MR)-based relaxation parameters of tendons and ligaments is challenging due to their very short transverse relaxation times, requiring application of ultra-short echo-time (UTE) imaging sequences. We quantify both T1 and T2⁎ in the quadriceps and patellar tendons of healthy volunteers at a field strength of 3 T and visualize the results based on 3D segmentation by using bivariate histogram analysis. We applied a 3D ultra-short echo-time imaging sequence with either variable repetition times (VTR) or variable flip angles (VFA) for T1 quantification in combination with multi-echo acquisition for extracting T2⁎. The values of both relaxation parameters were subsequently binned for bivariate histogram analysis and corresponding cluster identification, which were subsequently visualized. Based on manually-drawn regions of interest in the tendons on the relaxation parameter maps, T1 and T2⁎ boundaries were selected in the bivariate histogram to segment the quadriceps and patellar tendons and visualize the relaxation times by 3D volumetric rendering. Segmentation of bone marrow, fat, muscle and tendons was successfully performed based on the bivariate histogram analysis. Based on the segmentation results mean T2⁎ relaxation times, over the entire tendon volumes averaged over all subjects, were 1.8 ms ± 0.1 ms and 1.4 ms ± 0.2 ms for the patellar and quadriceps tendons, respectively. The mean T1 value of the patellar tendon, averaged over all subjects, was 527 ms ± 42 ms and 476 ms ± 40 ms for the VFA and VTR acquisitions, respectively. The quadriceps tendon had higher mean T1 values of 662 ms ± 97 ms (VFA method) and 637 ms ± 40 ms (VTR method) compared to the patellar tendon. 3D volumetric visualization of the relaxation times revealed that T1 values are not constant over the volume of both tendons, but vary locally. This work provided additional data to build upon the scarce literature available on relaxation times in the quadriceps and patellar tendons. We were able to segment both tendons and to visualize the relaxation parameter distributions over the entire tendon volumes. Y1 - 2019 U6 - https://doi.org/10.1016/j.mri.2019.07.015 VL - 63 IS - 11 SP - 29 EP - 36 ER - TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - An as-invariant-as-possible GL+(3)-based Statistical Shape Model T2 - Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA) N2 - We describe a novel nonlinear statistical shape model basedon differential coordinates viewed as elements of GL+(3). We adopt an as-invariant-as possible framework comprising a bi-invariant Lie group mean and a tangent principal component analysis based on a unique GL+(3)-left-invariant, O(3)-right-invariant metric. Contrary to earlier work that equips the coordinates with a specifically constructed group structure, our method employs the inherent geometric structure of the group-valued data and therefore features an improved statistical power in identifying shape differences. We demonstrate this in experiments on two anatomical datasets including comparison to the standard Euclidean as well as recent state-of-the-art nonlinear approaches to statistical shape modeling. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-33226-6_23 VL - 11846 SP - 219 EP - 228 PB - Springer ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - A Surface-Theoretic Approach for Statistical Shape Modeling N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. We evaluate the performance of our model w.r.t. shape-based classification of pathological malformations of the human knee and show that it outperforms the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model's ability of capturing natural biological shape variability, we carry out an analysis of specificity and generalization ability. T3 - ZIB-Report - 19-20 KW - Statistical shape analysis KW - Principal geodesic analysis KW - Lie groups KW - Classification KW - Manifold valued statistics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74497 SN - 1438-0064 ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - An as-invariant-as-possible GL+(3)-based Statistical Shape Model N2 - We describe a novel nonlinear statistical shape model basedon differential coordinates viewed as elements of GL+(3). We adopt an as-invariant-as possible framework comprising a bi-invariant Lie group mean and a tangent principal component analysis based on a unique GL+(3)-left-invariant, O(3)-right-invariant metric. Contrary to earlier work that equips the coordinates with a specifically constructed group structure, our method employs the inherent geometric structure of the group-valued data and therefore features an improved statistical power in identifying shape differences. We demonstrate this in experiments on two anatomical datasets including comparison to the standard Euclidean as well as recent state-of-the-art nonlinear approaches to statistical shape modeling. T3 - ZIB-Report - 19-46 KW - Statistical shape analysis KW - Tangent principal component analysis KW - Lie groups KW - Classification KW - Manifold valued statistics Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-74566 SN - 1438-0064 ER - TY - CHAP A1 - Sahu, Manish A1 - Strömsdörfer, Ronja A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part III N2 - Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis'15 dataset) highlight the effectiveness of the proposed Endo-Sim2Real method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-59716-0_75 VL - 12263 PB - Springer Nature ER - TY - JOUR A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Surgical phase recognition by learning phase transitions JF - Current Directions in Biomedical Engineering (CDBME) N2 - Automatic recognition of surgical phases is an important component for developing an intra-operative context-aware system. Prior work in this area focuses on recognizing short-term tool usage patterns within surgical phases. However, the difference between intra- and inter-phase tool usage patterns has not been investigated for automatic phase recognition. We developed a Recurrent Neural Network (RNN), in particular a state-preserving Long Short Term Memory (LSTM) architecture to utilize the long-term evolution of tool usage within complete surgical procedures. For fully automatic tool presence detection from surgical video frames, a Convolutional Neural Network (CNN) based architecture namely ZIBNet is employed. Our proposed approach outperformed EndoNet by 8.1% on overall precision for phase detection tasks and 12.5% on meanAP for tool recognition tasks. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/cdbme-2020-0037 N1 - Nomination for the Best-Paper Award VL - 6 IS - 1 SP - 20200037 PB - De Gruyter ER - TY - GEN A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Analyzing laparoscopic cholecystectomy with deep learning: automatic detection of surgical tools and phases T2 - 28th International Congress of the European Association for Endoscopic Surgery (EAES) N2 - Motivation: The ever-rising volume of patients, high maintenance cost of operating rooms and time consuming analysis of surgical skills are fundamental problems that hamper the practical training of the next generation of surgeons. The hospitals prefer to keep the surgeons busy in real operations over training young surgeons for obvious economic reasons. One fundamental need in surgical training is the reduction of the time needed by the senior surgeon to review the endoscopic procedures performed by the young surgeon while minimizing the subjective bias in evaluation. The unprecedented performance of deep learning ushers the new age of data-driven automatic analysis of surgical skills. Method: Deep learning is capable of efficiently analyzing thousands of hours of laparoscopic video footage to provide an objective assessment of surgical skills. However, the traditional end-to-end setting of deep learning (video in, skill assessment out) is not explainable. Our strategy is to utilize the surgical process modeling framework to divide the surgical process into understandable components. This provides the opportunity to employ deep learning for superior yet automatic detection and evaluation of several aspects of laparoscopic cholecystectomy such as surgical tool and phase detection. We employ ZIBNet for the detection of surgical tool presence. ZIBNet employs pre-processing based on tool usage imbalance, a transfer learned 50-layer residual network (ResNet-50) and temporal smoothing. To encode the temporal evolution of tool usage (over the entire video sequence) that relates to the surgical phases, Long Short Term Memory (LSTM) units are employed with long-term dependency. Dataset: We used CHOLEC 80 dataset that consists of 80 videos of laparoscopic cholecystectomy performed by 13 surgeons, divided equally for training and testing. In these videos, up to three different tools (among 7 types of tools) can be present in a frame. Results: The mean average precision of the detection of all tools is 93.5 ranging between 86.8 and 99.3, a significant improvement (p <0.01) over the previous state-of-the-art. We observed that less frequent tools like Scissors, Irrigator, Specimen Bag etc. are more related to phase transitions. The overall precision (recall) of the detection of all surgical phases is 79.6 (81.3). Conclusion: While this is not the end goal for surgical skill analysis, the development of such a technological platform is essential toward a data-driven objective understanding of surgical skills. In future, we plan to investigate surgeon-in-the-loop analysis and feedback for surgical skill analysis. Y1 - 2020 UR - https://academy.eaes.eu/eaes/2020/28th/298882/manish.sahu.analyzing.laparoscopic.cholecystectomy.with.deep.learning.html?f=listing%3D0%2Abrowseby%3D8%2Asortby%3D2 ER - TY - JOUR A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Rigid Motion Invariant Statistical Shape Modeling based on Discrete Fundamental Forms JF - Medical Image Analysis N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. Additionally, as planar configurations form a submanifold in shape space, our representation allows for effective estimation of quasi-isometric surfaces flattenings. We evaluate the performance of our model w.r.t. shape-based classification of hippocampus and femur malformations due to Alzheimer's disease and osteoarthritis, respectively. In particular, we achieve state-of-the-art accuracies outperforming the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model's ability of capturing biological shape variability, we carry out an analysis of specificity and generalization ability. Y1 - 2021 U6 - https://doi.org/10.1016/j.media.2021.102178 VL - 73 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Simulation-to-Real domain adaptation with teacher-student learning for endoscopic instrument segmentation JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose Segmentation of surgical instruments in endoscopic video streams is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts. Methods We introduce a teacher–student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the challenges in simulation-to-real unsupervised domain adaptation for endoscopic image segmentation. Results Empirical results on three datasets highlight the effectiveness of the proposed framework over current approaches for the endoscopic instrument segmentation task. Additionally, we provide analysis of major factors affecting the performance on all datasets to highlight the strengths and failure modes of our approach. Conclusions We show that our proposed approach can successfully exploit the unlabeled real endoscopic video frames and improve generalization performance over pure simulation-based training and the previous state-of-the-art. This takes us one step closer to effective segmentation of surgical instrument in the annotation scarce setting. Y1 - 2021 U6 - https://doi.org/10.1007/s11548-021-02383-4 N1 - Honorary Mention: Machine Learning for Computer-Assisted Intervention (CAI) Award @IPCAI2021 N1 - Honorary Mention: Audience Award for Best Innovation @IPCAI2021 VL - 16 SP - 849 EP - 859 PB - Springer Nature ER - TY - CHAP A1 - Estacio, Laura A1 - Ehlke, Moritz A1 - Tack, Alexander A1 - Castro-Gutierrez, Eveling A1 - Lamecker, Hans A1 - Mora, Rensso A1 - Zachow, Stefan T1 - Unsupervised Detection of Disturbances in 2D Radiographs T2 - 2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI) N2 - We present a method based on a generative model for detection of disturbances such as prosthesis, screws, zippers, and metals in 2D radiographs. The generative model is trained in an unsupervised fashion using clinical radiographs as well as simulated data, none of which contain disturbances. Our approach employs a latent space consistency loss which has the benefit of identifying similarities, and is enforced to reconstruct X-rays without disturbances. In order to detect images with disturbances, an anomaly score is computed also employing the Frechet distance between the input X-ray and the reconstructed one using our generative model. Validation was performed using clinical pelvis radiographs. We achieved an AUC of 0.77 and 0.83 with clinical and synthetic data, respectively. The results demonstrated a good accuracy of our method for detecting outliers as well as the advantage of utilizing synthetic data. Y1 - 2021 U6 - https://doi.org/10.1109/ISBI48211.2021.9434091 SP - 367 EP - 370 ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Geodesic B-Score for Improved Assessment of Knee Osteoarthritis N2 - Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions. T3 - ZIB-Report - 21-09 KW - Statistical shape analysis KW - Osteoarthritis KW - Geometric statistics KW - Riemannian manifolds Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81930 SN - 1438-0064 ER - TY - JOUR A1 - Tack, Alexander A1 - Preim, Bernhard A1 - Zachow, Stefan T1 - Fully automated Assessment of Knee Alignment from Full-Leg X-Rays employing a "YOLOv4 And Resnet Landmark regression Algorithm" (YARLA): Data from the Osteoarthritis Initiative JF - Computer Methods and Programs in Biomedicine N2 - We present a method for the quantification of knee alignment from full-leg X-Rays. A state-of-the-art object detector, YOLOv4, was trained to locate regions of interests (ROIs) in full-leg X-Ray images for the hip joint, the knee, and the ankle. Residual neural networks (ResNets) were trained to regress landmark coordinates for each ROI.Based on the detected landmarks the knee alignment, i.e., the hip-knee-ankle (HKA) angle, was computed. The accuracy of landmark detection was evaluated by a comparison to manually placed landmarks for 360 legs in 180 X-Rays. The accuracy of HKA angle computations was assessed on the basis of 2,943 X-Rays. Results of YARLA were compared to the results of two independent image reading studies(Cooke; Duryea) both publicly accessible via the Osteoarthritis Initiative. The agreement was evaluated using Spearman's Rho, and weighted kappa as well as regarding the correspondence of the class assignment (varus/neutral/valgus). The average difference between YARLA and manually placed landmarks was less than 2.0+- 1.5 mm for all structures (hip, knee, ankle). The average mismatch between HKA angle determinations of Cooke and Duryea was 0.09 +- 0.63°; YARLA resulted in a mismatch of 0.10 +- 0.74° compared to Cooke and of 0.18 +- 0.64° compared to Duryea. Cooke and Duryea agreed almost perfectly with respect to a weighted kappa value of 0.86, and showed an excellent reliability as measured by a Spearman's Rho value of 0.99. Similar values were achieved by YARLA, i.e., a weighted kappa value of0.83 and 0.87 and a Spearman's Rho value of 0.98 and 0.99 to Cooke and Duryea,respectively. Cooke and Duryea agreed in 92% of all class assignments and YARLA did so in 90% against Cooke and 92% against Duryea. In conclusion, YARLA achieved results comparable to those of human experts and thus provides a basis for an automated assessment of knee alignment in full-leg X-Rays. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.cmpb.2021.106080 VL - 205 IS - 106080 ER - TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Geodesic B-Score for Improved Assessment of Knee Osteoarthritis T2 - Proc. Information Processing in Medical Imaging (IPMI) N2 - Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-78191-0_14 SP - 177 EP - 188 ER - TY - JOUR A1 - Hembus, Jessica A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - Bader, Rainer T1 - Establishment of a rolling-sliding test bench to analyze abrasive wear propagation of different bearing materials for knee implants JF - Applied Sciences N2 - Currently, new materials for knee implants need to be extensively and expensive tested in a knee wear simulator in a realized design. However, using a rolling-sliding test bench, these materials can be examined under the same test conditions but with simplified geometries. In the present study, the test bench was optimized, and forces were adapted to the physiological contact pressure in the knee joint using the available geometric parameters. Various polymers made of polyethylene and polyurethane articulating against test wheels made of cobalt-chromium and aluminum titanate were tested in the test bench using adapted forces based on ISO 14243-1. Polyurethane materials showed distinctly higher wear rates than polyethylene materials and showed inadequate wear resistance for use as knee implant material. Thus, the rolling-sliding test bench is an adaptable test setup for evaluating newly developed bearing materials for knee implants. It combines the advantages of screening and simulator tests and allows testing of various bearing materials under physiological load and tribological conditions of the human knee joint. The wear behavior of different material compositions and the influence of surface geometry and quality can be initially investigated without the need to produce complex implant prototypes of total knee endoprosthesis or interpositional spacers. Y1 - 2021 U6 - https://doi.org/10.3390/app11041886 VL - 11 IS - 4 ER -