@inproceedings{HoffmannZachow2011, author = {Hoffmann, Ren{\´e} and Zachow, Stefan}, title = {Non-invasive approach to shed new light on the buoyancy business of chambered cephalopods (Mollusca)}, series = {Proc. of the Intl. Assoc. for Mathematical Geosciences, Salzburg}, booktitle = {Proc. of the Intl. Assoc. for Mathematical Geosciences, Salzburg}, doi = {10.5242/iamg.2011.0163}, pages = {1 -- 11}, year = {2011}, language = {en} } @article{RybakKussLameckeretal.2010, author = {Rybak, J{\"u}rgen and Kuß, Anja and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian and Lienhard, Matthias and Singer, Jochen and Neubert, Kerstin and Menzel, Randolf}, title = {The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System}, series = {Front. Syst. Neurosci.}, volume = {4}, journal = {Front. Syst. Neurosci.}, number = {30}, doi = {10.3389/fnsys.2010.00030}, year = {2010}, language = {en} } @article{GallowayKahntRammetal.2013, author = {Galloway, Francis and Kahnt, Max and Ramm, Heiko and Worsley, Peter and Zachow, Stefan and Nair, Prasanth and Taylor, Mark}, title = {A large scale finite element study of a cementless osseointegrated tibial tray}, series = {Journal of Biomechanics}, volume = {46}, journal = {Journal of Biomechanics}, number = {11}, doi = {/10.1016/j.jbiomech.2013.04.021}, pages = {1900 -- 1906}, year = {2013}, language = {en} } @article{ZachowLameckerZoeckleretal.2009, author = {Zachow, Stefan and Lamecker, Hans and Z{\"o}ckler, Maja and Haberl, Ernst}, title = {Computergest{\"u}tzte Planung zur chirurgischen Korrektur von fr{\"u}hkindlichen Sch{\"a}delfehlbildungen (Craniosynostosen)}, series = {Face 02/09, Int. Mag. of Orofacial Esthetics, Oemus Journale Leipzig}, journal = {Face 02/09, Int. Mag. of Orofacial Esthetics, Oemus Journale Leipzig}, pages = {48 -- 53}, year = {2009}, language = {en} } @article{ZahnGrotjohannRammetal., author = {Zahn, Robert and Grotjohann, Sarah and Ramm, Heiko and Zachow, Stefan and Pumberger, Matthias and Putzier, Michael and Perka, Carsten and Tohtz, Stephan}, title = {Influence of pelvic tilt on functional acetabular orientation}, series = {Technology and Health Care}, volume = {25}, journal = {Technology and Health Care}, number = {3}, publisher = {IOS Press}, doi = {10.3233/THC-161281}, pages = {557 -- 565}, language = {en} } @article{LemanisKornZachowetal., author = {Lemanis, Robert and Korn, Dieter and Zachow, Stefan and Rybacki, Erik and Hoffmann, Ren{\´e}}, title = {The Evolution and Development of Cephalopod Chambers and Their Shape}, series = {PLOS ONE}, volume = {11}, journal = {PLOS ONE}, number = {3}, doi = {10.1371/journal.pone.0151404}, abstract = {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.}, language = {en} } @article{DunlopApanaskevichLehmannetal.2016, author = {Dunlop, Jason and Apanaskevich, Dmitry and Lehmann, Jens and Hoffmann, Rene and Fusseis, Florian and Ehlke, Moritz and Zachow, Stefan and Xiao, Xianghui}, title = {Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus}, series = {BMC Evolutionary Biology}, volume = {16}, journal = {BMC Evolutionary Biology}, number = {1}, doi = {10.1186/s12862-016-0777-y}, year = {2016}, abstract = {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.}, language = {en} } @article{BernardSalamancaThunbergetal., author = {Bernard, Florian and Salamanca, Luis and Thunberg, Johan and Tack, Alexander and Jentsch, Dennis and Lamecker, Hans and Zachow, Stefan and Hertel, Frank and Goncalves, Jorge and Gemmar, Peter}, title = {Shape-aware Surface Reconstruction from Sparse Data}, series = {arXiv}, journal = {arXiv}, pages = {1602.08425v1}, abstract = {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.}, language = {en} } @article{LemanisZachowHoffmann, author = {Lemanis, Robert and Zachow, Stefan and Hoffmann, Ren{\´e}}, title = {Comparative cephalopod shell strength and the role of septum morphology on stress distribution}, series = {PeerJ}, volume = {4}, journal = {PeerJ}, doi = {10.7717/peerj.2434}, pages = {e2434}, abstract = {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.}, language = {en} } @article{BrueningGoubergritsHepptetal., author = {Br{\"u}ning, Jan and Goubergrits, Leonid and Heppt, Werner and Zachow, Stefan and Hildebrandt, Thomas}, title = {Numerical Analysis of Nasal Breathing - A Pilot Study}, series = {Facial Plastic Surgery}, volume = {33}, journal = {Facial Plastic Surgery}, number = {4}, doi = {doi:10.1055/s-0037-1603789}, pages = {388 -- 395}, abstract = {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.}, language = {en} } @misc{WeiserErdmannSchenkletal.2017, author = {Weiser, Martin and Erdmann, Bodo and Schenkl, Sebastian and Muggenthaler, Holger and Hubig, Michael and Mall, Gita and Zachow, Stefan}, title = {Uncertainty in Temperature-Based Determination of Time of Death}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63818}, year = {2017}, abstract = {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.}, language = {en} } @inproceedings{BaumMahlowLameckeretal., author = {Baum, Daniel and Mahlow, Kristin and Lamecker, Hans and Zachow, Stefan and M{\"u}ller, Johannes and Hege, Hans-Christian}, title = {The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis)}, series = {Abstract in DigitalSpecimen 2014}, booktitle = {Abstract in DigitalSpecimen 2014}, abstract = {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.}, language = {en} } @misc{AmbellanTackWilsonetal., author = {Ambellan, Felix and Tack, Alexander and Wilson, Dave and Anglin, Carolyn and Lamecker, Hans and Zachow, Stefan}, title = {Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66052}, abstract = {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.}, language = {en} } @misc{JoachimskyAmbellanZachow, author = {Joachimsky, Robert and Ambellan, Felix and Zachow, Stefan}, title = {Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung fr{\"u}her Gonarthrose}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66064}, abstract = {Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein h{\"a}ufiges Krankheitsbild unter {\"a}lteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder gesch{\"a}digter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfl{\"a}che erh{\"o}hen und so der teilweise oder vollst{\"a}ndige Gelenkersatz hinausgez{\"o}gert oder vermieden werden. In dieser Arbeit pr{\"a}sentieren wir eine Planungssoftware f{\"u}r 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 ausgew{\"a}hlt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. F{\"u}r jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern R{\"u}ckmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterst{\"u}tzt somit als Entscheidungshilfe die behandelnden {\"A}rzte bei der patientenspezifischen Spacerauswahl.}, language = {de} } @article{WeiserErdmannSchenkletal., author = {Weiser, Martin and Erdmann, Bodo and Schenkl, Sebastian and Muggenthaler, Holger and Hubig, Michael and Mall, Gita and Zachow, Stefan}, title = {Uncertainty in Temperature-Based Determination of Time of Death}, series = {Heat and Mass Transfer}, volume = {54}, journal = {Heat and Mass Transfer}, number = {9}, publisher = {Springer}, doi = {10.1007/s00231-018-2324-4}, pages = {2815 -- 2826}, abstract = {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.}, language = {en} } @article{BernardSalamancaThunbergetal., author = {Bernard, Florian and Salamanca, Luis and Thunberg, Johan and Tack, Alexander and Jentsch, Dennis and Lamecker, Hans and Zachow, Stefan and Hertel, Frank and Goncalves, Jorge and Gemmar, Peter}, title = {Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds}, series = {Medical Image Analysis}, volume = {38}, journal = {Medical Image Analysis}, doi = {10.1016/j.media.2017.02.005}, pages = {77 -- 89}, abstract = {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.}, language = {en} } @article{LubeFlackCotofanaetal., author = {Lube, Juliane and Flack, Natasha and Cotofana, Sebastian and {\"O}zkurtul, Orkun and Woodley, Stephanie and Zachow, Stefan and Hammer, Niels}, title = {Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature}, series = {Surgical and Radiologic Anatomy}, volume = {39}, journal = {Surgical and Radiologic Anatomy}, number = {8}, doi = {10.1007/s00276-016-1807-6}, pages = {849 -- 857}, abstract = {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.}, language = {en} } @inproceedings{MukhopadhyayMorilloZachowetal., author = {Mukhopadhyay, Anirban and Morillo, Oscar and Zachow, Stefan and Lamecker, Hans}, title = {Robust and Accurate Appearance Models Based on Joint Dictionary Learning Data from the Osteoarthritis Initiative}, series = {Lecture Notes in Computer Science, Patch-Based Techniques in Medical Imaging. Patch-MI 2016}, volume = {9993}, booktitle = {Lecture Notes in Computer Science, Patch-Based Techniques in Medical Imaging. Patch-MI 2016}, doi = {10.1007/978-3-319-47118-1_4}, pages = {25 -- 33}, abstract = {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.}, language = {en} } @article{SahuMukhopadhyaySzengeletal., author = {Sahu, Manish and Mukhopadhyay, Anirban and Szengel, Angelika and Zachow, Stefan}, title = {Addressing multi-label imbalance problem of Surgical Tool Detection using CNN}, series = {International Journal of Computer Assisted Radiology and Surgery}, volume = {12}, journal = {International Journal of Computer Assisted Radiology and Surgery}, number = {6}, publisher = {Springer}, doi = {10.1007/s11548-017-1565-x}, pages = {1013 -- 1020}, abstract = {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.}, language = {en} } @article{SchenklMuggenthalerHubigetal.2017, author = {Schenkl, Sebastian and Muggenthaler, Holger and Hubig, Michael and Erdmann, Bodo and Weiser, Martin and Zachow, Stefan and Heinrich, Andreas and G{\"u}ttler, Felix Victor and Teichgr{\"a}ber, Ulf and Mall, Gita}, title = {Automatic CT-based finite element model generation for temperature-based death time estimation: feasibility study and sensitivity analysis}, series = {International Journal of Legal Medicine}, volume = {131}, journal = {International Journal of Legal Medicine}, number = {3}, doi = {doi:10.1007/s00414-016-1523-0}, pages = {699 -- 712}, year = {2017}, abstract = {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.}, language = {en} } @article{Zachow, author = {Zachow, Stefan}, title = {Computational Planning in Facial Surgery}, series = {Facial Plastic Surgery}, volume = {31}, journal = {Facial Plastic Surgery}, number = {5}, doi = {10.1055/s-0035-1564717}, pages = {446 -- 462}, abstract = {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.}, language = {en} } @misc{LamasRodriguezEhlkeHoffmannetal., author = {Lamas-Rodr{\´i}guez, Juli{\´a}n and Ehlke, Moritz and Hoffmann, Ren{\´e} and Zachow, Stefan}, title = {GPU-accelerated denoising of large tomographic data sets with low SNR}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56339}, abstract = {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.}, language = {en} } @article{ZahnGrotjohannRammetal., author = {Zahn, Robert and Grotjohann, Sarah and Ramm, Heiko and Zachow, Stefan and Putzier, Michael and Perka, Carsten and Tohtz, Stephan}, title = {Pelvic tilt compensates for increased acetabular anteversion}, series = {International Orthopaedics}, volume = {40}, journal = {International Orthopaedics}, number = {8}, doi = {10.1007/s00264-015-2949-6}, pages = {1571 -- 1575}, abstract = {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.}, language = {en} } @incollection{LameckerZachow, author = {Lamecker, Hans and Zachow, Stefan}, title = {Statistical Shape Modeling of Musculoskeletal Structures and Its Applications}, series = {Computational Radiology for Orthopaedic Interventions}, volume = {23}, booktitle = {Computational Radiology for Orthopaedic Interventions}, publisher = {Springer}, isbn = {978-3-319-23481-6}, doi = {10.1007/978-3-319-23482-3}, pages = {1 -- 23}, abstract = {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.}, language = {en} } @article{ZachowHeppt, author = {Zachow, Stefan and Heppt, Werner}, title = {The Facial Profile}, series = {Facial Plastic Surgery}, volume = {31}, journal = {Facial Plastic Surgery}, number = {5}, doi = {10.1055/s-0035-1566132}, pages = {419 -- 420}, abstract = {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.}, language = {en} } @inproceedings{RammVictoriaMorilloTodtetal.2013, author = {Ramm, Heiko and Victoria Morillo, Oscar Salvador and Todt, Ingo and Schirmacher, Hartmut and Ernst, Arneborg and Zachow, Stefan and Lamecker, Hans}, title = {Visual Support for Positioning Hearing Implants}, series = {Proceedings of the 12th annual meeting of the CURAC society}, booktitle = {Proceedings of the 12th annual meeting of the CURAC society}, editor = {Freysinger, Wolfgang}, pages = {116 -- 120}, year = {2013}, language = {en} } @article{KainmuellerLameckerHelleretal.2013, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Heller, Markus O. and Weber, Britta and Hege, Hans-Christian and Zachow, Stefan}, title = {Omnidirectional Displacements for Deformable Surfaces}, series = {Medical Image Analysis}, volume = {17}, journal = {Medical Image Analysis}, number = {4}, publisher = {Elsevier}, doi = {10.1016/j.media.2012.11.006}, pages = {429 -- 441}, year = {2013}, language = {en} } @article{LamasRodriguezHerasArgueelloetal.2013, author = {Lamas-Rodr{\´i}guez, Juli{\´a}n and Heras, Dora Blanco and Arg{\"u}ello, Francisco and Kainm{\"u}ller, Dagmar and Zachow, Stefan and B{\´o}o, Montserrat}, title = {GPU-accelerated level-set segmentation}, series = {Journal of Real-Time Image Processing}, journal = {Journal of Real-Time Image Processing}, publisher = {Springer Berlin Heidelberg}, issn = {1861-8200}, doi = {10.1007/s11554-013-0378-6}, pages = {1 -- 15}, year = {2013}, language = {en} } @article{HoffmannSchultzSchellhornetal., author = {Hoffmann, Ren{\´e} and Schultz, Julia A. and Schellhorn, Rico and Rybacki, Erik and Keupp, Helmut and Gerden, S. R. and Lemanis, Robert and Zachow, Stefan}, title = {Non-invasive imaging methods applied to neo- and paleontological cephalopod research}, series = {Biogeosciences}, volume = {11}, journal = {Biogeosciences}, number = {10}, doi = {10.5194/bg-11-2721-2014}, pages = {2721 -- 2739}, abstract = {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.}, language = {en} } @inproceedings{vonBergDworzakKlinderetal.2011, author = {von Berg, Jens and Dworzak, Jalda and Klinder, Tobias and Manke, Dirk and Lamecker, Hans and Zachow, Stefan and Lorenz, Cristian}, title = {Temporal Subtraction of Chest Radiographs Compensating Pose Differences}, series = {SPIE Medical Imaging}, booktitle = {SPIE Medical Imaging}, year = {2011}, language = {en} } @inproceedings{BindernagelKainmuellerSeimetal.2011, author = {Bindernagel, Matthias and Kainm{\"u}ller, Dagmar and Seim, Heiko and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian}, title = {An Articulated Statistical Shape Model of the Human Knee}, series = {Bildverarbeitung f{\"u}r die Medizin 2011}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2011}, publisher = {Springer}, doi = {10.1007/978-3-642-19335-4_14}, pages = {59 -- 63}, year = {2011}, language = {en} } @inproceedings{KahntGallowaySeimetal.2011, author = {Kahnt, Max and Galloway, Francis and Seim, Heiko and Lamecker, Hans and Taylor, Mark and Zachow, Stefan}, title = {Robust and Intuitive Meshing of Bone-Implant Compounds}, series = {CURAC}, booktitle = {CURAC}, address = {Magdeburg}, pages = {71 -- 74}, year = {2011}, language = {en} } @misc{SKGBSetal.2011, author = {SK, Saevarsson and GB, Sharma and S, Montgomery and KCT, Ho and Ramm, Heiko and Lieck, Robert and Zachow, Stefan and C, Anglin}, title = {Kinematic Comparison Between Gender Specific and Traditional Femoral Implants}, series = {Proceedings of the 11th Alberta Biomedical Engineering (BME) Conference (Poster)}, journal = {Proceedings of the 11th Alberta Biomedical Engineering (BME) Conference (Poster)}, pages = {80}, year = {2011}, language = {en} } @incollection{DeuflhardDoesselLouisetal.2008, author = {Deuflhard, Peter and D{\"o}ssel, Olaf and Louis, Alfred and Zachow, Stefan}, title = {Mehr Mathematik wagen in der Medizin}, series = {acatech diskutiert, Produktionsfaktor Mathematik - Wie Mathematik Technik und Wirtschaft bewegt}, booktitle = {acatech diskutiert, Produktionsfaktor Mathematik - Wie Mathematik Technik und Wirtschaft bewegt}, publisher = {Springer}, doi = {10.1007/978-3-540-89435-3}, pages = {435 -- 459}, year = {2008}, language = {en} } @inproceedings{KainmuellerLameckerZachowetal.2008, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian}, title = {Coupling Deformable Models for Multi-object Segmentation}, series = {Proc. Int. Symp. on Computational Models for Biomedical Simulation (ISBMS)}, booktitle = {Proc. Int. Symp. on Computational Models for Biomedical Simulation (ISBMS)}, doi = {10.1007/978-3-540-70521-5_8}, pages = {69 -- 78}, year = {2008}, language = {en} } @inproceedings{KainmuellerLameckerZachowetal.2008, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Zachow, Stefan and Heller, Markus O. and Hege, Hans-Christian}, title = {Multi-Object Segmentation with Coupled Deformable Models}, series = {Proc. Medical Image Understanding and Analysis}, booktitle = {Proc. Medical Image Understanding and Analysis}, pages = {34 -- 38}, year = {2008}, language = {en} } @inproceedings{SeimKainmuellerKussetal.2008, author = {Seim, Heiko and Kainm{\"u}ller, Dagmar and Kuss, Anja and Lamecker, Hans and Zachow, Stefan and Menzel, Randolf and Rybak, Juergen}, title = {Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models}, series = {Proc. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain}, booktitle = {Proc. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain}, doi = {10.3389/conf.neuro.11.2008.01.064}, year = {2008}, language = {en} } @inproceedings{DworzakLameckervonBergetal.2008, author = {Dworzak, Jalda and Lamecker, Hans and von Berg, Jens and Klinder, Tobias and Lorenz, Cristian and Kainm{\"u}ller, Dagmar and Seim, Heiko and Hege, Hans-Christian and Zachow, Stefan}, title = {Towards model-based 3-D reconstruction of the human rib cage from radiographs}, series = {Proc. 7. Jahrestagung der Deutschen Gesellschaft f{\"u}r Computer-Roboterassistierte Chirurgie (CURAC)}, booktitle = {Proc. 7. Jahrestagung der Deutschen Gesellschaft f{\"u}r Computer-Roboterassistierte Chirurgie (CURAC)}, pages = {193 -- 196}, year = {2008}, language = {en} } @inproceedings{SeimKainmuellerHelleretal.2008, author = {Seim, Heiko and Kainm{\"u}ller, Dagmar and Heller, Markus O. and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian}, title = {Automatic Segmentation of the Pelvic Bones from CT Data Based on a Statistical Shape Model}, series = {Eurographics Workshop on Visual Computing for Biomedicine (VCBM)}, booktitle = {Eurographics Workshop on Visual Computing for Biomedicine (VCBM)}, address = {Delft, Netherlands}, pages = {93 -- 100}, year = {2008}, language = {en} } @incollection{DeuflhardDoesselLouisetal.2010, author = {Deuflhard, Peter and D{\"o}ssel, Olaf and Louis, Alfred and Zachow, Stefan}, title = {More Mathematics into Medicine!}, series = {Production Factor Mathematics}, booktitle = {Production Factor Mathematics}, publisher = {Springer}, pages = {357 -- 378}, year = {2010}, language = {en} } @inproceedings{SeimKainmuellerLameckeretal.2010, author = {Seim, Heiko and Kainm{\"u}ller, Dagmar and Lamecker, Hans and Bindernagel, Matthias and Malinowski, Jana and Zachow, Stefan}, title = {Model-based Auto-Segmentation of Knee Bones and Cartilage in MRI Data}, series = {Proc. MICCAI Workshop Medical Image Analysis for the Clinic}, booktitle = {Proc. MICCAI Workshop Medical Image Analysis for the Clinic}, editor = {v. Ginneken, B.}, pages = {215 -- 223}, year = {2010}, language = {en} } @misc{EhlkeRammLameckeretal.2012, author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Zachow, Stefan}, title = {Efficient projection and deformation of volumetric shape and intensity models for accurate simulation of X-ray images}, series = {Eurographics Workshop on Visual Computing for Biomedicine (NVIDIA best poster award)}, journal = {Eurographics Workshop on Visual Computing for Biomedicine (NVIDIA best poster award)}, year = {2012}, language = {en} } @article{RammKahntZachow2012, author = {Ramm, Heiko and Kahnt, Max and Zachow, Stefan}, title = {Patientenspezifische Simulationsmodelle f{\"u}r die funktionelle Analyse von k{\"u}nstlichem Gelenkersatz}, series = {Computer Aided Medical Engineering (CaMe)}, volume = {3}, journal = {Computer Aided Medical Engineering (CaMe)}, number = {2}, pages = {30 -- 36}, year = {2012}, language = {de} } @inproceedings{KahntRammLameckeretal.2012, author = {Kahnt, Max and Ramm, Heiko and Lamecker, Hans and Zachow, Stefan}, title = {Feature-Preserving, Multi-Material Mesh Generation using Hierarchical Oracles}, series = {Proc. MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed)}, volume = {7599}, booktitle = {Proc. MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed)}, editor = {Levine, Joshua A. and Paulsen, Rasmus R. and Zhang, Yongjie}, pages = {101 -- 111}, year = {2012}, language = {en} } @incollection{RammZachow2012, author = {Ramm, Heiko and Zachow, Stefan}, title = {Computergest{\"u}tzte Planung f{\"u}r die individuelle Implantatversorgung}, series = {Health Academy}, volume = {16}, booktitle = {Health Academy}, editor = {Niederlag, Wolfgang and Lemke, Heinz and Peitgen, Heinz-Otto and Lehrach, Hans}, pages = {145 -- 158}, year = {2012}, language = {de} } @article{KainmuellerLameckerSeimetal.2009, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Seim, Heiko and Zachow, Stefan}, title = {Multi-object segmentation of head bones}, series = {MIDAS Journal}, journal = {MIDAS Journal}, year = {2009}, language = {en} } @inproceedings{SeimKainmuellerLameckeretal.2009, author = {Seim, Heiko and Kainm{\"u}ller, Dagmar and Lamecker, Hans and Zachow, Stefan}, title = {A System for Unsupervised Extraction of Orthopaedic Parameters from CT Data}, series = {GI Workshop Softwareassistenten - Computerunterst{\"u}tzung f{\"u}r die medizinische Diagnose und Therapieplanung}, booktitle = {GI Workshop Softwareassistenten - Computerunterst{\"u}tzung f{\"u}r die medizinische Diagnose und Therapieplanung}, address = {L{\"u}beck, Germany}, pages = {1328 -- 1337}, year = {2009}, language = {en} } @inproceedings{KainmuellerLameckerSeimetal.2009, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Seim, Heiko and Zinser, Max and Zachow, Stefan}, title = {Automatic Extraction of Mandibular Nerve and Bone from Cone-Beam CT Data}, series = {Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)}, booktitle = {Proceedings of Medical Image Computing and Computer Assisted Intervention (MICCAI)}, editor = {Yang, Guang-Zhong and J. Hawkes, David and Rueckert, Daniel and Noble, J. Alison and J. Taylor, Chris}, address = {London, UK}, pages = {76 -- 83}, year = {2009}, language = {en} } @inproceedings{KainmuellerLameckerZachowetal.2009, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian}, title = {An Articulated Statistical Shape Model for Accurate Hip Joint Segmentation}, series = {EBMC 2009. Int. Conf. of the IEEE Eng. in Med. and Biol. Society (EMBC)}, booktitle = {EBMC 2009. Int. Conf. of the IEEE Eng. in Med. and Biol. Society (EMBC)}, address = {Minneapolis, USA}, pages = {6345 -- 6351}, year = {2009}, language = {en} } @inproceedings{SeimKainmuellerHelleretal.2009, author = {Seim, Heiko and Kainm{\"u}ller, Dagmar and Heller, Markus O. and Zachow, Stefan and Hege, Hans-Christian}, title = {Automatic Extraction of Anatomical Landmarks from Medical Image Data: An Evaluation of Different Methods}, series = {Proc. of IEEE Int. Symposium on Biomedical Imaging (ISBI)}, booktitle = {Proc. of IEEE Int. Symposium on Biomedical Imaging (ISBI)}, address = {Boston, MA, USA}, pages = {538 -- 541}, year = {2009}, language = {en} } @article{KainmuellerLameckerZachow2009, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Zachow, Stefan}, title = {Multi-object Segmentation with Coupled Deformable Models}, series = {Annals of the British Machine Vision Association (BMVA)}, volume = {5}, journal = {Annals of the British Machine Vision Association (BMVA)}, pages = {1 -- 10}, year = {2009}, language = {en} } @article{ZachowMuiggHildebrandtetal.2009, author = {Zachow, Stefan and Muigg, Philipp and Hildebrandt, Thomas and Doleisch, Helmut and Hege, Hans-Christian}, title = {Visual Exploration of Nasal Airflow}, series = {IEEE Transactions on Visualization and Computer Graphics}, volume = {15}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {8}, doi = {10.1109/TVCG.2009.198}, pages = {1407 -- 1414}, year = {2009}, language = {en} } @article{ZachowDeuflhard2008, author = {Zachow, Stefan and Deuflhard, Peter}, title = {Computergest{\"u}tzte Planung in der kraniofazialen Chirurgie}, series = {Face 01/08, Int. Mag. of Orofacial Esthetics}, journal = {Face 01/08, Int. Mag. of Orofacial Esthetics}, publisher = {Oemus Journale Leipzig}, pages = {43 -- 49}, year = {2008}, language = {en} } @inproceedings{ZilskeLameckerZachow2008, author = {Zilske, Michael and Lamecker, Hans and Zachow, Stefan}, title = {Adaptive Remeshing of Non-Manifold Surfaces}, series = {Eurographics 2008 Annex to the Conf. Proc.}, booktitle = {Eurographics 2008 Annex to the Conf. Proc.}, pages = {207 -- 211}, year = {2008}, language = {en} } @inproceedings{SeimLameckerZachow2008, author = {Seim, Heiko and Lamecker, Hans and Zachow, Stefan}, title = {Segmentation of Bony Structures with Ligament Attachment Sites}, series = {Bildverarbeitung f{\"u}r die Medizin 2008}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2008}, publisher = {Springer}, doi = {10.1007/978-3-540-78640-5_42}, pages = {207 -- 211}, year = {2008}, language = {en} } @inproceedings{NeugebauerJanigaZachowetal.2008, author = {Neugebauer, Mathias and Janiga, Gabor and Zachow, Stefan and Krischek, {\"O}zlem and Preim, Bernhard}, title = {Generierung qualitativ hochwertiger Modelle f{\"u}r die Simulation von Blutfluss in zerebralen Aneurysmen}, series = {Proc. of Simulation and Visualization 2008}, booktitle = {Proc. of Simulation and Visualization 2008}, editor = {Hauser, Helwig}, pages = {221 -- 235}, year = {2008}, language = {en} } @inproceedings{DornheimBornZachowetal.2008, author = {Dornheim, Jana and Born, Silvia and Zachow, Stefan and Gessat, Michael and Wellein, Daniela and Strauß, Gero and Preim, Bernhard and Bartz, Dirk}, title = {Bildanalyse, Visualisierung und Modellerstellung f{\"u}r die Implantatplanung im Mittelohr}, series = {Proc. of Simulation and Visualization 2008}, booktitle = {Proc. of Simulation and Visualization 2008}, editor = {Hauser, Helwig}, pages = {139 -- 154}, year = {2008}, language = {en} } @article{SteinmannBartschZachowetal.2008, author = {Steinmann, Alexander and Bartsch, Peter and Zachow, Stefan and Hildebrandt, Thomas}, title = {Breathing Easily: Simulation of airflow in human noses can become a useful rhinosurgery planning tool}, series = {ANSYS Advantage}, volume = {Vol. II, No. 1}, journal = {ANSYS Advantage}, pages = {30 -- 31}, year = {2008}, language = {en} } @article{WeiserZachowDeuflhard2010, author = {Weiser, Martin and Zachow, Stefan and Deuflhard, Peter}, title = {Craniofacial Surgery Planning Based on Virtual Patient Models}, series = {it - Information Technology}, volume = {52}, journal = {it - Information Technology}, number = {5}, publisher = {Oldenbourg Verlagsgruppe}, doi = {10.1524/itit.2010.0600}, pages = {258 -- 263}, year = {2010}, language = {en} } @incollection{ZachowHahnLange2010, author = {Zachow, Stefan and Hahn, Horst and Lange, Thomas}, title = {Computerassistierte Chirugieplanung}, series = {Computerassistierte Chirurgie}, booktitle = {Computerassistierte Chirurgie}, editor = {Schlag, Peter and Eulenstein, Sebastian and Lange, Thomas}, publisher = {Elsevier}, pages = {119 -- 149}, year = {2010}, language = {en} } @inproceedings{KainmuellerLameckerSeimetal.2010, author = {Kainm{\"u}ller, Dagmar and Lamecker, Hans and Seim, Heiko and Zachow, Stefan and Hege, Hans-Christian}, title = {Improving Deformable Surface Meshes through Omni-directional Displacements and MRFs}, series = {Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI)}, volume = {6361}, booktitle = {Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI)}, editor = {Navab, Tianzi and P. W. Pluim, Josien and Viergever, Max}, publisher = {Springer}, doi = {10.1007/978-3-642-15705-9_28}, pages = {227 -- 234}, year = {2010}, language = {en} } @inproceedings{ZachowKubiackMalinowskietal.2010, author = {Zachow, Stefan and Kubiack, Kim and Malinowski, Jana and Lamecker, Hans and Essig, Harald and Gellrich, Nils-Claudius}, title = {Modellgest{\"u}tzte chirurgische Rekonstruktion komplexer Mittelgesichtsfrakturen}, series = {Proc. BMT, Biomed Tech 2010}, volume = {55 (Suppl 1)}, booktitle = {Proc. BMT, Biomed Tech 2010}, publisher = {Walter de Gruyter-Verlag}, pages = {107 -- 108}, year = {2010}, language = {de} } @inproceedings{LameckerKainmuellerSeimetal.2010, author = {Lamecker, Hans and Kainm{\"u}ller, Dagmar and Seim, Heiko and Zachow, Stefan}, title = {Automatische 3D Rekonstruktion des Unterkiefers und der Mandibul{\"a}rnerven auf Basis dentaler Bildgebung}, series = {Proc. BMT, Biomed Tech}, volume = {55 (Suppl. 1)}, booktitle = {Proc. BMT, Biomed Tech}, publisher = {Walter de Gruyter-Verlag}, pages = {35 -- 36}, year = {2010}, language = {en} } @article{DworzakLameckervonBergetal.2010, author = {Dworzak, Jalda and Lamecker, Hans and von Berg, Jens and Klinder, Tobias and Lorenz, Cristian and Kainm{\"u}ller, Dagmar and Seim, Heiko and Hege, Hans-Christian and Zachow, Stefan}, title = {3D Reconstruction of the Human Rib Cage from 2D Projection Images using a Statistical Shape Model}, series = {Int. J. Comput. Assist. Radiol. Surg.}, volume = {5}, journal = {Int. J. Comput. Assist. Radiol. Surg.}, number = {2}, publisher = {Springer}, issn = {1861-6410}, doi = {10.1007/s11548-009-0390-2}, pages = {111 -- 124}, year = {2010}, language = {en} } @misc{KamerNoserLameckeretal.2006, author = {Kamer, Lukas and Noser, Hansrudi and Lamecker, Hans and Zachow, Stefan and Wittmers, Antonia and Kaup, Thomas and Schramm, Alexander and Hammer, Beat}, title = {Three-dimensional statistical shape analysis - A useful tool for developing a new type of orbital implant?}, publisher = {AO Development Institute, New Products Brochure 2/06}, pages = {20 -- 21}, year = {2006}, language = {en} } @article{HepptHildebrandtSteinmannetal.2007, author = {Heppt, Werner and Hildebrandt, Thomas and Steinmann, Alexander and Zachow, Stefan}, title = {Aesthetic and Function in Rhinoplasty}, series = {Springer Journal}, volume = {264 (Suppl 1), RL 126}, journal = {Springer Journal}, pages = {307}, year = {2007}, language = {en} } @inproceedings{ZachowZilskeHege2007, author = {Zachow, Stefan and Zilske, Michael and Hege, Hans-Christian}, title = {3D Reconstruction of Individual Anatomy from Medical Image Data: Segmentation and Geometry Processing}, series = {25. ANSYS Conference \& CADFEM Users' Meeting}, booktitle = {25. ANSYS Conference \& CADFEM Users' Meeting}, address = {Dresden}, year = {2007}, language = {en} } @article{GessatZachowBurgertetal.2007, author = {Gessat, Michael and Zachow, Stefan and Burgert, Oliver and Lemke, Heinz}, title = {Geometric Meshes in Medical Applications - Steps towards a specification of Geometric Models in DICOM}, series = {Int. J. of Computer Assisted Radiology and Surgery (CARS)}, journal = {Int. J. of Computer Assisted Radiology and Surgery (CARS)}, doi = {10.1007/s11548-007-0112-6}, pages = {440 -- 442}, year = {2007}, language = {en} } @article{HildebrandtZachowSteinmannetal.2007, author = {Hildebrandt, Thomas and Zachow, Stefan and Steinmann, Alexander and Heppt, Werner}, title = {Innovation in der Funktionell-{\"A}sthetischen Nasenchirurgie: Rhino-CFD}, series = {Face, Int. Mag. of Orofacial Esthetics}, journal = {Face, Int. Mag. of Orofacial Esthetics}, publisher = {Oemus Journale Leipzig}, pages = {20 -- 23}, year = {2007}, language = {en} } @article{ZachowSteinmannHildebrandtetal.2007, author = {Zachow, Stefan and Steinmann, Alexander and Hildebrandt, Thomas and Heppt, Werner}, title = {Understanding nasal airflow via CFD simulation and visualization}, series = {Proc. Computer Aided Surgery around the Head}, journal = {Proc. Computer Aided Surgery around the Head}, pages = {173 -- 176}, year = {2007}, language = {en} } @article{LameckerKamerWittmersetal.2007, author = {Lamecker, Hans and Kamer, Lukas and Wittmers, Antonia and Zachow, Stefan and Kaup, Thomas and Schramm, Alexander and Noser, Hansrudi and Hammer, Beat}, title = {A method for the three-dimensional statistical shape analysis of the bony orbit}, series = {Proc. Computer Aided Surgery around the Head}, journal = {Proc. Computer Aided Surgery around the Head}, pages = {94 -- 97}, year = {2007}, language = {en} } @inproceedings{ZachowLameckerElsholtzetal.2005, author = {Zachow, Stefan and Lamecker, Hans and Elsholtz, Barbara and Stiller, Michael}, title = {Reconstruction of mandibular dysplasia using a statistical 3D shape model}, series = {Proc. Computer Assisted Radiology and Surgery (CARS)}, booktitle = {Proc. Computer Assisted Radiology and Surgery (CARS)}, address = {Berlin, Germany}, doi = {10.1016/j.ics.2005.03.339}, pages = {1238 -- 1243}, year = {2005}, language = {en} } @inproceedings{NkenkeHaeuslerNeukametal.2005, author = {Nkenke, Emeka and H{\"a}usler, Gerd and Neukam, Friedrich and Zachow, Stefan}, title = {Streak artifact correction of CT data by optical 3D imaging in the simulation of orthognathic surgery}, series = {Computer Assisted Radiology and Surgery (CARS)}, booktitle = {Computer Assisted Radiology and Surgery (CARS)}, address = {Berlin Germany}, doi = {doi:10.1016/j.ics.2005.03.278}, year = {2005}, language = {en} } @inproceedings{NkenkeZachowHaeusler2005, author = {Nkenke, Emeka and Zachow, Stefan and H{\"a}usler, Gerd}, title = {Fusion von optischen 3D- und CT-Daten des Gebisses zur Metallartefaktkorrektur vor computerassistierter Planung MKG-chirurgischer Eingriffe}, series = {Symposium der Arbeitsgemeinschaf f{\"u}r Kieferchirurgie}, booktitle = {Symposium der Arbeitsgemeinschaf f{\"u}r Kieferchirurgie}, address = {Bad Homburg v.d.H}, year = {2005}, language = {en} } @article{LameckerZachowHaberletal.2005, author = {Lamecker, Hans and Zachow, Stefan and Haberl, Hannes and Stiller, Michael}, title = {Medical applications for statistical shape models}, series = {Computer Aided Surgery around the Head, Fortschritt-Berichte VDI - Biotechnik/Medizintechnik}, volume = {17 (258)}, journal = {Computer Aided Surgery around the Head, Fortschritt-Berichte VDI - Biotechnik/Medizintechnik}, pages = {61}, year = {2005}, language = {en} } @article{LameckerZachowWittmersetal.2006, author = {Lamecker, Hans and Zachow, Stefan and Wittmers, Antonia and Weber, Britta and Hege, Hans-Christian and Elsholtz, Barbara and Stiller, Michael}, title = {Automatic segmentation of mandibles in low-dose CT-data}, series = {Int. J. Computer Assisted Radiology and Surgery}, volume = {1(1)}, journal = {Int. J. Computer Assisted Radiology and Surgery}, pages = {393 -- 395}, year = {2006}, language = {en} } @article{LameckerZachowHegeetal.2006, author = {Lamecker, Hans and Zachow, Stefan and Hege, Hans-Christian and Z{\"o}ckler, Maja}, title = {Surgical treatment of craniosynostosis based on a statistical 3D-shape model}, series = {Int. J. Computer Assisted Radiology and Surgery}, volume = {1(1)}, journal = {Int. J. Computer Assisted Radiology and Surgery}, doi = {10.1007/s11548-006-0024-x}, pages = {253 -- 254}, year = {2006}, language = {en} } @article{ZachowHegeDeuflhard2006, author = {Zachow, Stefan and Hege, Hans-Christian and Deuflhard, Peter}, title = {Computer assisted planning in cranio-maxillofacial surgery}, series = {Journal of Computing and Information Technology}, volume = {14(1)}, journal = {Journal of Computing and Information Technology}, pages = {53 -- 64}, year = {2006}, language = {en} } @article{ZachowLameckerElsholtzetal.2006, author = {Zachow, Stefan and Lamecker, Hans and Elsholtz, Barbara and Stiller, Michael}, title = {Is the course of the mandibular nerve deducible from the shape of the mandible?}, series = {Int. J. of Computer Assisted Radiology and Surgery}, journal = {Int. J. of Computer Assisted Radiology and Surgery}, publisher = {Springer}, pages = {415 -- 417}, year = {2006}, language = {en} } @article{ZachowSteinmannHildebrandtetal.2006, author = {Zachow, Stefan and Steinmann, Alexander and Hildebrandt, Thomas and Weber, Rainer and Heppt, Werner}, title = {CFD simulation of nasal airflow: Towards treatment planning for functional rhinosurgery}, series = {Int. J. of Computer Assisted Radiology and Surgery}, journal = {Int. J. of Computer Assisted Radiology and Surgery}, publisher = {Springer}, pages = {165 -- 167}, year = {2006}, language = {en} } @inproceedings{EhlkeFrenzelRammetal., author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Shandiz, Mohsen Akbari and Anglin, Carolyn and Zachow, Stefan}, title = {Towards Robust Measurement Of Pelvic Parameters From AP Radiographs Using Articulated 3D Models}, series = {Computer Assisted Radiology and Surgery (CARS)}, booktitle = {Computer Assisted Radiology and Surgery (CARS)}, abstract = {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.}, language = {en} } @misc{EhlkeFrenzelRammetal., author = {Ehlke, Moritz and Frenzel, Thomas and Ramm, Heiko and Shandiz, Mohsen Akbari and Anglin, Carolyn and Zachow, Stefan}, title = {Towards Robust Measurement of Pelvic Parameters from AP Radiographs using Articulated 3D Models}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-53707}, abstract = {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.}, language = {en} } @article{LemanisZachowFusseisetal., author = {Lemanis, Robert and Zachow, Stefan and Fusseis, Florian and Hoffmann, Ren{\´e}}, title = {A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells}, series = {Paleobiology}, volume = {41}, journal = {Paleobiology}, number = {2}, publisher = {Cambridge University Press}, address = {Cambridge}, doi = {10.1017/pab.2014.17}, pages = {313 -- 329}, abstract = {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.}, language = {en} } @inproceedings{TackZachow, author = {Tack, Alexander and Zachow, Stefan}, title = {Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative}, series = {IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)}, booktitle = {IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)}, doi = {10.1109/ISBI.2019.8759201}, pages = {40 -- 43}, abstract = {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.}, language = {en} } @inproceedings{NeumannHellwichZachow, author = {Neumann, Mario and Hellwich, Olaf and Zachow, Stefan}, title = {Localization and Classification of Teeth in Cone Beam CT using Convolutional Neural Networks}, series = {Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC)}, booktitle = {Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC)}, isbn = {978-3-00-063717-9}, pages = {182 -- 188}, abstract = {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.}, language = {en} } @inproceedings{JoachimskyMaIckingetal., author = {Joachimsky, Robert and Ma, Lihong and Icking, Christian and Zachow, Stefan}, title = {A Collision-Aware Articulated Statistical Shape Model of the Human Spine}, series = {Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC)}, booktitle = {Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC)}, pages = {58 -- 64}, abstract = {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).}, language = {en} } @article{KraemerMaggioniBrissonetal., author = {Kr{\"a}mer, Martin and Maggioni, Marta and Brisson, Nicholas and Zachow, Stefan and Teichgr{\"a}ber, Ulf and Duda, Georg and Reichenbach, J{\"u}rgen}, title = {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}, series = {Magnetic Resonance Imaging}, volume = {63}, journal = {Magnetic Resonance Imaging}, number = {11}, doi = {10.1016/j.mri.2019.07.015}, pages = {29 -- 36}, abstract = {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.}, language = {en} } @inproceedings{AmbellanZachowvonTycowicz, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {An as-invariant-as-possible GL+(3)-based Statistical Shape Model}, series = {Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA)}, volume = {11846}, booktitle = {Proc. 7th MICCAI workshop on Mathematical Foundations of Computational Anatomy (MFCA)}, publisher = {Springer}, doi = {10.1007/978-3-030-33226-6_23}, pages = {219 -- 228}, abstract = {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.}, language = {en} } @misc{AmbellanZachowvonTycowicz, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {A Surface-Theoretic Approach for Statistical Shape Modeling}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74497}, abstract = {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.}, language = {en} } @misc{AmbellanZachowvonTycowicz, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {An as-invariant-as-possible GL+(3)-based Statistical Shape Model}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74566}, abstract = {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.}, language = {en} } @inproceedings{SahuStroemsdoerferMukhopadhyayetal., author = {Sahu, Manish and Str{\"o}msd{\"o}rfer, Ronja and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation}, series = {Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part III}, volume = {12263}, booktitle = {Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part III}, publisher = {Springer Nature}, doi = {https://doi.org/10.1007/978-3-030-59716-0_75}, abstract = {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.}, language = {en} } @article{SahuSzengelMukhopadhyayetal.2020, author = {Sahu, Manish and Szengel, Angelika and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {Surgical phase recognition by learning phase transitions}, series = {Current Directions in Biomedical Engineering (CDBME)}, volume = {6}, journal = {Current Directions in Biomedical Engineering (CDBME)}, number = {1}, publisher = {De Gruyter}, doi = {https://doi.org/10.1515/cdbme-2020-0037}, pages = {20200037}, year = {2020}, abstract = {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.}, language = {en} } @misc{SahuSzengelMukhopadhyayetal., author = {Sahu, Manish and Szengel, Angelika and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {Analyzing laparoscopic cholecystectomy with deep learning: automatic detection of surgical tools and phases}, series = {28th International Congress of the European Association for Endoscopic Surgery (EAES)}, journal = {28th International Congress of the European Association for Endoscopic Surgery (EAES)}, abstract = {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.}, language = {en} } @article{AmbellanZachowvonTycowicz, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {Rigid Motion Invariant Statistical Shape Modeling based on Discrete Fundamental Forms}, series = {Medical Image Analysis}, volume = {73}, journal = {Medical Image Analysis}, doi = {10.1016/j.media.2021.102178}, abstract = {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.}, language = {en} } @article{SahuMukhopadhyayZachow, author = {Sahu, Manish and Mukhopadhyay, Anirban and Zachow, Stefan}, title = {Simulation-to-Real domain adaptation with teacher-student learning for endoscopic instrument segmentation}, series = {International Journal of Computer Assisted Radiology and Surgery}, volume = {16}, journal = {International Journal of Computer Assisted Radiology and Surgery}, publisher = {Springer Nature}, doi = {10.1007/s11548-021-02383-4}, pages = {849 -- 859}, abstract = {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.}, language = {en} } @inproceedings{EstacioEhlkeTacketal., author = {Estacio, Laura and Ehlke, Moritz and Tack, Alexander and Castro-Gutierrez, Eveling and Lamecker, Hans and Mora, Rensso and Zachow, Stefan}, title = {Unsupervised Detection of Disturbances in 2D Radiographs}, series = {2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)}, booktitle = {2021 IEEE 18th International Symposium on Biomedical Imaging (ISBI)}, doi = {10.1109/ISBI48211.2021.9434091}, pages = {367 -- 370}, abstract = {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.}, language = {en} } @misc{AmbellanZachowvonTycowicz, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {Geodesic B-Score for Improved Assessment of Knee Osteoarthritis}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81930}, abstract = {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.}, language = {en} } @article{TackPreimZachow, author = {Tack, Alexander and Preim, Bernhard and Zachow, Stefan}, title = {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}, series = {Computer Methods and Programs in Biomedicine}, volume = {205}, journal = {Computer Methods and Programs in Biomedicine}, number = {106080}, doi = {https://doi.org/10.1016/j.cmpb.2021.106080}, abstract = {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.}, language = {de} } @inproceedings{AmbellanZachowvonTycowicz, author = {Ambellan, Felix and Zachow, Stefan and von Tycowicz, Christoph}, title = {Geodesic B-Score for Improved Assessment of Knee Osteoarthritis}, series = {Proc. Information Processing in Medical Imaging (IPMI)}, booktitle = {Proc. Information Processing in Medical Imaging (IPMI)}, doi = {10.1007/978-3-030-78191-0_14}, pages = {177 -- 188}, abstract = {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.}, language = {en} } @article{HembusAmbellanZachowetal.2021, author = {Hembus, Jessica and Ambellan, Felix and Zachow, Stefan and Bader, Rainer}, title = {Establishment of a rolling-sliding test bench to analyze abrasive wear propagation of different bearing materials for knee implants}, series = {Applied Sciences}, volume = {11}, journal = {Applied Sciences}, number = {4}, doi = {10.3390/app11041886}, pages = {15}, year = {2021}, abstract = {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.}, language = {en} }