@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} }