TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Zöckler, Maja T1 - Surgical treatment of craniosynostosis based on a statistical 3D-shape model JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2006 U6 - https://doi.org/10.1007/s11548-006-0024-x VL - 1(1) SP - 253 EP - 254 ER - TY - GEN A1 - Sahu, Manish A1 - Dill, Sabrina A1 - Mukhopadyay, Anirban A1 - Zachow, Stefan T1 - Surgical Tool Presence Detection for Cataract Procedures N2 - This article outlines the submission to the CATARACTS challenge for automatic tool presence detection [1]. Our approach for this multi-label classification problem comprises labelset-based sampling, a CNN architecture and temporal smothing as described in [3], which we call ZIB-Res-TS. T3 - ZIB-Report - 18-28 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69110 SN - 1438-0064 ER - TY - JOUR A1 - Sahu, Manish A1 - Szengel, Angelika A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Surgical phase recognition by learning phase transitions JF - Current Directions in Biomedical Engineering (CDBME) N2 - Automatic recognition of surgical phases is an important component for developing an intra-operative context-aware system. Prior work in this area focuses on recognizing short-term tool usage patterns within surgical phases. However, the difference between intra- and inter-phase tool usage patterns has not been investigated for automatic phase recognition. We developed a Recurrent Neural Network (RNN), in particular a state-preserving Long Short Term Memory (LSTM) architecture to utilize the long-term evolution of tool usage within complete surgical procedures. For fully automatic tool presence detection from surgical video frames, a Convolutional Neural Network (CNN) based architecture namely ZIBNet is employed. Our proposed approach outperformed EndoNet by 8.1% on overall precision for phase detection tasks and 12.5% on meanAP for tool recognition tasks. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1515/cdbme-2020-0037 N1 - Nomination for the Best-Paper Award VL - 6 IS - 1 SP - 20200037 PB - De Gruyter ER - TY - CHAP A1 - Nkenke, Emeka A1 - Häusler, Gerd A1 - Neukam, Friedrich A1 - Zachow, Stefan T1 - Streak artifact correction of CT data by optical 3D imaging in the simulation of orthognathic surgery T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/doi:10.1016/j.ics.2005.03.278 CY - Berlin Germany ER - TY - GEN A1 - Ambellan, Felix A1 - Lamecker, Hans A1 - von Tycowicz, Christoph A1 - Zachow, Stefan T1 - Statistical Shape Models - Understanding and Mastering Variation in Anatomy N2 - In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring. T3 - ZIB-Report - 19-13 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72699 SN - 1438-0064 ER - TY - CHAP A1 - Ambellan, Felix A1 - Lamecker, Hans A1 - von Tycowicz, Christoph A1 - Zachow, Stefan ED - Rea, Paul M. T1 - Statistical Shape Models - Understanding and Mastering Variation in Anatomy T2 - Biomedical Visualisation N2 - In our chapter we are describing how to reconstruct three-dimensional anatomy from medical image data and how to build Statistical 3D Shape Models out of many such reconstructions yielding a new kind of anatomy that not only allows quantitative analysis of anatomical variation but also a visual exploration and educational visualization. Future digital anatomy atlases will not only show a static (average) anatomy but also its normal or pathological variation in three or even four dimensions, hence, illustrating growth and/or disease progression. Statistical Shape Models (SSMs) are geometric models that describe a collection of semantically similar objects in a very compact way. SSMs represent an average shape of many three-dimensional objects as well as their variation in shape. The creation of SSMs requires a correspondence mapping, which can be achieved e.g. by parameterization with a respective sampling. If a corresponding parameterization over all shapes can be established, variation between individual shape characteristics can be mathematically investigated. We will explain what Statistical Shape Models are and how they are constructed. Extensions of Statistical Shape Models will be motivated for articulated coupled structures. In addition to shape also the appearance of objects will be integrated into the concept. Appearance is a visual feature independent of shape that depends on observers or imaging techniques. Typical appearances are for instance the color and intensity of a visual surface of an object under particular lighting conditions, or measurements of material properties with computed tomography (CT) or magnetic resonance imaging (MRI). A combination of (articulated) statistical shape models with statistical models of appearance lead to articulated Statistical Shape and Appearance Models (a-SSAMs).After giving various examples of SSMs for human organs, skeletal structures, faces, and bodies, we will shortly describe clinical applications where such models have been successfully employed. Statistical Shape Models are the foundation for the analysis of anatomical cohort data, where characteristic shapes are correlated to demographic or epidemiologic data. SSMs consisting of several thousands of objects offer, in combination with statistical methods ormachine learning techniques, the possibility to identify characteristic clusters, thus being the foundation for advanced diagnostic disease scoring. Y1 - 2019 SN - 978-3-030-19384-3 SN - 978-3-030-19385-0 U6 - https://doi.org/10.1007/978-3-030-19385-0_5 VL - 3 IS - 1156 SP - 67 EP - 84 PB - Springer Nature Switzerland AG ET - 1 ER - TY - CHAP A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Statistical Shape Modeling of Musculoskeletal Structures and Its Applications T2 - Computational Radiology for Orthopaedic Interventions N2 - Statistical shape models (SSM) describe the shape variability contained in a given population. They are able to describe large populations of complex shapes with few degrees of freedom. This makes them a useful tool for a variety of tasks that arise in computer-aided madicine. In this chapter we are going to explain the basic methodology of SSMs and present a variety of examples, where SSMs have been successfully applied. Y1 - 2016 SN - 978-3-319-23481-6 U6 - https://doi.org/10.1007/978-3-319-23482-3 VL - 23 SP - 1 EP - 23 PB - Springer ER - TY - CHAP A1 - Lamecker, Hans A1 - Zöckler, Maja A1 - Haberl, Hannes A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - Statistical shape modeling for craniosynostosis planning T2 - 2nd International Conference Advanced Digital Technology in Head and Neck Reconstruction 2005, Abstract Volume Y1 - 2005 SP - 64 CY - Banff, Alberta ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Liu, Tuo A1 - Kahl, Christoph A1 - Andrea, Hildebrandt A1 - Zachow, Stefan T1 - Statistical Learning of Facial Expressions Improves Realism of Animated Avatar Faces JF - Frontiers in Virtual Reality Y1 - 2021 U6 - https://doi.org/10.3389/frvir.2021.619811 VL - 2 SP - 1 EP - 13 PB - Frontiers ER - TY - GEN A1 - Grewe, Carl Martin A1 - Le Roux, Gabriel A1 - Pilz, Sven-Kristofer A1 - Zachow, Stefan T1 - Spotting the Details: The Various Facets of Facial Expressions N2 - 3D Morphable Models (MM) are a popular tool for analysis and synthesis of facial expressions. They represent plausible variations in facial shape and appearance within a low-dimensional parameter space. Fitted to a face scan, the model's parameters compactly encode its expression patterns. This expression code can be used, for instance, as a feature in automatic facial expression recognition. For accurate classification, an MM that can adequately represent the various characteristic facets and variants of each expression is necessary. Currently available MMs are limited in the diversity of expression patterns. We present a novel high-quality Facial Expression Morphable Model built from a large-scale face database as a tool for expression analysis and synthesis. Establishment of accurate dense correspondence, up to finest skin features, enables a detailed statistical analysis of facial expressions. Various characteristic shape patterns are identified for each expression. The results of our analysis give rise to a new facial expression code. We demonstrate the advantages of such a code for the automatic recognition of expressions, and compare the accuracy of our classifier to state-of-the-art. T3 - ZIB-Report - 18-06 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-67696 SN - 1438-0064 ER - TY - CHAP A1 - Grewe, Carl Martin A1 - le Roux, Gabriel A1 - Pilz, Sven-Kristofer A1 - Zachow, Stefan T1 - Spotting the Details: The Various Facets of Facial Expressions T2 - IEEE International Conference on Automatic Face and Gesture Recognition Y1 - 2018 U6 - https://doi.org/10.1109/FG.2018.00049 SP - 286 EP - 293 ER - TY - CHAP A1 - Zachow, Stefan A1 - Weiser, Martin A1 - Hege, Hans-Christian A1 - Deuflhard, Peter ED - Payan, Y. T1 - Soft Tissue Prediction in Computer Assisted Maxillofacial Surgery Planning T2 - Biomechanics Applied to Computer Assisted Surgery Y1 - 2005 SP - 277 EP - 298 PB - Research Signpost ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Simulation-to-Real domain adaptation with teacher-student learning for endoscopic instrument segmentation JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose Segmentation of surgical instruments in endoscopic video streams is essential for automated surgical scene understanding and process modeling. However, relying on fully supervised deep learning for this task is challenging because manual annotation occupies valuable time of the clinical experts. Methods We introduce a teacher–student learning approach that learns jointly from annotated simulation data and unlabeled real data to tackle the challenges in simulation-to-real unsupervised domain adaptation for endoscopic image segmentation. Results Empirical results on three datasets highlight the effectiveness of the proposed framework over current approaches for the endoscopic instrument segmentation task. Additionally, we provide analysis of major factors affecting the performance on all datasets to highlight the strengths and failure modes of our approach. Conclusions We show that our proposed approach can successfully exploit the unlabeled real endoscopic video frames and improve generalization performance over pure simulation-based training and the previous state-of-the-art. This takes us one step closer to effective segmentation of surgical instrument in the annotation scarce setting. Y1 - 2021 U6 - https://doi.org/10.1007/s11548-021-02383-4 N1 - Honorary Mention: Machine Learning for Computer-Assisted Intervention (CAI) Award @IPCAI2021 N1 - Honorary Mention: Audience Award for Best Innovation @IPCAI2021 VL - 16 SP - 849 EP - 859 PB - Springer Nature ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Mun, Seong T1 - Shape-based Modeling Approach for the Estimation of Individual Facial Mimics in Craniofacial Surgery Planning T2 - Proc. SPIE Medical Imaging 2002: Visualization, Image-Guided Procedures, and Display Y1 - 2002 VL - 4681 SP - 242 EP - 248 CY - San Diego, USA target ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse Data JF - arXiv N2 - The reconstruction of an object's shape or surface from a set of 3D points is a common topic in materials and life sciences, computationally handled in computer graphics. Such points usually stem from optical or tactile 3D coordinate measuring equipment. Surface reconstruction also appears in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or the alignment of intra-operative navigation and preoperative planning data. In contrast to mere 3D point clouds, medical imaging yields contextual information on the 3D point data that can be used to adopt prior information on the shape that is to be reconstructed from the measurements. In this work we propose to use a statistical shape model (SSM) as a prior for surface reconstruction. The prior knowledge is represented by a point distribution model (PDM) that is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we reformulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given measurements are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are oriented according to the surface normals at the PDM points, a surface-based tting is accomplished. By estimating the parameters of the GMM in a maximum a posteriori manner, the reconstruction of the surface from the given measurements is achieved. Extensive experiments suggest that our proposed approach leads to superior surface reconstructions compared to Iterative Closest Point (ICP) methods. Y1 - 2016 SP - 1602.08425v1 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds JF - Medical Image Analysis N2 - The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. Y1 - 2017 UR - http://www.sciencedirect.com/science/article/pii/S1361841517300233 U6 - https://doi.org/10.1016/j.media.2017.02.005 VL - 38 SP - 77 EP - 89 ER - TY - GEN A1 - Sharma, Gulshan A1 - Saevarsson, Stefan A1 - Amiri, Shahram A1 - Montgomery, Sigrun A1 - Ramm, Heiko A1 - Lichti, Derek A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Sequential-Biplane Radiography for Measuring Pre and Post Total Knee Arthroplasty Kinematics T2 - 58th Annual Meeting of the Orthopaedic Research Society (ORS) Y1 - 2012 CY - San Francisco, CA ER - TY - CHAP A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Segmentation of Bony Structures with Ligament Attachment Sites T2 - Bildverarbeitung für die Medizin 2008 Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-78640-5_42 SP - 207 EP - 211 PB - Springer ER - TY - GEN A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Akbari Shandiz, Mohsen A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Robust Measurement of Natural Acetabular Orientation from AP Radiographs using Articulated 3D Shape and Intensity Models T3 - ZIB-Report - 14-12 KW - articulated shape and intensity models KW - 3D reconstruction KW - acetabular orientation KW - image registration Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-49824 SN - 1438-0064 ER - TY - CHAP A1 - Kahnt, Max A1 - Galloway, Francis A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Taylor, Mark A1 - Zachow, Stefan T1 - Robust and Intuitive Meshing of Bone-Implant Compounds T2 - CURAC Y1 - 2011 SP - 71 EP - 74 CY - Magdeburg ER - TY - CHAP A1 - Mukhopadhyay, Anirban A1 - Morillo, Oscar A1 - Zachow, Stefan A1 - Lamecker, Hans T1 - Robust and Accurate Appearance Models Based on Joint Dictionary Learning Data from the Osteoarthritis Initiative T2 - Lecture Notes in Computer Science, Patch-Based Techniques in Medical Imaging. Patch-MI 2016 N2 - Deformable model-based approaches to 3D image segmentation have been shown to be highly successful. Such methodology requires an appearance model that drives the deformation of a geometric model to the image data. Appearance models are usually either created heuristically or through supervised learning. Heuristic methods have been shown to work effectively in many applications but are hard to transfer from one application (imaging modality/anatomical structure) to another. On the contrary, supervised learning approaches can learn patterns from a collection of annotated training data. In this work, we show that the supervised joint dictionary learning technique is capable of overcoming the traditional drawbacks of the heuristic approaches. Our evaluation based on two different applications (liver/CT and knee/MR) reveals that our approach generates appearance models, which can be used effectively and efficiently in a deformable model-based segmentation framework. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-47118-1_4 VL - 9993 SP - 25 EP - 33 ER - TY - JOUR A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Rigid Motion Invariant Statistical Shape Modeling based on Discrete Fundamental Forms JF - Medical Image Analysis N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. Additionally, as planar configurations form a submanifold in shape space, our representation allows for effective estimation of quasi-isometric surfaces flattenings. We evaluate the performance of our model w.r.t. shape-based classification of hippocampus and femur malformations due to Alzheimer's disease and osteoarthritis, respectively. In particular, we achieve state-of-the-art accuracies outperforming the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model's ability of capturing biological shape variability, we carry out an analysis of specificity and generalization ability. Y1 - 2021 U6 - https://doi.org/10.1016/j.media.2021.102178 VL - 73 ER - TY - GEN A1 - Grewe, C. Martin A1 - Zachow, Stefan T1 - Release of the FexMM for the Open Virtual Mirror Framework N2 - THIS MODEL IS FOR NON-COMMERCIAL RESEARCH PURPOSES. ONLY MEMBERS OF UNIVERSITIES OR NON-COMMERCIAL RESEARCH INSTITUTES ARE ELIGIBLE TO APPLY. 1. Download, fill, and sign the form available from: https://media.githubusercontent.com/media/mgrewe/ovmf/main/data/fexmm_license_agreement.pdf 2. Send the signed form to: fexmm@zib.de NOTE: Use an official email address of your institution for the request. Y1 - 2021 U6 - https://doi.org/10.12752/8532 ER - TY - JOUR A1 - Campoli, Gianni A1 - Baka, Nora A1 - Kaptein, Bart A1 - Valstar, Edward A1 - Zachow, Stefan A1 - Weinans, Harrie A1 - Zadpoor, Amir Abbas T1 - Relationship between the shape and density distribution of the femur and its natural frequencies of vibration JF - Journal of Biomechanics N2 - It has been recently suggested that mechanical loads applied at frequencies close to the natural frequencies of bone could enhance bone apposition due to the resonance phenomenon. Other applications of bone modal analysis are also suggested. For the above-mentioned applications, it is important to understand how patient-specific bone shape and density distribution influence the natural frequencies of bones. We used finite element models to study the effects of bone shape and density distribution on the natural frequencies of the femur in free boundary conditions. A statistical shape and appearance model that describes shape and density distribution independently was created, based on a training set of 27 femora. The natural frequencies were then calculated for different shape modes varied around the mean shape while keeping the mean density distribution, for different appearance modes around the mean density distribution while keeping the mean bone shape, and for the 27 training femora. Single shape or appearance modes could cause up to 15% variations in the natural frequencies with certain modes having the greatest impact. For the actual femora, shape and density distribution changed the natural frequencies by up to 38%. First appearance mode that describes the general cortical bone thickness and trabecular bone density had one of the strongest impacts. The first appearance mode could therefore provide a sensitive measure of general bone health and disease progression. Since shape and density could cause large variations in the calculated natural frequencies, patient-specific FE models are needed for accurate estimation of bone natural frequencies. Y1 - 2014 U6 - https://doi.org/10.1016/j.jbiomech.2014.08.008 VL - 47 SP - 3334 EP - 3343 PB - Elsevier ER - TY - CHAP A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Reconstruction of mandibular dysplasia using a statistical 3D shape model T2 - Proc. Computer Assisted Radiology and Surgery (CARS) Y1 - 2005 U6 - https://doi.org/10.1016/j.ics.2005.03.339 SP - 1238 EP - 1243 CY - Berlin, Germany ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Galloway, Robert T1 - Realistic prediction of individual facial emotion expressions for craniofacial surgery simulations T2 - Proc. SPIE medical Imaging 2003 Y1 - 2003 U6 - https://doi.org/10.1117/12.479584 VL - 5029 SP - 520 EP - 527 CY - San Diego, CA, USA ER - TY - JOUR A1 - Saevarsson, Stefan A1 - Sharma, Gulshan A1 - Amiri, Shahram A1 - Montgomery, Sigrun A1 - Ramm, Heiko A1 - Lichti, Derek A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Radiological method for measuring patellofemoral tracking and tibiofemoral kinematics before and after total knee replacement JF - Bone and Joint Research Y1 - 2012 UR - http://www.bjr.boneandjoint.org.uk/content/1/10/263.short U6 - https://doi.org/10.1302/2046-3758.110.2000117 VL - 1 IS - 10 SP - 263 EP - 271 ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Pelvic tilt compensates for increased acetabular anteversion JF - International Orthopaedics N2 - Pelvic tilt determines functional orientation of the acetabulum. In this study, we investigated the interaction of pelvic tilt and functional acetabular anteversion (AA) in supine position. Y1 - 2015 U6 - https://doi.org/10.1007/s00264-015-2949-6 VL - 40 IS - 8 SP - 1571 EP - 1575 ER - TY - JOUR A1 - Lube, Juliane A1 - Flack, Natasha A1 - Cotofana, Sebastian A1 - Özkurtul, Orkun A1 - Woodley, Stephanie A1 - Zachow, Stefan A1 - Hammer, Niels T1 - Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature JF - Surgical and Radiologic Anatomy N2 - Purpose: Morphological data pertaining to the pelvis and lower extremity muscles are increasingly being used in biomechanical modeling to compare healthy and pathological conditions. Very few data sets exist that encompass all of the muscles of the lower limb, allowing for comparisons between regions. The aims of this study were to (a) provide physiological cross-sectional area (PCSA) data for the pelvic, thigh, and leg muscles in young, healthy participants, using magnetic resonance imaging (MRI), and (b) to compare these data with summarized PCSAs obtained from the literature. Materials and Methods: Six young and healthy volunteers participated and were scanned using 3 T MRI. PCSAs were calculated from volumetric segmentations obtained bilaterally of 28 muscles/muscle groups of the pelvis, thigh, and leg. These data were compared to published, summarized PCSA data derived from cadaveric, computed tomography, MRI and ultrasound studies. Results: The PCSA of the pelvis, thigh, and leg muscles tended to be 20–130% larger in males than in females, except for the gemelli which were 34% smaller in males, and semitendinosus and triceps surae which did not differ (<20% different). The dominant and the non-dominant sides showed similar and minutely different PCSA with less than 18% difference between sides. Comparison to other studies revealed wide ranges within, and large differences between, the cadaveric and imaging PCSA data. Comparison of the PCSA of this study and published literature revealed major differences in the iliopsoas, gluteus minimus, tensor fasciae latae, gemelli, obturator internus, biceps femoris, quadriceps femoris, and the deep leg flexor muscles. Conclusions: These volume-derived PCSAs of the pelvic and lower limb muscles alongside the data synthesised from the literature may serve as a basis for comparative and biomechanical studies of the living and healthy young, and enable calculation of muscle forces. Comparison of the literature revealed large variations in PCSA from each of the different investigative modalities, hampering omparability between studies. Sample size, age, post-mortem changes of muscle tone, chemical fixation of cadaveric tissues, and the underlying physics of the imaging techniques may potentially influence PCSA calculations. Y1 - 2017 U6 - https://doi.org/10.1007/s00276-016-1807-6 VL - 39 IS - 8 SP - 849 EP - 857 ER - TY - JOUR A1 - Ramm, Heiko A1 - Kahnt, Max A1 - Zachow, Stefan T1 - Patientenspezifische Simulationsmodelle für die funktionelle Analyse von künstlichem Gelenkersatz JF - Computer Aided Medical Engineering (CaMe) Y1 - 2012 VL - 3 IS - 2 SP - 30 EP - 36 ER - TY - CHAP A1 - Zachow, Stefan A1 - Lueth, Tim A1 - Stalling, Detlev A1 - Hein, Andreas A1 - Klein, Martin A1 - Menneking, Horst T1 - Optimized Arrangement of Osseointegrated Implants: A Surgical Planning System for the Fixation of Facial Protheses T2 - Computer Assisted Radiology and Surgery (CARS’99) Y1 - 1999 SP - 942 EP - 946 PB - Elsevier Science B.V. ER - TY - CHAP A1 - Zachow, Stefan A1 - Hierl, Thomas A1 - Erdmann, Bodo T1 - On the Predictability of tissue changes after osteotomy planning in maxillofacial surgery T2 - Computer Assisted Radiology and Surgery (CARS) Y1 - 2004 U6 - https://doi.org/10.1016/j.ics.2004.03.043 SP - 648 EP - 653 CY - Chicago, USA ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Deuflhard, Peter A1 - Hege, Hans-Christian T1 - On constitutive modeling of soft tissue for the long-term prediction of cranio-maxillofacial surgery outcome T2 - International Congress Series, CARS2003, Computer Assisted Radiology and Surgery, Proceedings of the 17th International Congress and Exhibition Y1 - 2003 U6 - https://doi.org/10.1016/S0531-5131(03)00500-4 VL - 1256 SP - 343 EP - 348 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Heller, Markus O. A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Omnidirectional Displacements for Deformable Surfaces JF - Medical Image Analysis Y1 - 2013 U6 - https://doi.org/10.1016/j.media.2012.11.006 VL - 17 IS - 4 SP - 429 EP - 441 PB - Elsevier ER - TY - JOUR A1 - Brüning, Jan A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Numerical Analysis of Nasal Breathing - A Pilot Study JF - Facial Plastic Surgery N2 - Background: Currently, there is no fully sufficient way to differentiate between symptomatic and normal nasal breathing. Using the nose’s total resistance is disputed as a valid means to objectify nasal airflow, and the need for a more comprehensive diagnostic method is increasing. This work’s aim was to test a novel approach considering intranasal wall shear stress as well as static pressure maps obtained by computational fluid dynamics (CFD). Methods: X-ray computed tomography (CT) scan data of six symptom-free subjects and seven symptomatic patients were used. Patient-specific geometries of the nasal cavity were segmented from these data sets. Inspiratory and expiratory steady airflow simulations were performed using CFD. Calculated static pressures and wall shear stresses (WSS) were mapped onto a common template of the nasal septum, allowing for comparison of these parameters between the two patient groups. Results: Significant differences in wall shear stress distributions during the inspiratory phase could be identified between the two groups, whereas no differences were found for the expiratory phase. It is assumed that one essential feature of normal nasal breathing probably consists in distinctively different intranasal flow fields for inspiration and expiration. This is in accordance with previous investigations. Conclusion: The proposed method seems to be a promising tool for developing a new kind of patient-specific assessment of nasal breathing. However, more studies and a greater case number of data with an expanded focus, would be ideal. Y1 - 2017 U6 - https://doi.org/doi:10.1055/s-0037-1603789 VL - 33 IS - 4 SP - 388 EP - 395 ER - TY - JOUR A1 - Hoffmann, René A1 - Schultz, Julia A. A1 - Schellhorn, Rico A1 - Rybacki, Erik A1 - Keupp, Helmut A1 - Gerden, S. R. A1 - Lemanis, Robert A1 - Zachow, Stefan T1 - Non-invasive imaging methods applied to neo- and paleontological cephalopod research JF - Biogeosciences N2 - Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied. Y1 - 2014 U6 - https://doi.org/10.5194/bg-11-2721-2014 N1 - To access the corresponding discussion paper go to www.biogeosciences-discuss.net/10/18803/2013/ - Biogeosciences Discuss., 10, 18803-18851, 2013 VL - 11 IS - 10 SP - 2721 EP - 2739 ER - TY - GEN A1 - Hoffmann, René A1 - Schultz, Julia A. A1 - Schellhorn, Rico A1 - Rybacki, Erik A1 - Keupp, Helmut A1 - Lemanis, Robert A1 - Zachow, Stefan T1 - Non-invasive imaging methods applied to neo- and paleo-ontological cephalopod research N2 - Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum/maximum size of objects that can be studied, the degree of post-processing needed and availability. The main application of the methods is seen in morphometry and volumetry of cephalopod shells. In particular we present a method for precise buoyancy calculation. Therefore, cephalopod shells were scanned together with different reference bodies, an approach developed in medical sciences. It is necessary to know the volume of the reference bodies, which should have similar absorption properties like the object of interest. Exact volumes can be obtained from surface scanning. Depending on the dimensions of the study object different computed tomography techniques were applied. T3 - ZIB-Report - 14-18 Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-50300 SN - 1438-0064 ER - TY - CHAP A1 - Hoffmann, René A1 - Zachow, Stefan T1 - Non-invasive approach to shed new light on the buoyancy business of chambered cephalopods (Mollusca) T2 - Proc. of the Intl. Assoc. for Mathematical Geosciences, Salzburg Y1 - 2011 U6 - https://doi.org/10.5242/iamg.2011.0163 SP - 1 EP - 11 ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heller, Markus O. A1 - Hege, Hans-Christian T1 - Multi-Object Segmentation with Coupled Deformable Models T2 - Proc. Medical Image Understanding and Analysis Y1 - 2008 SP - 34 EP - 38 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Multi-object Segmentation with Coupled Deformable Models JF - Annals of the British Machine Vision Association (BMVA) Y1 - 2009 VL - 5 SP - 1 EP - 10 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan T1 - Multi-object segmentation of head bones JF - MIDAS Journal Y1 - 2009 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - More Mathematics into Medicine! T2 - Production Factor Mathematics Y1 - 2010 UR - http://www.springer.com/mathematics/book/978-3-642-11247-8 SP - 357 EP - 378 PB - Springer ER - TY - CHAP A1 - Zachow, Stefan A1 - Weiser, Martin A1 - Deuflhard, Peter ED - Niederlag, Wolfgang ED - Lemke, Heinz ED - Meixensberger, Jürgen ED - Baumann, Michael T1 - Modellgestützte Operationsplanung in der Kopfchirurgie T2 - Modellgestützte Therapie Y1 - 2008 SP - 140 EP - 156 PB - Health Academy ER - TY - CHAP A1 - Zachow, Stefan A1 - Kubiack, Kim A1 - Malinowski, Jana A1 - Lamecker, Hans A1 - Essig, Harald A1 - Gellrich, Nils-Claudius T1 - Modellgestützte chirurgische Rekonstruktion komplexer Mittelgesichtsfrakturen T2 - Proc. BMT, Biomed Tech 2010 Y1 - 2010 VL - 55 (Suppl 1) SP - 107 EP - 108 PB - Walter de Gruyter-Verlag ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Kuss, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Menzel, Randolf A1 - Rybak, Juergen T1 - Model-based autosegmentation of the central brain of the honeybee, Apis mellifera, using active statistical shape models T2 - Proc. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain Y1 - 2008 U6 - https://doi.org/10.3389/conf.neuro.11.2008.01.064 ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Bindernagel, Matthias A1 - Malinowski, Jana A1 - Zachow, Stefan ED - v. Ginneken, B. T1 - Model-based Auto-Segmentation of Knee Bones and Cartilage in MRI Data T2 - Proc. MICCAI Workshop Medical Image Analysis for the Clinic Y1 - 2010 SP - 215 EP - 223 ER - TY - JOUR A1 - Dunlop, Jason A1 - Apanaskevich, Dmitry A1 - Lehmann, Jens A1 - Hoffmann, Rene A1 - Fusseis, Florian A1 - Ehlke, Moritz A1 - Zachow, Stefan A1 - Xiao, Xianghui T1 - Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus JF - BMC Evolutionary Biology N2 - Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases. Y1 - 2016 U6 - https://doi.org/10.1186/s12862-016-0777-y VL - 16 IS - 1 ER - TY - CHAP A1 - Stalling, Detlev A1 - Seebaß, Martin A1 - Zachow, Stefan T1 - Mehrschichtige Oberflächenmodelle zur computergestützten Planung in der Chirurgie T2 - Bildverarbeitung für die Medizin 1999 - Algorithmen, Anwendungen Y1 - 1999 SP - 203 EP - 207 PB - Springer-Verlag, Berlin ER - TY - GEN A1 - Stalling, Detlev A1 - Seebass, Martin A1 - Zachow, Stefan T1 - Mehrschichtige Oberflächenmodelle zur computergestützten Planung in der Chirurgie N2 - Polygonale Schädelmodelle bilden ein wichtiges Hilfsmittel für computergestützte Planungen im Bereich der plastischen Chirurgie. Wir beschreiben, wie derartige Modelle automatisch aus hochaufgelösten CT-Datensätzen erzeugt werden können. Durch einen lokal steuerbaren Simplifizierungsalgorithmus werden die Modelle so weit vereinfacht, daß auch auf kleineren Graphikcomputern interaktives Arbeiten möglich wird. Die Verwendung eines speziellen Transparenzmodells ermöglicht den ungehinderten Blick auf die bei der Planung relevanten Knochenstrukturen und läßt den Benutzer zugleich die Kopfumrisse des Patienten erkennen. T3 - ZIB-Report - TR-98-05 KW - Isoflächen KW - Simplifizierung KW - Transparenzen Y1 - 1998 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-5661 ER - TY - GEN A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - Mehr Mathematik wagen in der Medizin N2 - Der Artikel gibt einen Einblick in das reiche Feld der Zusammenarbeit zwischen Mathematik und Medizin. Beispielhaft werden drei Erfolgsmodelle dargestellt: Medizinische Bildgebung, mathematische Modellierung und Biosignalverarbeitung im Bereich der Dynamik des Herzens sowie mathematische Modellierung und Simulation in der Krebstherapie Hyperthermie und der Mund-Kiefer-Gesichts-Chirurgie. In allen Fällen existiert ein Gleichklang der Interessen von Medizin und Mathematik: Beide Disziplinen wollen die Resultate schnell und zuverlässig. Für die Klinik heißt das, dass notwendige Rechnungen in möglichst kurzer Zeit, und zwar auf dem PC, ablaufen müssen und dass die Resultate so genau und belastbar sein müssen, dass medizinische Entscheidungen darauf aufbauen können. Für die Mathematik folgt daraus, dass höchste Anforderungen an die Effizienz der verwendeten Algorithmen und die darauf aufbauende Software in Numerik und Visualisierung zu stellen sind. Jedes Kapitel endet mit einer Darstellung der Perspektive des jeweiligen Gebietes. Abschließend werden mögliche Handlungsoptionen für Politik und Wirtschaft diskutiert. T3 - ZIB-Report - 08-25 Y1 - 2008 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-10776 SN - 1438-0064 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - Mehr Mathematik wagen in der Medizin T2 - acatech diskutiert, Produktionsfaktor Mathematik - Wie Mathematik Technik und Wirtschaft bewegt Y1 - 2008 U6 - https://doi.org/10.1007/978-3-540-89435-3 SP - 435 EP - 459 PB - Springer ER - TY - JOUR A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Haberl, Hannes A1 - Stiller, Michael T1 - Medical applications for statistical shape models JF - Computer Aided Surgery around the Head, Fortschritt-Berichte VDI - Biotechnik/Medizintechnik Y1 - 2005 VL - 17 (258) SP - 61 ER - TY - CHAP A1 - Krämer, Martin A1 - Herrmann, Karl-Heinz A1 - Boeth, Heide A1 - Tycowicz, Christoph von A1 - König, Christian A1 - Zachow, Stefan A1 - Ehrig, Rainald A1 - Hege, Hans-Christian A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - Measuring 3D knee dynamics using center out radial ultra-short echo time trajectories with a low cost experimental setup T2 - ISMRM (International Society for Magnetic Resonance in Medicine), 23rd Annual Meeting 2015, Toronto, Canada Y1 - 2015 ER - TY - JOUR A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Maxillofacial surgery planning with 3D soft tissue prediction - modeling, planning, simulation JF - 2. Int. Conf. on Advanced Digital Technology in Head and Neck Reconstruction, Abstract 33 Y1 - 2005 SP - 64 CY - Banff, Alberta, CA ER - TY - GEN A1 - Deuflhard, Peter A1 - Zachow, Stefan T1 - Mathematische Therapie- und Operationsplanung Y1 - 2012 SP - 89 EP - 90 PB - Berliner Wirtschaftsgespräche e.V. CY - Berlin ER - TY - JOUR A1 - Deuflhard, Peter A1 - Weiser, Martin A1 - Zachow, Stefan T1 - Mathematics in Facial Surgery JF - AMS Notices Y1 - 2006 VL - 53 IS - 9 SP - 1012 EP - 1016 ER - TY - CHAP A1 - Neumann, Mario A1 - Hellwich, Olaf A1 - Zachow, Stefan T1 - Localization and Classification of Teeth in Cone Beam CT using Convolutional Neural Networks T2 - Proc. of the 18th annual conference on Computer- and Robot-assisted Surgery (CURAC) N2 - In dentistry, software-based medical image analysis and visualization provide efficient and accurate diagnostic and therapy planning capabilities. We present an approach for the automatic recognition of tooth types and positions in digital volume tomography (DVT). By using deep learning techniques in combination with dimensionality reduction through non-planar reformatting of the jaw anatomy, DVT data can be efficiently processed and teeth reliably recognized and classified, even in the presence of imaging artefacts, missing or dislocated teeth. We evaluated our approach, which is based on 2D Convolutional Neural Networks (CNNs), on 118 manually annotated cases of clinical DVT datasets. Our proposed method correctly classifies teeth with an accuracy of 94% within a limit of 2mm distance to ground truth labels. Y1 - 2019 SN - 978-3-00-063717-9 SP - 182 EP - 188 ER - TY - CHAP A1 - Amiranashvili, Tamaz A1 - Lüdke, David A1 - Li, Hongwei A1 - Menze, Bjoern A1 - Zachow, Stefan T1 - Learning Shape Reconstruction from Sparse Measurements with Neural Implicit Functions T2 - Medical Imaging with Deep Learning N2 - Reconstructing anatomical shapes from sparse or partial measurements relies on prior knowledge of shape variations that occur within a given population. Such shape priors are learned from example shapes, obtained by segmenting volumetric medical images. For existing models, the resolution of a learned shape prior is limited to the resolution of the training data. However, in clinical practice, volumetric images are often acquired with highly anisotropic voxel sizes, e.g. to reduce image acquisition time in MRI or radiation exposure in CT imaging. The missing shape information between the slices prohibits existing methods to learn a high-resolution shape prior. We introduce a method for high-resolution shape reconstruction from sparse measurements without relying on high-resolution ground truth for training. Our method is based on neural implicit shape representations and learns a continuous shape prior only from highly anisotropic segmentations. Furthermore, it is able to learn from shapes with a varying field of view and can reconstruct from various sparse input configurations. We demonstrate its effectiveness on two anatomical structures: vertebra and femur, and successfully reconstruct high-resolution shapes from sparse segmentations, using as few as three orthogonal slices. Y1 - 2022 ER - TY - JOUR A1 - Amiranashvili, Tamaz A1 - Lüdke, David A1 - Li, Hongwei Bran A1 - Zachow, Stefan A1 - Menze, Bjoern T1 - Learning continuous shape priors from sparse data with neural implicit functions JF - Medical Image Analysis N2 - Statistical shape models are an essential tool for various tasks in medical image analysis, including shape generation, reconstruction and classification. Shape models are learned from a population of example shapes, which are typically obtained through segmentation of volumetric medical images. In clinical practice, highly anisotropic volumetric scans with large slice distances are prevalent, e.g., to reduce radiation exposure in CT or image acquisition time in MR imaging. For existing shape modeling approaches, the resolution of the emerging model is limited to the resolution of the training shapes. Therefore, any missing information between slices prohibits existing methods from learning a high-resolution shape prior. We propose a novel shape modeling approach that can be trained on sparse, binary segmentation masks with large slice distances. This is achieved through employing continuous shape representations based on neural implicit functions. After training, our model can reconstruct shapes from various sparse inputs at high target resolutions beyond the resolution of individual training examples. We successfully reconstruct high-resolution shapes from as few as three orthogonal slices. Furthermore, our shape model allows us to embed various sparse segmentation masks into a common, low-dimensional latent space — independent of the acquisition direction, resolution, spacing, and field of view. We show that the emerging latent representation discriminates between healthy and pathological shapes, even when provided with sparse segmentation masks. Lastly, we qualitatively demonstrate that the emerging latent space is smooth and captures characteristic modes of shape variation. We evaluate our shape model on two anatomical structures: the lumbar vertebra and the distal femur, both from publicly available datasets. Y1 - 2024 U6 - https://doi.org/10.1016/j.media.2024.103099 VL - 94 SP - 103099 ER - TY - CHAP A1 - Lüdke, David A1 - Amiranashvili, Tamaz A1 - Ambellan, Felix A1 - Ezhov, Ivan A1 - Menze, Bjoern A1 - Zachow, Stefan T1 - Landmark-free Statistical Shape Modeling via Neural Flow Deformations T2 - Medical Image Computing and Computer Assisted Intervention - MICCAI 2022 N2 - Statistical shape modeling aims at capturing shape variations of an anatomical structure that occur within a given population. Shape models are employed in many tasks, such as shape reconstruction and image segmentation, but also shape generation and classification. Existing shape priors either require dense correspondence between training examples or lack robustness and topological guarantees. We present FlowSSM, a novel shape modeling approach that learns shape variability without requiring dense correspondence between training instances. It relies on a hierarchy of continuous deformation flows, which are parametrized by a neural network. Our model outperforms state-of-the-art methods in providing an expressive and robust shape prior for distal femur and liver. We show that the emerging latent representation is discriminative by separating healthy from pathological shapes. Ultimately, we demonstrate its effectiveness on two shape reconstruction tasks from partial data. Our source code is publicly available (https://github.com/davecasp/flowssm). Y1 - 2022 U6 - https://doi.org/10.1007/978-3-031-16434-7_44 VL - 13432 PB - Springer, Cham ER - TY - GEN A1 - Grewe, Carl Martin A1 - Lamecker, Hans A1 - Zachow, Stefan ED - Hermanussen, Michael T1 - Landmark-based Statistical Shape Analysis T2 - Auxology - Studying Human Growth and Development url Y1 - 2013 UR - http://www.schweizerbart.de/publications/detail/isbn/9783510652785 SP - 199 EP - 201 PB - Schweizerbart Verlag, Stuttgart ER - TY - GEN A1 - Sharma, Gulshan A1 - Ho, Karen A1 - Saevarsson, Stefan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Knee Pose and Geometry Pre- and Post-Total Knee Arthroplasty Using Computed Tomography T2 - 58th Annual Meeting of the Orthopaedic Research Society (ORS) Y1 - 2012 CY - San Francisco, CA ER - TY - GEN A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative (Supplementary Material) N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. Y1 - 2018 U6 - https://doi.org/10.12752/4.TMZ.1.0 N1 - Supplementary data to reproduce results from the related publication, including convolutional neural networks' weights. ER - TY - JOUR A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative JF - Osteoarthritis and Cartilage N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. Y1 - 2018 U6 - https://doi.org/10.1016/j.joca.2018.02.907 VL - 26 IS - 5 SP - 680 EP - 688 ER - TY - GEN A1 - Tack, Alexander A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Knee Menisci Segmentation using Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - Abstract: Objective: To present a novel method for automated segmentation of knee menisci from MRIs. To evaluate quantitative meniscal biomarkers for osteoarthritis (OA) estimated thereof. Method: A segmentation method employing convolutional neural networks in combination with statistical shape models was developed. Accuracy was evaluated on 88 manual segmentations. Meniscal volume, tibial coverage, and meniscal extrusion were computed and tested for differences between groups of OA, joint space narrowing (JSN), and WOMAC pain. Correlation between computed meniscal extrusion and MOAKS experts' readings was evaluated for 600 subjects. Suitability of biomarkers for predicting incident radiographic OA from baseline to 24 months was tested on a group of 552 patients (184 incident OA, 386 controls) by performing conditional logistic regression. Results: Segmentation accuracy measured as Dice Similarity Coefficient was 83.8% for medial menisci (MM) and 88.9% for lateral menisci (LM) at baseline, and 83.1% and 88.3% at 12-month follow-up. Medial tibial coverage was significantly lower for arthritic cases compared to non-arthritic ones. Medial meniscal extrusion was significantly higher for arthritic knees. A moderate correlation between automatically computed medial meniscal extrusion and experts' readings was found (ρ=0.44). Mean medial meniscal extrusion was significantly greater for incident OA cases compared to controls (1.16±0.93 mm vs. 0.83±0.92 mm; p<0.05). Conclusion: Especially for medial menisci an excellent segmentation accuracy was achieved. Our meniscal biomarkers were validated by comparison to experts' readings as well as analysis of differences w.r.t groups of OA, JSN, and WOMAC pain. It was confirmed that medial meniscal extrusion is a predictor for incident OA. T3 - ZIB-Report - 18-15 Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-68038 SN - 1438-0064 VL - 26 IS - 5 SP - 680 EP - 688 ER - TY - JOUR A1 - Saevarsson, Stefan A1 - Sharma, Gulshan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Hutchison, Carol A1 - Werle, Jason A1 - Montgomery, Sigrun A1 - Romeo, Carolina A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Kinematic Differences Between Gender Specific And Traditional Knee Implants JF - The Journal of Arthroplasty Y1 - 2013 U6 - https://doi.org/10.1016/j.arth.2013.01.021 VL - 28 IS - 9 SP - 1543 EP - 1550 ER - TY - CHAP A1 - Stefan, Saevarsson A1 - Gulshan, Sharma A1 - Sigrun, Montgomery A1 - Karen, Ho A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Hutchison, Carol A1 - Jason, Werle A1 - Carolyn, Anglin T1 - Kinematic Comparison Between Gender Specific and Traditional Femoral Implants T2 - 67th Canadian Orthopaedic Association (COA) Annual Meeting Y1 - 2012 ER - TY - GEN A1 - SK, Saevarsson A1 - GB, Sharma A1 - S, Montgomery A1 - KCT, Ho A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - C, Anglin T1 - Kinematic Comparison Between Gender Specific and Traditional Femoral Implants T2 - Proceedings of the 11th Alberta Biomedical Engineering (BME) Conference (Poster) Y1 - 2011 SP - 80 ER - TY - JOUR A1 - Zachow, Stefan A1 - Lamecker, Hans A1 - Elsholtz, Barbara A1 - Stiller, Michael T1 - Is the course of the mandibular nerve deducible from the shape of the mandible? JF - Int. J. of Computer Assisted Radiology and Surgery Y1 - 2006 SP - 415 EP - 417 PB - Springer ER - TY - JOUR A1 - Hoffmann, René A1 - Lemanis, Robert A1 - Falkenberg, Janina A1 - Schneider, Steffen A1 - Wesendonk, Hendrik A1 - Zachow, Stefan T1 - Integrating 2D and 3D shell morphology to disentangle the palaeobiology of ammonoids: A virtual approach JF - Palaeontology N2 - We demonstrate, based on data derived from computed tomography, that integrating 2D and 3D morphological data of ammonoid shells represent an important new approach to disentangle the palaeobiology of ammonoids. Characterization of ammonite morphology has long been constrained to 2D data and only a few studies collect ontogenetic data in 180° steps. We combine this traditional approach with 3D data collected from high-resolution nano-computed tomography. For this approach, ontogenetic morphological data of the hollow shell of a juvenile ammonite Kosmoceras (Jurassic, Callovian) is collected. 2D data is collected in 10° steps and show significant changes in shell morphology. Preserved hollow spines show multiple mineralized membranes never reported before, representing temporal changes of the ammonoid mantle tissue. 3D data show that chamber volumes do not always increase exponentially, as was generally assumed, but may represent a proxy for life events, e.g. stress phases. Furthermore, chamber volume cannot be simply derived from septal spacing in forms comparable to Kosmoceras. Vogel numbers, a 3D parameter for chamber shape, of Kosmoceras are similar to other ammonoids (Arnsbergites, Amauroceras) and modern cephalopods (Nautilus, Spirula). Two methods to virtually document the suture line ontogeny, used to document phylogenetic relationships of larger taxonomic entities, were applied for the first time and seem a promising alternative to hand drawings. The curvature of the chamber surfaces increases during ontogeny due to increasing strength of ornamentation and septal complexity. As increasing curvature may allow for faster handling of cameral liquid, it could compensate for decreasing SA/V ratios through ontogeny. Y1 - 2017 UR - http://dx.doi.org/10.1111/pala.12328 U6 - https://doi.org/10.1111/pala.12328 VL - 61 IS - 1 SP - 89 EP - 104 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Zachow, Stefan A1 - Steinmann, Alexander A1 - Heppt, Werner T1 - Innovation in der Funktionell-Ästhetischen Nasenchirurgie: Rhino-CFD JF - Face, Int. Mag. of Orofacial Esthetics Y1 - 2007 SP - 20 EP - 23 PB - Oemus Journale Leipzig ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Pumberger, Matthias A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Influence of pelvic tilt on functional acetabular orientation JF - Technology and Health Care Y1 - 2016 U6 - https://doi.org/10.3233/THC-161281 VL - 25 IS - 3 SP - 557 EP - 565 PB - IOS Press ER - TY - CHAP A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Seim, Heiko A1 - Zachow, Stefan A1 - Hege, Hans-Christian ED - Navab, Tianzi ED - P. W. Pluim, Josien ED - Viergever, Max T1 - Improving Deformable Surface Meshes through Omni-directional Displacements and MRFs T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2010 U6 - https://doi.org/10.1007/978-3-642-15705-9_28 VL - 6361 SP - 227 EP - 234 PB - Springer ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Zeilhofer, Hans-Florian A1 - Sader, Robert T1 - Improved 3D Osteotomy Planning in Cranio-Maxillofacial Surgery T2 - Proc. Medical Image Computing and Computer-Assisted Intervention (MICCAI 2001) Y1 - 2001 U6 - https://doi.org/10.1007/3-540-45468-3_57 SP - 473 EP - 481 CY - Utrecht, The Netherlands ER - TY - JOUR A1 - Lamas-Rodríguez, Julián A1 - Heras, Dora Blanco A1 - Argüello, Francisco A1 - Kainmüller, Dagmar A1 - Zachow, Stefan A1 - Bóo, Montserrat T1 - GPU-accelerated level-set segmentation JF - Journal of Real-Time Image Processing Y1 - 2013 UR - http://dx.doi.org/10.1007/s11554-013-0378-6 U6 - https://doi.org/10.1007/s11554-013-0378-6 SN - 1861-8200 SP - 1 EP - 15 PB - Springer Berlin Heidelberg ER - TY - GEN A1 - Lamas-Rodríguez, Julián A1 - Ehlke, Moritz A1 - Hoffmann, René A1 - Zachow, Stefan T1 - GPU-accelerated denoising of large tomographic data sets with low SNR BT - Application for non-invasive analysis of paleontological data N2 - Enhancements in tomographic imaging techniques facilitate non-destructive methods for visualizing fossil structures. However, to penetrate dense materials such as sediments or pyrites, image acquisition is typically performed with high beam energy and very sensitive image intensifiers, leading to artifacts and noise in the acquired data. The analysis of delicate fossil structures requires the images to be captured in maximum resolution, resulting in large data sets of several giga bytes (GB) in size. Since the structural information of interest is often almost in the same spatial range as artifacts and noise, image processing and segmentation algorithms have to cope with a very low signal-to-noise ratio (SNR). Within this report we present a study on the performance of a collection of denoising algorithms applied to a very noisy fossil dataset. The study shows that a non-local means (NLM) filter, in case it is properly configured, is able to remove a considerable amount of noise while preserving most of the structural information of interest. Based on the results of this study, we developed a software tool within ZIBAmira that denoises large tomographic datasets using an adaptive, GPU-accelerated NLM filter. With the help of our implementation a user can interactively configure the filter's parameters and thus its effectiveness with respect to the data of interest, while the filtering response is instantly visualized for a preselected region of interest (ROI). Our implementation efficiently denoises even large fossil datasets in a reasonable amount of time. T3 - ZIB-Report - 15-14 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56339 SN - 1438-0064 ER - TY - JOUR A1 - Gessat, Michael A1 - Zachow, Stefan A1 - Burgert, Oliver A1 - Lemke, Heinz T1 - Geometric Meshes in Medical Applications - Steps towards a specification of Geometric Models in DICOM JF - Int. J. of Computer Assisted Radiology and Surgery (CARS) Y1 - 2007 U6 - https://doi.org/10.1007/s11548-007-0112-6 SP - 440 EP - 442 ER - TY - GEN A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Geodesic B-Score for Improved Assessment of Knee Osteoarthritis N2 - Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions. T3 - ZIB-Report - 21-09 KW - Statistical shape analysis KW - Osteoarthritis KW - Geometric statistics KW - Riemannian manifolds Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81930 SN - 1438-0064 ER - TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - Geodesic B-Score for Improved Assessment of Knee Osteoarthritis T2 - Proc. Information Processing in Medical Imaging (IPMI) N2 - Three-dimensional medical imaging enables detailed understanding of osteoarthritis structural status. However, there remains a vast need for automatic, thus, reader-independent measures that provide reliable assessment of subject-specific clinical outcomes. To this end, we derive a consistent generalization of the recently proposed B-score to Riemannian shape spaces. We further present an algorithmic treatment yielding simple, yet efficient computations allowing for analysis of large shape populations with several thousand samples. Our intrinsic formulation exhibits improved discrimination ability over its Euclidean counterpart, which we demonstrate for predictive validity on assessing risks of total knee replacement. This result highlights the potential of the geodesic B-score to enable improved personalized assessment and stratification for interventions. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-78191-0_14 SP - 177 EP - 188 ER - TY - CHAP A1 - Neugebauer, Mathias A1 - Janiga, Gabor A1 - Zachow, Stefan A1 - Krischek, Özlem A1 - Preim, Bernhard ED - Hauser, Helwig T1 - Generierung qualitativ hochwertiger Modelle für die Simulation von Blutfluss in zerebralen Aneurysmen T2 - Proc. of Simulation and Visualization 2008 Y1 - 2008 SP - 221 EP - 235 ER - TY - JOUR A1 - Oeltze-Jaffra, Steffen A1 - Meuschke, Monique A1 - Neugebauer, Mathias A1 - Saalfeld, Sylvia A1 - Lawonn, Kai A1 - Janiga, Gabor A1 - Hege, Hans-Christian A1 - Zachow, Stefan A1 - Preim, Bernhard T1 - Generation and Visual Exploration of Medical Flow Data: Survey, Research Trends, and Future Challenges JF - Computer Graphics Forum N2 - Simulations and measurements of blood and air flow inside the human circulatory and respiratory system play an increasingly important role in personalized medicine for prevention, diagnosis, and treatment of diseases. This survey focuses on three main application areas. (1) Computational Fluid Dynamics (CFD) simulations of blood flow in cerebral aneurysms assist in predicting the outcome of this pathologic process and of therapeutic interventions. (2) CFD simulations of nasal airflow allow for investigating the effects of obstructions and deformities and provide therapy decision support. (3) 4D Phase-Contrast (4D PC) Magnetic Resonance Imaging (MRI) of aortic hemodynamics supports the diagnosis of various vascular and valve pathologies as well as their treatment. An investigation of the complex and often dynamic simulation and measurement data requires the coupling of sophisticated visualization, interaction, and data analysis techniques. In this paper, we survey the large body of work that has been conducted within this realm. We extend previous surveys by incorporating nasal airflow, addressing the joint investigation of blood flow and vessel wall properties, and providing a more fine-granular taxonomy of the existing techniques. From the survey, we extract major research trends and identify open problems and future challenges. The survey is intended for researchers interested in medical flow but also more general, in the combined visualization of physiology and anatomy, the extraction of features from flow field data and feature-based visualization, the visual comparison of different simulation results, and the interactive visual analysis of the flow field and derived characteristics. Y1 - 2019 U6 - https://doi.org/10.1111/cgf.13394 VL - 38 IS - 1 SP - 87 EP - 125 PB - Wiley ER - TY - CHAP A1 - Nkenke, Emeka A1 - Zachow, Stefan A1 - Häusler, Gerd T1 - Fusion von optischen 3D- und CT-Daten des Gebisses zur Metallartefaktkorrektur vor computerassistierter Planung MKG-chirurgischer Eingriffe T2 - Symposium der Arbeitsgemeinschaf für Kieferchirurgie Y1 - 2005 CY - Bad Homburg v.d.H ER - TY - JOUR A1 - Nkenke, Emeka A1 - Zachow, Stefan A1 - Benz, Michaela A1 - Maier, Tobias A1 - Veit, Klaus A1 - Kramer, Manuel A1 - Benz, St. A1 - Häusler, Gerd A1 - Neukam, Friedrich A1 - Lell, Michael T1 - Fusion of computed tomography data and optical 3D images of the dentition for streak artefact correction in the simulation of orthognathic surgery JF - Journal of Dento-Maxillofacial Radiology Y1 - 2004 U6 - https://doi.org/10.1259/dmfr/27071199 VL - 33 SP - 226 EP - 232 ER - TY - JOUR A1 - Tack, Alexander A1 - Preim, Bernhard A1 - Zachow, Stefan T1 - Fully automated Assessment of Knee Alignment from Full-Leg X-Rays employing a "YOLOv4 And Resnet Landmark regression Algorithm" (YARLA): Data from the Osteoarthritis Initiative JF - Computer Methods and Programs in Biomedicine N2 - We present a method for the quantification of knee alignment from full-leg X-Rays. A state-of-the-art object detector, YOLOv4, was trained to locate regions of interests (ROIs) in full-leg X-Ray images for the hip joint, the knee, and the ankle. Residual neural networks (ResNets) were trained to regress landmark coordinates for each ROI.Based on the detected landmarks the knee alignment, i.e., the hip-knee-ankle (HKA) angle, was computed. The accuracy of landmark detection was evaluated by a comparison to manually placed landmarks for 360 legs in 180 X-Rays. The accuracy of HKA angle computations was assessed on the basis of 2,943 X-Rays. Results of YARLA were compared to the results of two independent image reading studies(Cooke; Duryea) both publicly accessible via the Osteoarthritis Initiative. The agreement was evaluated using Spearman's Rho, and weighted kappa as well as regarding the correspondence of the class assignment (varus/neutral/valgus). The average difference between YARLA and manually placed landmarks was less than 2.0+- 1.5 mm for all structures (hip, knee, ankle). The average mismatch between HKA angle determinations of Cooke and Duryea was 0.09 +- 0.63°; YARLA resulted in a mismatch of 0.10 +- 0.74° compared to Cooke and of 0.18 +- 0.64° compared to Duryea. Cooke and Duryea agreed almost perfectly with respect to a weighted kappa value of 0.86, and showed an excellent reliability as measured by a Spearman's Rho value of 0.99. Similar values were achieved by YARLA, i.e., a weighted kappa value of0.83 and 0.87 and a Spearman's Rho value of 0.98 and 0.99 to Cooke and Duryea,respectively. Cooke and Duryea agreed in 92% of all class assignments and YARLA did so in 90% against Cooke and 92% against Duryea. In conclusion, YARLA achieved results comparable to those of human experts and thus provides a basis for an automated assessment of knee alignment in full-leg X-Rays. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.cmpb.2021.106080 VL - 205 IS - 106080 ER - TY - CHAP A1 - Grewe, Carl Martin A1 - Zachow, Stefan T1 - Fully Automated and Highly Accurate Dense Correspondence for Facial Surfaces T2 - Computer Vision – ECCV 2016 Workshops N2 - We present a novel framework for fully automated and highly accurate determination of facial landmarks and dense correspondence, e.g. a topologically identical mesh of arbitrary resolution, across the entire surface of 3D face models. For robustness and reliability of the proposed approach, we are combining 2D landmark detectors and 3D statistical shape priors with a variational matching method. Instead of matching faces in the spatial domain only, we employ image registration to align the 2D parametrization of the facial surface to a planar template we call the Unified Facial Parameter Domain (ufpd). This allows us to simultaneously match salient photometric and geometric facial features using robust image similarity measures while reasonably constraining geometric distortion in regions with less significant features. We demonstrate the accuracy of the dense correspondence established by our framework on the BU3DFE database with 2500 facial surfaces and show, that our framework outperforms current state-of-the-art methods with respect to the fully automated location of facial landmarks. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-48881-3_38 VL - 9914 SP - 552 EP - 568 PB - Springer International Publishing ER - TY - CHAP A1 - Hege, Hans-Christian A1 - Schirmacher, Hartmut A1 - Westerhoff, Malte A1 - Lamecker, Hans A1 - Prohaska, Steffen A1 - Zachow, Stefan T1 - From Image Data to Three-Dimensional Models - Case Studies on the Impact of 3D Patient Models T2 - Proceedings of the Japan Korea Computer Graphics Conference 2002 Y1 - 2002 PB - Kanazawa University CY - Kanazawa City, Ishikawa, Japan ER - TY - JOUR A1 - Hochfeld, Mascha A1 - Lamecker, Hans A1 - Thomale, Ulrich W. A1 - Schulz, Matthias A1 - Zachow, Stefan A1 - Haberl, Hannes T1 - Frame-based cranial reconstruction JF - Journal of Neurosurgery: Pediatrics N2 - The authors report on the first experiences with the prototype of a surgical tool for cranial remodeling. The device enables the surgeon to transfer statistical information, represented in a model, into the disfigured bone. The model is derived from a currently evolving databank of normal head shapes. Ultimately, the databank will provide a set of standard models covering the statistical range of normal head shapes, thus providing the required template for any standard remodeling procedure as well as customized models for intended overcorrection. To date, this technique has been used in the surgical treatment of 14 infants (age range 6-12 months) with craniosynostosis. In all 14 cases, the designated esthetic result, embodied by the selected model, has been achieved, without morbidity or mortality. Frame-based reconstruction provides the required tools to precisely realize the surgical reproduction of the model shape. It enables the establishment of a self-referring system, feeding back postoperative growth patterns, recorded by 3D follow-up, into the model design. Y1 - 2014 U6 - https://doi.org/10.3171/2013.11.PEDS1369 VL - 13 IS - 3 SP - 319 EP - 323 ER - TY - CHAP A1 - Zachow, Stefan A1 - Gladilin, Evgeny A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - Finite-Element Simulation of Soft Tissue Deformation T2 - Computer Assisted Radiology and Surgey (CARS) Y1 - 2000 SP - 23 EP - 28 PB - Elsevier Science B.V. ER - TY - CHAP A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan ED - Levine, Joshua A. ED - Paulsen, Rasmus R. ED - Zhang, Yongjie T1 - Feature-Preserving, Multi-Material Mesh Generation using Hierarchical Oracles T2 - Proc. MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed) Y1 - 2012 VL - 7599 SP - 101 EP - 111 ER - TY - CHAP A1 - Gladilin, Evgeny A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Deuflhard, Peter T1 - FE-based heuristic approach for the estimation of person-specific facial mimics T2 - Proceedings of Euro-Par 2001: 5-th International Symposium on Computer Methods Y1 - 2001 CY - Rome, Italy ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes N2 - We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements. T3 - ZIB-Report - 13-38 KW - digitally reconstructed radiographs KW - volume rendering KW - mesh deformation KW - statistical shape and intensity models KW - image registration KW - GPU acceleration Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-41896 SN - 1438-0064 ER - TY - JOUR A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Fast Generation of Virtual X-ray Images for Reconstruction of 3D Anatomy JF - IEEE Transactions on Visualization and Computer Graphics Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-35928 VL - 19 IS - 12 SP - 2673 EP - 2682 ER - TY - JOUR A1 - Grewe, Carl Martin A1 - Schreiber, Lisa A1 - Zachow, Stefan T1 - Fast and Accurate Digital Morphometry of Facial Expressions JF - Facial Plastic Surgery Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564720 VL - 31 IS - 05 SP - 431 EP - 438 PB - Thieme Medical Publishers CY - New York ER - TY - GEN A1 - Grewe, Carl Martin A1 - Zachow, Stefan ED - Doll, Nikola ED - Bredekamp, Horst ED - Schäffner, Wolfgang T1 - Face to Face-Interface T2 - +ultra. Knowledge & Gestaltung Y1 - 2017 SP - 320 EP - 321 PB - Seemann Henschel ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Bessler, Stefan A1 - Zachow, Stefan T1 - Evaluation of the Intranasal Flow Field through Computational Fluid Dynamics (CFD) JF - Journal of Facial and Plastic Surgery Y1 - 2013 UR - https://www.thieme-connect.de/DOI/DOI?10.1055/s-0033-1341591 U6 - https://doi.org/10.1055/s-0033-1341591 VL - 29 IS - 2 SP - 93 EP - 98 PB - Thieme ER - TY - CHAP A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Wilson, Dave A1 - Anglin, Carolyn A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data T2 - Proceedings of the Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie (CURAC) N2 - In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients’ distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated. KW - Total Knee Arthoplasty KW - Sparse Geometry Reconstruction KW - Statistical Shape Models Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65339 VL - 16 SP - 24 EP - 30 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Wilson, Dave A1 - Anglin, Carolyn A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data N2 - In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients’ distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated. T3 - ZIB-Report - 17-71 KW - Knee Arthroplasty KW - Sparse Geometry Reconstruction KW - Statistical Shape Models Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66052 SN - 1438-0064 ER - TY - JOUR A1 - Hembus, Jessica A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - Bader, Rainer T1 - Establishment of a rolling-sliding test bench to analyze abrasive wear propagation of different bearing materials for knee implants JF - Applied Sciences N2 - Currently, new materials for knee implants need to be extensively and expensive tested in a knee wear simulator in a realized design. However, using a rolling-sliding test bench, these materials can be examined under the same test conditions but with simplified geometries. In the present study, the test bench was optimized, and forces were adapted to the physiological contact pressure in the knee joint using the available geometric parameters. Various polymers made of polyethylene and polyurethane articulating against test wheels made of cobalt-chromium and aluminum titanate were tested in the test bench using adapted forces based on ISO 14243-1. Polyurethane materials showed distinctly higher wear rates than polyethylene materials and showed inadequate wear resistance for use as knee implant material. Thus, the rolling-sliding test bench is an adaptable test setup for evaluating newly developed bearing materials for knee implants. It combines the advantages of screening and simulator tests and allows testing of various bearing materials under physiological load and tribological conditions of the human knee joint. The wear behavior of different material compositions and the influence of surface geometry and quality can be initially investigated without the need to produce complex implant prototypes of total knee endoprosthesis or interpositional spacers. Y1 - 2021 U6 - https://doi.org/10.3390/app11041886 VL - 11 IS - 4 ER - TY - CHAP A1 - Sahu, Manish A1 - Strömsdörfer, Ronja A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - Endo-Sim2Real: Consistency learning-based domain adaptation for instrument segmentation T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part III N2 - Surgical tool segmentation in endoscopic videos is an important component of computer assisted interventions systems. Recent success of image-based solutions using fully-supervised deep learning approaches can be attributed to the collection of big labeled datasets. However, the annotation of a big dataset of real videos can be prohibitively expensive and time consuming. Computer simulations could alleviate the manual labeling problem, however, models trained on simulated data do not generalize to real data. This work proposes a consistency-based framework for joint learning of simulated and real (unlabeled) endoscopic data to bridge this performance generalization issue. Empirical results on two data sets (15 videos of the Cholec80 and EndoVis'15 dataset) highlight the effectiveness of the proposed Endo-Sim2Real method for instrument segmentation. We compare the segmentation of the proposed approach with state-of-the-art solutions and show that our method improves segmentation both in terms of quality and quantity. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-59716-0_75 VL - 12263 PB - Springer Nature ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric shape and intensity models for accurate simulation of X-ray images T2 - Eurographics Workshop on Visual Computing for Biomedicine (NVIDIA best poster award) Y1 - 2012 ER -