TY - CHAP A1 - Ambellan, Felix A1 - Zachow, Stefan A1 - von Tycowicz, Christoph T1 - A Surface-Theoretic Approach for Statistical Shape Modeling T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI), Part IV N2 - We present a novel approach for nonlinear statistical shape modeling that is invariant under Euclidean motion and thus alignment-free. By analyzing metric distortion and curvature of shapes as elements of Lie groups in a consistent Riemannian setting, we construct a framework that reliably handles large deformations. Due to the explicit character of Lie group operations, our non-Euclidean method is very efficient allowing for fast and numerically robust processing. This facilitates Riemannian analysis of large shape populations accessible through longitudinal and multi-site imaging studies providing increased statistical power. We evaluate the performance of our model w.r.t. shape-based classification of pathological malformations of the human knee and show that it outperforms the standard Euclidean as well as a recent nonlinear approach especially in presence of sparse training data. To provide insight into the model’s ability of capturing natural biological shape variability, we carry out an analysis of specificity and generalization ability. Y1 - 2019 U6 - https://doi.org/10.1007/978-3-030-32251-9_3 VL - 11767 SP - 21 EP - 29 PB - Springer ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Schmidt, Nora Laura A1 - Lamecker, Hans A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Goubergrits, Leonid T1 - The Healthy Nasal Cavity - Characteristics of Morphology and Related Airflow Based on a Statistical Shape Model Viewed from a Surgeon’s Perspective JF - Facial Plastic Surgery N2 - Functional surgery on the nasal framework requires referential criteria to objectively assess nasal breathing for indication and follow-up. Thismotivated us to generate amean geometry of the nasal cavity based on a statistical shape model. In this study, the authors could demonstrate that the introduced nasal cavity’s mean geometry features characteristics of the inner shape and airflow, which are commonly observed in symptom-free subjects. Therefore, the mean geometry might serve as a reference-like model when one considers qualitative aspects. However, to facilitate quantitative considerations and statistical inference, further research is necessary. Additionally, the authorswere able to obtain details about the importance of the isthmus nasi and the inferior turbinate for the intranasal airstream. KW - statistical shape model KW - nasal cavity KW - nasal breathing KW - nasal airflow KW - isthmus nasi KW - inferior turbinate Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677721 VL - 35 IS - 1 SP - 9 EP - 13 ER - TY - JOUR A1 - Hildebrandt, Thomas A1 - Bruening, Jan Joris A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Heppt, Werner A1 - Schmidt, Nora A1 - Goubergrits, Leonid T1 - Digital Analysis of Nasal Airflow Facilitating Decision Support in Rhinosurgery JF - Facial Plastic Surgery N2 - Successful functional surgery on the nasal framework requires reliable and comprehensive diagnosis. In this regard, the authors introduce a new methodology: Digital Analysis of Nasal Airflow (diANA). It is based on computational fluid dynamics, a statistical shape model of the healthy nasal cavity and rhinologic expertise. diANA necessitates an anonymized tomographic dataset of the paranasal sinuses including the complete nasal cavity and, when available, clinical information. The principle of diANA is to compare the morphology and the respective airflow of an individual nose with those of a reference. This enablesmorphometric aberrations and consecutive flow field anomalies to localize and quantify within a patient’s nasal cavity. Finally, an elaborated expert opinion with instructive visualizations is provided. Using diANA might support surgeons in decision-making, avoiding unnecessary surgery, gaining more precision, and target-orientation for indicated operations. KW - nasal airflow simulation KW - nasal breathing KW - statistical shape model KW - diANA KW - nasal obstruction KW - rhinorespiratory homeostasis Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1677720 VL - 35 IS - 1 SP - 1 EP - 8 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 - JOUR A1 - Al Hajj, Hassan A1 - Sahu, Manish A1 - Lamard, Mathieu A1 - Conze, Pierre-Henri A1 - Roychowdhury, Soumali A1 - Hu, Xiaowei A1 - Marsalkaite, Gabija A1 - Zisimopoulos, Odysseas A1 - Dedmari, Muneer Ahmad A1 - Zhao, Fenqiang A1 - Prellberg, Jonas A1 - Galdran, Adrian A1 - Araujo, Teresa A1 - Vo, Duc My A1 - Panda, Chandan A1 - Dahiya, Navdeep A1 - Kondo, Satoshi A1 - Bian, Zhengbing A1 - Bialopetravicius, Jonas A1 - Qiu, Chenghui A1 - Dill, Sabrina A1 - Mukhopadyay, Anirban A1 - Costa, Pedro A1 - Aresta, Guilherme A1 - Ramamurthy, Senthil A1 - Lee, Sang-Woong A1 - Campilho, Aurelio A1 - Zachow, Stefan A1 - Xia, Shunren A1 - Conjeti, Sailesh A1 - Armaitis, Jogundas A1 - Heng, Pheng-Ann A1 - Vahdat, Arash A1 - Cochener, Beatrice A1 - Quellec, Gwenole T1 - CATARACTS: Challenge on Automatic Tool Annotation for cataRACT Surgery JF - Medical Image Analysis N2 - Surgical tool detection is attracting increasing attention from the medical image analysis community. The goal generally is not to precisely locate tools in images, but rather to indicate which tools are being used by the surgeon at each instant. The main motivation for annotating tool usage is to design efficient solutions for surgical workflow analysis, with potential applications in report generation, surgical training and even real-time decision support. Most existing tool annotation algorithms focus on laparoscopic surgeries. However, with 19 million interventions per year, the most common surgical procedure in the world is cataract surgery. The CATARACTS challenge was organized in 2017 to evaluate tool annotation algorithms in the specific context of cataract surgery. It relies on more than nine hours of videos, from 50 cataract surgeries, in which the presence of 21 surgical tools was manually annotated by two experts. With 14 participating teams, this challenge can be considered a success. As might be expected, the submitted solutions are based on deep learning. This paper thoroughly evaluates these solutions: in particular, the quality of their annotations are compared to that of human interpretations. Next, lessons learnt from the differential analysis of these solutions are discussed. We expect that they will guide the design of efficient surgery monitoring tools in the near future. Y1 - 2019 U6 - https://doi.org/10.1016/j.media.2018.11.008 N1 - Best paper award - Computer Graphics Night 2020 (TU Darmstadt) VL - 52 IS - 2 SP - 24 EP - 41 PB - Elsevier ER - TY - GEN A1 - Tack, Alexander A1 - Zachow, Stefan T1 - Accurate Automated Volumetry of Cartilage of the Knee using Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - Volumetry of the cartilage of the knee, as needed for the assessment of knee osteoarthritis (KOA), is typically performed in a tedious and subjective process. We present an automated segmentation-based method for the quantification of cartilage volume by employing 3D Convolutional Neural Networks (CNNs). CNNs were trained in a supervised manner using magnetic resonance imaging data as well as cartilage volumetry readings given by clinical experts for 1378 subjects. It was shown that 3D CNNs can be employed for cartilage volumetry with an accuracy similar to expert volumetry readings. In future, accurate automated cartilage volumetry might support both, diagnosis of KOA as well as assessment of KOA progression via longitudinal analysis. T3 - ZIB-Report - 19-05 KW - Deep Learning KW - imaging biomarker KW - radiomics KW - cartilage morphometry KW - volume assessment Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-71439 SN - 1438-0064 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging (MRI) that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs).The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures.The shape models and neural networks employed are trained using data from the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets from the SKI10 challenge.For the first time, an accuracy equivalent to the inter-observer variability of human readers is achieved in this challenge.Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We make the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation.In conclusion, combining localized classification via CNNs with statistical anatomical knowledge via SSMs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. T3 - ZIB-Report - 19-06 Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-72704 SN - 1438-0064 N1 - Innovation Excellence Award 2020 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative (Supplementary Material) T2 - Medical Image Analysis N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The shape models and neural networks employed are trained using data of the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets of the SKI10 challenge. For the first time, an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We made the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation. In conclusion, combining statistical anatomical knowledge via SSMs with the localized classification via CNNs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. Y1 - 2019 U6 - https://doi.org/10.12752/4.ATEZ.1.0 N1 - OAI-ZIB dataset VL - 52 IS - 2 SP - 109 EP - 118 ER - TY - JOUR A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative JF - Medical Image Analysis N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The shape models and neural networks employed are trained using data of the Osteoarthritis Initiative (OAI) and the MICCAI grand challenge "Segmentation of Knee Images 2010" (SKI10), respectively. We evaluate our method on 40 validation and 50 submission datasets of the SKI10 challenge. For the first time, an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for data from the OAI, i.e. 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy for both OAI datasets. We made the 507 manual segmentations as well as our experimental setup publicly available to further aid research in the field of medical image segmentation. In conclusion, combining statistical anatomical knowledge via SSMs with the localized classification via CNNs results in a state-of-the-art segmentation method for knee bones and cartilage from MRI data. Y1 - 2019 U6 - https://doi.org/10.1016/j.media.2018.11.009 VL - 52 IS - 2 SP - 109 EP - 118 ER - TY - JOUR A1 - Akbari Shandiz, Mohsen A1 - Boulos, Paul A1 - Sævarsson, Stefan A1 - Ramm, Heiko A1 - Fu, Chun Kit A1 - Miller, Stephen A1 - Zachow, Stefan A1 - Anglin, Carolyn T1 - Changes in Knee Shape and Geometry Resulting from Total Knee Arthroplasty JF - Journal of Engineering in Medicine N2 - Changes in knee shape and geometry resulting from total knee arthroplasty can affect patients in numerous important ways: pain, function, stability, range of motion, and kinematics. Quantitative data concerning these changes have not been previously available, to our knowledge, yet are essential to understand individual experiences of total knee arthroplasty and thereby improve outcomes for all patients. The limiting factor has been the challenge of accurately measuring these changes. Our study objective was to develop a conceptual framework and analysis method to investigate changes in knee shape and geometry, and prospectively apply it to a sample total knee arthroplasty population. Using clinically available computed tomography and radiography imaging systems, the three-dimensional knee shape and geometry of nine patients (eight varus and one valgus) were compared before and after total knee arthroplasty. All patients had largely good outcomes after their total knee arthroplasty. Knee shape changed both visually and numerically. On average, the distal condyles were slightly higher medially and lower laterally (range: +4.5 mm to −4.4 mm), the posterior condyles extended farther out medially but not laterally (range: +1.8 to −6.4 mm), patellofemoral distance increased throughout flexion by 1.8–3.5 mm, and patellar thickness alone increased by 2.9 mm (range: 0.7–5.2 mm). External femoral rotation differed preop and postop. Joint line distance, taking cartilage into account, changed by +0.7 to −1.5 mm on average throughout flexion. Important differences in shape and geometry were seen between pre-total knee arthroplasty and post-total knee arthroplasty knees. While this is qualitatively known, this is the first study to report it quantitatively, an important precursor to identifying the reasons for the poor outcome of some patients. Using the developed protocol and visualization techniques to compare patients with good versus poor clinical outcomes could lead to changes in implant design, implant selection, component positioning, and surgical technique. Recommendations based on this sample population are provided. Intraoperative and postoperative feedback could ultimately improve patient satisfaction. Y1 - 2018 UR - http://journals.sagepub.com/eprint/ZVgNrNESA9EjIcaFWSjb/full U6 - https://doi.org/10.1177/0954411917743274 VL - 232 IS - 1 SP - 67 EP - 79 ER - TY - JOUR A1 - von Tycowicz, Christoph A1 - Ambellan, Felix A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - An Efficient Riemannian Statistical Shape Model using Differential Coordinates JF - Medical Image Analysis N2 - We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidean structure. A key advantage of our framework is that statistics in a manifold shape space becomes numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidean approach in terms of shape-based classification of morphological disorders. Y1 - 2018 U6 - https://doi.org/10.1016/j.media.2017.09.004 VL - 43 IS - 1 SP - 1 EP - 9 ER - TY - JOUR A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death JF - Heat and Mass Transfer N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. Y1 - 2018 U6 - https://doi.org/10.1007/s00231-018-2324-4 VL - 54 IS - 9 SP - 2815 EP - 2826 PB - Springer ER - TY - CHAP A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Ehlke, Moritz A1 - Zachow, Stefan T1 - Automated Segmentation of Knee Bone and Cartilage combining Statistical Shape Knowledge and Convolutional Neural Networks: Data from the Osteoarthritis Initiative T2 - Medical Imaging with Deep Learning N2 - We present a method for the automated segmentation of knee bones and cartilage from magnetic resonance imaging, that combines a priori knowledge of anatomical shape with Convolutional Neural Networks (CNNs). The proposed approach incorporates 3D Statistical Shape Models (SSMs) as well as 2D and 3D CNNs to achieve a robust and accurate segmentation of even highly pathological knee structures. The method is evaluated on data of the MICCAI grand challenge "Segmentation of Knee Images 2010". For the first time an accuracy equivalent to the inter-observer variability of human readers has been achieved in this challenge. Moreover, the quality of the proposed method is thoroughly assessed using various measures for 507 manual segmentations of bone and cartilage, and 88 additional manual segmentations of cartilage. Our method yields sub-voxel accuracy. In conclusion, combining of anatomical knowledge using SSMs with localized classification via CNNs results in a state-of-the-art segmentation method. Y1 - 2018 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 (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 - Hoffmann, Rene A1 - Lemanis, Robert A1 - Wulff, Lena A1 - Zachow, Stefan A1 - Lukeneder, Alexander A1 - Klug, Christian A1 - Keupp, Helmut T1 - Traumatic events in the life of the deep-sea cephalopod mollusc, the coleoid Spirula spirula JF - ScienceDirect: Deep Sea Research Part I - Oceanographic Research N2 - Here, we report on different types of shell pathologies of the enigmatic deep-sea (mesopelagic) cephalopod Spirula spirula. For the first time, we apply non-invasive imaging methods to: document trauma-induced changes in shell shapes, reconstruct the different causes and effects of these pathologies, unravel the etiology, and attempt to quantify the efficiency of the buoyancy apparatus. We have analysed 2D and 3D shell parameters from eleven shells collected as beach findings from the Canary Islands (Gran Canaria and Fuerteventura), West-Australia, and the Maldives. All shells were scanned with a nanotom-m computer tomograph. Seven shells were likely injured by predator attacks: fishes, cephalopods or crustaceans, one specimen was infested by an endoparasite (potentially Digenea) and one shell shows signs of inflammation and one shell shows large fluctuations of chamber volumes without any signs of pathology. These fluctuations are potential indicators of a stressed environment. Pathological shells represent the most deviant morphologies of a single species and can therefore be regarded as morphological end-members. The changes in the shell volume / chamber volume ratio were assessed in order to evaluate the functional tolerance of the buoyancy apparatus showing that these had little effect. Y1 - 2018 U6 - https://doi.org/10.1016/j.dsr.2018.10.007 VL - 142 IS - 12 SP - 127 EP - 144 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 - 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 - Krämer, Martin A1 - Maggioni, Marta A1 - Tycowicz, Christoph von A1 - Brisson, Nick A1 - Zachow, Stefan A1 - Duda, Georg A1 - Reichenbach, Jürgen T1 - Ultra-short echo-time (UTE) imaging of the knee with curved surface reconstruction-based extraction of the patellar tendon T2 - ISMRM (International Society for Magnetic Resonance in Medicine), 26th Annual Meeting 2018, Paris, France N2 - Due to very short T2 relaxation times, imaging of tendons is typically performed using ultra-short echo-time (UTE) acquisition techniques. In this work, we combined an echo-train shifted multi-echo 3D UTE imaging sequence with a 3D curved surface reconstruction to virtually extract the patellar tendon from an acquired 3D UTE dataset. Based on the analysis of the acquired multi-echo data, a T2* relaxation time parameter map was calculated and interpolated to the curved surface of the patellar tendon. Y1 - 2018 ER - TY - CHAP A1 - Joachimsky, Robert A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung früher Gonarthrose T2 - Proceedings of the Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie (CURAC) N2 - Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein häufiges Krankheitsbild unter älteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder geschädigter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfläche erhöhen und so der teilweise oder vollständige Gelenkersatz hinausgezögert oder vermieden werden. In dieser Arbeit präsentieren wir eine Planungssoftware für die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgewählt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. Für jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern Rückmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterstützt somit als Entscheidungshilfe die behandelnden Ärzte bei der patientenspezifischen Spacerauswahl. KW - Osteoarthrose KW - Kniegelenk KW - Medizinische Planung KW - Visualisierung Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65321 VL - 16 SP - 106 EP - 111 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 - Moldenhauer, Marian A1 - Weiser, Martin A1 - Zachow, Stefan T1 - Adaptive Algorithms for Optimal Hip Implant Positioning JF - PAMM N2 - In an aging society where the number of joint replacements rises, it is important to also increase the longevity of implants. In particular hip implants have a lifetime of at most 15 years. This derives primarily from pain due to implant migration, wear, inflammation, and dislocation, which is affected by the positioning of the implant during the surgery. Current joint replacement practice uses 2D software tools and relies on the experience of surgeons. Especially the 2D tools fail to take the patients’ natural range of motion as well as stress distribution in the 3D joint induced by different daily motions into account. Optimizing the hip joint implant position for all possible parametrized motions under the constraint of a contact problem is prohibitively expensive as there are too many motions and every position change demands a recalculation of the contact problem. For the reduction of the computational effort, we use adaptive refinement on the parameter domain coupled with the interpolation method of Kriging. A coarse initial grid is to be locally refined using goal-oriented error estimation, reducing locally high variances. This approach will be combined with multi-grid optimization such that numerical errors are reduced. Y1 - 2017 U6 - https://doi.org/10.1002/pamm.201710071 VL - 17 IS - 1 SP - 203 EP - 204 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 - JOUR A1 - Brüning, Jan A1 - Goubergrits, Leonid A1 - Heppt, Werner A1 - Zachow, Stefan A1 - Hildebrandt, Thomas T1 - Numerical Analysis of Nasal Breathing - A Pilot Study JF - Facial Plastic Surgery N2 - Background: Currently, there is no fully sufficient way to differentiate between symptomatic and normal nasal breathing. Using the nose’s total resistance is disputed as a valid means to objectify nasal airflow, and the need for a more comprehensive diagnostic method is increasing. This work’s aim was to test a novel approach considering intranasal wall shear stress as well as static pressure maps obtained by computational fluid dynamics (CFD). Methods: X-ray computed tomography (CT) scan data of six symptom-free subjects and seven symptomatic patients were used. Patient-specific geometries of the nasal cavity were segmented from these data sets. Inspiratory and expiratory steady airflow simulations were performed using CFD. Calculated static pressures and wall shear stresses (WSS) were mapped onto a common template of the nasal septum, allowing for comparison of these parameters between the two patient groups. Results: Significant differences in wall shear stress distributions during the inspiratory phase could be identified between the two groups, whereas no differences were found for the expiratory phase. It is assumed that one essential feature of normal nasal breathing probably consists in distinctively different intranasal flow fields for inspiration and expiration. This is in accordance with previous investigations. Conclusion: The proposed method seems to be a promising tool for developing a new kind of patient-specific assessment of nasal breathing. However, more studies and a greater case number of data with an expanded focus, would be ideal. Y1 - 2017 U6 - https://doi.org/doi:10.1055/s-0037-1603789 VL - 33 IS - 4 SP - 388 EP - 395 ER - TY - GEN A1 - Weiser, Martin A1 - Erdmann, Bodo A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Mall, Gita A1 - Zachow, Stefan T1 - Uncertainty in Temperature-Based Determination of Time of Death N2 - Temperature-based estimation of time of death (ToD) can be per- formed either with the help of simple phenomenological models of corpse cooling or with detailed mechanistic (thermodynamic) heat transfer mod- els. The latter are much more complex, but allow a higher accuracy of ToD estimation as in principle all relevant cooling mechanisms can be taken into account. The potentially higher accuracy depends on the accuracy of tissue and environmental parameters as well as on the geometric resolution. We in- vestigate the impact of parameter variations and geometry representation on the estimated ToD based on a highly detailed 3D corpse model, that has been segmented and geometrically reconstructed from a computed to- mography (CT) data set, differentiating various organs and tissue types. From that we identify the most crucial parameters to measure or estimate, and obtain a local uncertainty quantifcation for the ToD. T3 - ZIB-Report - 17-18 KW - forensic medicine KW - determination of time of death KW - heat transfer equation KW - sensitivity i.r.t. thermal parameters KW - sensitivity i.r.t. geometric resolution Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63818 SN - 1438-0064 ER - TY - GEN A1 - Ambellan, Felix A1 - Tack, Alexander A1 - Wilson, Dave A1 - Anglin, Carolyn A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Evaluating two methods for Geometry Reconstruction from Sparse Surgical Navigation Data N2 - In this study we investigate methods for fitting a Statistical Shape Model (SSM) to intraoperatively acquired point cloud data from a surgical navigation system. We validate the fitted models against the pre-operatively acquired Magnetic Resonance Imaging (MRI) data from the same patients. We consider a cohort of 10 patients who underwent navigated total knee arthroplasty. As part of the surgical protocol the patients’ distal femurs were partially digitized. All patients had an MRI scan two months pre-operatively. The MRI data were manually segmented and the reconstructed bone surfaces used as ground truth against which the fit was compared. Two methods were used to fit the SSM to the data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). For both approaches, the difference between model fit and ground truth surface averaged less than 1.7 mm and excellent correspondence with the distal femoral morphology can be demonstrated. T3 - ZIB-Report - 17-71 KW - Knee Arthroplasty KW - Sparse Geometry Reconstruction KW - Statistical Shape Models Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66052 SN - 1438-0064 ER - TY - GEN A1 - Joachimsky, Robert A1 - Ambellan, Felix A1 - Zachow, Stefan T1 - Computerassistierte Auswahl und Platzierung von interpositionalen Spacern zur Behandlung früher Gonarthrose N2 - Degenerative Gelenkerkrankungen, wie die Osteoarthrose, sind ein häufiges Krankheitsbild unter älteren Erwachsenen. Hierbei verringert sich u.a. der Gelenkspalt aufgrund degenerierten Knorpels oder geschädigter Menisci. Ein in den Gelenkspalt eingebrachter interpositionaler Spacer soll die mit der Osteoarthrose einhergehende verringerte Gelenkkontaktfläche erhöhen und so der teilweise oder vollständige Gelenkersatz hinausgezögert oder vermieden werden. In dieser Arbeit präsentieren wir eine Planungssoftware für die Auswahl und Positionierung eines interpositionalen Spacers am Patientenmodell. Auf einer MRT-basierten Bildsegmentierung aufbauend erfolgt eine geometrische Rekonstruktion der 3D-Anatomie des Kniegelenks. Anhand dieser wird der Gelenkspalt bestimmt, sowie ein Spacer ausgewählt und algorithmisch vorpositioniert. Die Positionierung des Spacers ist durch den Benutzer jederzeit interaktiv anpassbar. Für jede Positionierung eines Spacers wird ein Fitness-Wert zur Knieanatomie des jeweiligen Patienten berechnet und den Nutzern Rückmeldung hinsichtlich Passgenauigkeit gegeben. Die Software unterstützt somit als Entscheidungshilfe die behandelnden Ärzte bei der patientenspezifischen Spacerauswahl. T3 - ZIB-Report - 17-72 KW - Osteoarthrose KW - Kniegelenk KW - Medizinische Planung KW - Visualisierung Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66064 SN - 1438-0064 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse 3D Point-Clouds JF - Medical Image Analysis N2 - The reconstruction of an object’s shape or surface from a set of 3D points plays an important role in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or in the process of aligning intra-operative navigation and preoperative planning data. In such scenarios, one usually has to deal with sparse data, which significantly aggravates the problem of reconstruction. However, medical applications often provide contextual information about the 3D point data that allow to incorporate prior knowledge about the shape that is to be reconstructed. To this end, we propose the use of a statistical shape model (SSM) as a prior for surface reconstruction. The SSM is represented by a point distribution model (PDM), which is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we formulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given points are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are “oriented” according to the surface normals at the PDM points, a surface-based fitting is accomplished. Estimating the parameters of the GMM in a maximum a posteriori manner yields the reconstruction of the surface from the given data points. We compare our method to the extensively used Iterative Closest Points method on several different anatomical datasets/SSMs (brain, femur, tibia, hip, liver) and demonstrate superior accuracy and robustness on sparse data. Y1 - 2017 UR - http://www.sciencedirect.com/science/article/pii/S1361841517300233 U6 - https://doi.org/10.1016/j.media.2017.02.005 VL - 38 SP - 77 EP - 89 ER - TY - JOUR A1 - Lube, Juliane A1 - Flack, Natasha A1 - Cotofana, Sebastian A1 - Özkurtul, Orkun A1 - Woodley, Stephanie A1 - Zachow, Stefan A1 - Hammer, Niels T1 - Pelvic and lower extremity physiological cross-sectional areas: An MRI study of the living young and comparison to published research literature JF - Surgical and Radiologic Anatomy N2 - Purpose: Morphological data pertaining to the pelvis and lower extremity muscles are increasingly being used in biomechanical modeling to compare healthy and pathological conditions. Very few data sets exist that encompass all of the muscles of the lower limb, allowing for comparisons between regions. The aims of this study were to (a) provide physiological cross-sectional area (PCSA) data for the pelvic, thigh, and leg muscles in young, healthy participants, using magnetic resonance imaging (MRI), and (b) to compare these data with summarized PCSAs obtained from the literature. Materials and Methods: Six young and healthy volunteers participated and were scanned using 3 T MRI. PCSAs were calculated from volumetric segmentations obtained bilaterally of 28 muscles/muscle groups of the pelvis, thigh, and leg. These data were compared to published, summarized PCSA data derived from cadaveric, computed tomography, MRI and ultrasound studies. Results: The PCSA of the pelvis, thigh, and leg muscles tended to be 20–130% larger in males than in females, except for the gemelli which were 34% smaller in males, and semitendinosus and triceps surae which did not differ (<20% different). The dominant and the non-dominant sides showed similar and minutely different PCSA with less than 18% difference between sides. Comparison to other studies revealed wide ranges within, and large differences between, the cadaveric and imaging PCSA data. Comparison of the PCSA of this study and published literature revealed major differences in the iliopsoas, gluteus minimus, tensor fasciae latae, gemelli, obturator internus, biceps femoris, quadriceps femoris, and the deep leg flexor muscles. Conclusions: These volume-derived PCSAs of the pelvic and lower limb muscles alongside the data synthesised from the literature may serve as a basis for comparative and biomechanical studies of the living and healthy young, and enable calculation of muscle forces. Comparison of the literature revealed large variations in PCSA from each of the different investigative modalities, hampering omparability between studies. Sample size, age, post-mortem changes of muscle tone, chemical fixation of cadaveric tissues, and the underlying physics of the imaging techniques may potentially influence PCSA calculations. Y1 - 2017 U6 - https://doi.org/10.1007/s00276-016-1807-6 VL - 39 IS - 8 SP - 849 EP - 857 ER - TY - JOUR A1 - Sahu, Manish A1 - Mukhopadhyay, Anirban A1 - Szengel, Angelika A1 - Zachow, Stefan T1 - Addressing multi-label imbalance problem of Surgical Tool Detection using CNN JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: A fully automated surgical tool detection framework is proposed for endoscopic video streams. State-of-the-art surgical tool detection methods rely on supervised one-vs-all or multi-class classification techniques, completely ignoring the co-occurrence relationship of the tools and the associated class imbalance. Methods: In this paper, we formulate tool detection as a multi-label classification task where tool co-occurrences are treated as separate classes. In addition, imbalance on tool co-occurrences is analyzed and stratification techniques are employed to address the imbalance during Convolutional Neural Network (CNN) training. Moreover, temporal smoothing is introduced as an online post-processing step to enhance run time prediction. Results: Quantitative analysis is performed on the M2CAI16 tool detection dataset to highlight the importance of stratification, temporal smoothing and the overall framework for tool detection. Conclusion: The analysis on tool imbalance, backed by the empirical results indicates the need and superiority of the proposed framework over state-of-the-art techniques. Y1 - 2017 UR - https://link.springer.com/article/10.1007/s11548-017-1565-x U6 - https://doi.org/10.1007/s11548-017-1565-x N1 - Selected for final oral presentation VL - 12 IS - 6 SP - 1013 EP - 1020 PB - Springer ER - TY - JOUR A1 - Schenkl, Sebastian A1 - Muggenthaler, Holger A1 - Hubig, Michael A1 - Erdmann, Bodo A1 - Weiser, Martin A1 - Zachow, Stefan A1 - Heinrich, Andreas A1 - Güttler, Felix Victor A1 - Teichgräber, Ulf A1 - Mall, Gita T1 - Automatic CT-based finite element model generation for temperature-based death time estimation: feasibility study and sensitivity analysis JF - International Journal of Legal Medicine N2 - Temperature based death time estimation is based either on simple phenomenological models of corpse cooling or on detailed physical heat transfer models. The latter are much more complex, but allow a higher accuracy of death time estimation as in principle all relevant cooling mechanisms can be taken into account. Here, a complete work flow for finite element based cooling simulation models is presented. The following steps are demonstrated on CT-phantoms: • CT-scan • Segmentation of the CT images for thermodynamically relevant features of individual geometries • Conversion of the segmentation result into a Finite Element (FE) simulation model • Computation of the model cooling curve • Calculation of the cooling time For the first time in FE-based cooling time estimation the steps from the CT image over segmentation to FE model generation are semi-automatically performed. The cooling time calculation results are compared to cooling measurements performed on the phantoms under controlled conditions. In this context, the method is validated using different CTphantoms. Some of the CT phantoms thermodynamic material parameters had to be experimentally determined via independent experiments. Moreover the impact of geometry and material parameter uncertainties on the estimated cooling time is investigated by a sensitivity analysis. KW - temperature based death time estimation KW - finite element method KW - CT segmentation KW - sensitivity analysis Y1 - 2017 U6 - https://doi.org/doi:10.1007/s00414-016-1523-0 VL - 131 IS - 3 SP - 699 EP - 712 ER - TY - 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 - Wilson, David A1 - Anglin, Carolyn A1 - Ambellan, Felix A1 - Grewe, Carl Martin A1 - Tack, Alexander A1 - Lamecker, Hans A1 - Dunbar, Michael A1 - Zachow, Stefan T1 - Validation of three-dimensional models of the distal femur created from surgical navigation point cloud data for intraoperative and postoperative analysis of total knee arthroplasty JF - International Journal of Computer Assisted Radiology and Surgery N2 - Purpose: Despite the success of total knee arthroplasty there continues to be a significant proportion of patients who are dissatisfied. One explanation may be a shape mismatch between pre and post-operative distal femurs. The purpose of this study was to investigate a method to match a statistical shape model (SSM) to intra-operatively acquired point cloud data from a surgical navigation system, and to validate it against the pre-operative magnetic resonance imaging (MRI) data from the same patients. Methods: A total of 10 patients who underwent navigated total knee arthroplasty also had an MRI scan less than 2 months pre-operatively. The standard surgical protocol was followed which included partial digitization of the distal femur. Two different methods were employed to fit the SSM to the digitized point cloud data, based on (1) Iterative Closest Points (ICP) and (2) Gaussian Mixture Models (GMM). The available MRI data were manually segmented and the reconstructed three-dimensional surfaces used as ground truth against which the statistical shape model fit was compared. Results: For both approaches, the difference between the statistical shape model-generated femur and the surface generated from MRI segmentation averaged less than 1.7 mm, with maximum errors occurring in less clinically important areas. Conclusion: The results demonstrated good correspondence with the distal femoral morphology even in cases of sparse data sets. Application of this technique will allow for measurement of mismatch between pre and post-operative femurs retrospectively on any case done using the surgical navigation system and could be integrated into the surgical navigation unit to provide real-time feedback. Y1 - 2017 UR - https://link.springer.com/content/pdf/10.1007%2Fs11548-017-1630-5.pdf U6 - https://doi.org/10.1007/s11548-017-1630-5 VL - 12 IS - 12 SP - 2097 EP - 2105 PB - Springer 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 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Pumberger, Matthias A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Influence of pelvic tilt on functional acetabular orientation JF - Technology and Health Care Y1 - 2016 U6 - https://doi.org/10.3233/THC-161281 VL - 25 IS - 3 SP - 557 EP - 565 PB - IOS Press ER - TY - JOUR A1 - Lemanis, Robert A1 - Korn, Dieter A1 - Zachow, Stefan A1 - Rybacki, Erik A1 - Hoffmann, René T1 - The Evolution and Development of Cephalopod Chambers and Their Shape JF - PLOS ONE N2 - The Ammonoidea is a group of extinct cephalopods ideal to study evolution through deep time. The evolution of the planispiral shell and complexly folded septa in ammonoids has been thought to have increased the functional surface area of the chambers permitting enhanced metabolic functions such as: chamber emptying, rate of mineralization and increased growth rates throughout ontogeny. Using nano-computed tomography and synchrotron radiation based micro-computed tomography, we present the first study of ontogenetic changes in surface area to volume ratios in the phragmocone chambers of several phylogenetically distant ammonoids and extant cephalopods. Contrary to the initial hypothesis, ammonoids do not possess a persistently high relative chamber surface area. Instead, the functional surface area of the chambers is higher in earliest ontogeny when compared to Spirula spirula. The higher the functional surface area the quicker the potential emptying rate of the chamber; quicker chamber emptying rates would theoretically permit faster growth. This is supported by the persistently higher siphuncular surface area to chamber volume ratio we collected for the ammonite Amauroceras sp. compared to either S. spirula or nautilids. We demonstrate that the curvature of the surface of the chamber increases with greater septal complexity increasing the potential refilling rates. We further show a unique relationship between ammonoid chamber shape and size that does not exist in S. spirula or nautilids. This view of chamber function also has implications for the evolution of the internal shell of coleoids, relating this event to the decoupling of soft-body growth and shell growth. Y1 - 2016 U6 - https://doi.org/10.1371/journal.pone.0151404 VL - 11 IS - 3 ER - TY - JOUR A1 - Dunlop, Jason A1 - Apanaskevich, Dmitry A1 - Lehmann, Jens A1 - Hoffmann, Rene A1 - Fusseis, Florian A1 - Ehlke, Moritz A1 - Zachow, Stefan A1 - Xiao, Xianghui T1 - Microtomography of the Baltic amber tick Ixodes succineus reveals affinities with the modern Asian disease vector Ixodes ovatus JF - BMC Evolutionary Biology N2 - Background: Fossil ticks are extremely rare, whereby Ixodes succineus Weidner, 1964 from Eocene (ca. 44-49 Ma) Baltic amber is one of the oldest examples of a living hard tick genus (Ixodida: Ixodidae). Previous work suggested it was most closely related to the modern and widespread European sheep tick Ixodes ricinus (Linneaus, 1758). Results: Restudy using phase contrast synchrotron x-ray tomography yielded images of exceptional quality. These confirm the fossil's referral to Ixodes Latreille, 1795, but the characters resolved here suggest instead affinities with the Asian subgenus Partipalpiger Hoogstraal et al., 1973 and its single living (and medically significant) species Ixodes ovatus Neumann, 1899. We redescribe the amber fossil here as Ixodes (Partipalpiger) succineus. Conclusions: Our data suggest that Ixodes ricinus is unlikely to be directly derived from Weidner's amber species, but instead reveals that the Partipalpiger lineage was originally more widely distributed across the northern hemisphere. The closeness of Ixodes (P.) succineus to a living vector of a wide range of pathogens offers the potential to correlate its spatial and temporal position (northern Europe, nearly 50 million years ago) with the estimated origination dates of various tick-borne diseases. Y1 - 2016 U6 - https://doi.org/10.1186/s12862-016-0777-y VL - 16 IS - 1 ER - TY - JOUR A1 - Bernard, Florian A1 - Salamanca, Luis A1 - Thunberg, Johan A1 - Tack, Alexander A1 - Jentsch, Dennis A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hertel, Frank A1 - Goncalves, Jorge A1 - Gemmar, Peter T1 - Shape-aware Surface Reconstruction from Sparse Data JF - arXiv N2 - The reconstruction of an object's shape or surface from a set of 3D points is a common topic in materials and life sciences, computationally handled in computer graphics. Such points usually stem from optical or tactile 3D coordinate measuring equipment. Surface reconstruction also appears in medical image analysis, e.g. in anatomy reconstruction from tomographic measurements or the alignment of intra-operative navigation and preoperative planning data. In contrast to mere 3D point clouds, medical imaging yields contextual information on the 3D point data that can be used to adopt prior information on the shape that is to be reconstructed from the measurements. In this work we propose to use a statistical shape model (SSM) as a prior for surface reconstruction. The prior knowledge is represented by a point distribution model (PDM) that is associated with a surface mesh. Using the shape distribution that is modelled by the PDM, we reformulate the problem of surface reconstruction from a probabilistic perspective based on a Gaussian Mixture Model (GMM). In order to do so, the given measurements are interpreted as samples of the GMM. By using mixture components with anisotropic covariances that are oriented according to the surface normals at the PDM points, a surface-based tting is accomplished. By estimating the parameters of the GMM in a maximum a posteriori manner, the reconstruction of the surface from the given measurements is achieved. Extensive experiments suggest that our proposed approach leads to superior surface reconstructions compared to Iterative Closest Point (ICP) methods. Y1 - 2016 SP - 1602.08425v1 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Hoffmann, René T1 - Comparative cephalopod shell strength and the role of septum morphology on stress distribution JF - PeerJ N2 - The evolution of complexly folded septa in ammonoids has long been a controversial topic. Explanations of the function of these folded septa can be divided into physiological and mechanical hypotheses with the mechanical functions tending to find widespread support. The complexity of the cephalopod shell has made it difficult to directly test the mechanical properties of these structures without oversimplification of the septal morphology or extraction of a small sub-domain. However, the power of modern finite element analysis now permits direct testing of mechanical hypothesis on complete, empirical models of the shells taken from computed tomographic data. Here we compare, for the first time using empirical models, the capability of the shells of extant Nautilus pompilius, Spirula spirula, and the extinct ammonite Cadoceras sp. to withstand hydrostatic pressure and point loads. Results show hydrostatic pressure imparts highest stress on the final septum with the rest of the shell showing minimal compression. S. spirula shows the lowest stress under hydrostatic pressure while N. pompilius shows the highest stress. Cadoceras sp. shows the development of high stress along the attachment of the septal saddles with the shell wall. Stress due to point loads decreases when the point force is directed along the suture as opposed to the unsupported chamber wall. Cadoceras sp. shows the greatest decrease in stress between the point loads compared to all other models. Greater amplitude of septal flutes corresponds with greater stress due to hydrostatic pressure; however, greater amplitude decreases the stress magnitude of point loads directed along the suture. In our models, sutural complexity does not predict greater resistance to hydrostatic pressure but it does seem to increase resistance to point loads, such as would be from predators. This result permits discussion of palaeoecological reconstructions on the basis of septal morphology. We further suggest that the ratio used to characterize septal morphology in the septal strength index and in calculations of tensile strength of nacre are likely insufficient. A better understanding of the material properties of cephalopod nacre may allow the estimation of maximum depth limits of shelled cephalopods through finite element analysis. Y1 - 2016 U6 - https://doi.org/10.7717/peerj.2434 VL - 4 SP - e2434 ER - TY - 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 - 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 - GEN A1 - Tycowicz, Christoph von A1 - Ambellan, Felix A1 - Mukhopadhyay, Anirban A1 - Zachow, Stefan T1 - A Riemannian Statistical Shape Model using Differential Coordinates N2 - We propose a novel Riemannian framework for statistical analysis of shapes that is able to account for the nonlinearity in shape variation. By adopting a physical perspective, we introduce a differential representation that puts the local geometric variability into focus. We model these differential coordinates as elements of a Lie group thereby endowing our shape space with a non-Euclidian structure. A key advantage of our framework is that statistics in a manifold shape space become numerically tractable improving performance by several orders of magnitude over state-of-the-art. We show that our Riemannian model is well suited for the identification of intra-population variability as well as inter-population differences. In particular, we demonstrate the superiority of the proposed model in experiments on specificity and generalization ability. We further derive a statistical shape descriptor that outperforms the standard Euclidian approach in terms of shape-based classification of morphological disorders. T3 - ZIB-Report - 16-69 Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61175 UR - https://opus4.kobv.de/opus4-zib/frontdoor/index/index/docId/6485 SN - 1438-0064 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 - JOUR A1 - Zachow, Stefan T1 - Computational Planning in Facial Surgery JF - Facial Plastic Surgery N2 - This article reflects the research of the last two decades in computational planning for cranio-maxillofacial surgery. Model-guided and computer-assisted surgery planning has tremendously developed due to ever increasing computational capabilities. Simulators for education, planning, and training of surgery are often compared with flight simulators, where maneuvers are also trained to reduce a possible risk of failure. Meanwhile, digital patient models can be derived from medical image data with astonishing accuracy and thus can serve for model surgery to derive a surgical template model that represents the envisaged result. Computerized surgical planning approaches, however, are often still explorative, meaning that a surgeon tries to find a therapeutic concept based on his or her expertise using computational tools that are mimicking real procedures. Future perspectives of an improved computerized planning may be that surgical objectives will be generated algorithmically by employing mathematical modeling, simulation, and optimization techniques. Planning systems thus act as intelligent decision support systems. However, surgeons can still use the existing tools to vary the proposed approach, but they mainly focus on how to transfer objectives into reality. Such a development may result in a paradigm shift for future surgery planning. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1564717 VL - 31 IS - 5 SP - 446 EP - 462 ER - TY - GEN A1 - Lamas-Rodríguez, Julián A1 - Ehlke, Moritz A1 - Hoffmann, René A1 - Zachow, Stefan T1 - GPU-accelerated denoising of large tomographic data sets with low SNR BT - Application for non-invasive analysis of paleontological data N2 - Enhancements in tomographic imaging techniques facilitate non-destructive methods for visualizing fossil structures. However, to penetrate dense materials such as sediments or pyrites, image acquisition is typically performed with high beam energy and very sensitive image intensifiers, leading to artifacts and noise in the acquired data. The analysis of delicate fossil structures requires the images to be captured in maximum resolution, resulting in large data sets of several giga bytes (GB) in size. Since the structural information of interest is often almost in the same spatial range as artifacts and noise, image processing and segmentation algorithms have to cope with a very low signal-to-noise ratio (SNR). Within this report we present a study on the performance of a collection of denoising algorithms applied to a very noisy fossil dataset. The study shows that a non-local means (NLM) filter, in case it is properly configured, is able to remove a considerable amount of noise while preserving most of the structural information of interest. Based on the results of this study, we developed a software tool within ZIBAmira that denoises large tomographic datasets using an adaptive, GPU-accelerated NLM filter. With the help of our implementation a user can interactively configure the filter's parameters and thus its effectiveness with respect to the data of interest, while the filtering response is instantly visualized for a preselected region of interest (ROI). Our implementation efficiently denoises even large fossil datasets in a reasonable amount of time. T3 - ZIB-Report - 15-14 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56339 SN - 1438-0064 ER - TY - JOUR A1 - Zahn, Robert A1 - Grotjohann, Sarah A1 - Ramm, Heiko A1 - Zachow, Stefan A1 - Putzier, Michael A1 - Perka, Carsten A1 - Tohtz, Stephan T1 - Pelvic tilt compensates for increased acetabular anteversion JF - International Orthopaedics N2 - Pelvic tilt determines functional orientation of the acetabulum. In this study, we investigated the interaction of pelvic tilt and functional acetabular anteversion (AA) in supine position. Y1 - 2015 U6 - https://doi.org/10.1007/s00264-015-2949-6 VL - 40 IS - 8 SP - 1571 EP - 1575 ER - TY - JOUR A1 - Zachow, Stefan A1 - Heppt, Werner T1 - The Facial Profile JF - Facial Plastic Surgery N2 - Facial appearance in our societies is often associated with notions of attractiveness, juvenileness, beauty, success, and so forth. Hence, the role of facial plastic surgery is highly interrelated to a patient's desire to feature many of these positively connoted attributes, which of course, are subject of different cultural perceptions or social trends. To judge about somebody's facial appearance, appropriate quantitative measures as well as methods to obtain and compare individual facial features are required. This special issue on facial profile is intended to provide an overview on how facial characteristics are surgically managed in an interdisciplinary way based on experience, instrumentation, and modern technology to obtain an aesthetic facial appearance with harmonious facial proportions. The facial profile will be discussed within the context of facial aesthetics. Latest concepts for capturing facial morphology in high speed and impressive detail are presented for quantitative analysis of even subtle changes, aging effects, or facial expressions. In addition, the perception of facial profiles is evaluated based on eye tracking technology. Y1 - 2015 U6 - https://doi.org/10.1055/s-0035-1566132 VL - 31 IS - 5 SP - 419 EP - 420 ER - TY - CHAP A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Shandiz, Mohsen Akbari A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Towards Robust Measurement Of Pelvic Parameters From AP Radiographs Using Articulated 3D Models T2 - Computer Assisted Radiology and Surgery (CARS) N2 - Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph. KW - Articulated Models, Statistical Shape And Intensity Models, 2D/3D Anatomy Reconstruction, Pelvic Parameters Measurement, Total Hip Arthroplasty Y1 - 2015 ER - TY - GEN A1 - Ehlke, Moritz A1 - Frenzel, Thomas A1 - Ramm, Heiko A1 - Shandiz, Mohsen Akbari A1 - Anglin, Carolyn A1 - Zachow, Stefan T1 - Towards Robust Measurement of Pelvic Parameters from AP Radiographs using Articulated 3D Models N2 - Patient-specific parameters such as the orientation of the acetabulum or pelvic tilt are useful for custom planning for total hip arthroplasty (THA) and for evaluating the outcome of surgical interventions. The gold standard in obtaining pelvic parameters is from three-dimensional (3D) computed tomography (CT) imaging. However, this adds time and cost, exposes the patient to a substantial radiation dose, and does not allow for imaging under load (e.g. while the patient is standing). If pelvic parameters could be reliably derived from the standard anteroposterior (AP) radiograph, preoperative planning would be more widespread, and research analyses could be applied to retrospective data, after a postoperative issue is discovered. The goal of this work is to enable robust measurement of two surgical parameters of interest: the tilt of the anterior pelvic plane (APP) and the orientation of the natural acetabulum. We present a computer-aided reconstruction method to determine the APP and natural acetabular orientation from a single, preoperative X-ray. It can easily be extended to obtain other important preoperative and postoperative parameters solely based on a single AP radiograph. T3 - ZIB-Report - 15-11 KW - Articulated Models, Statistical Shape And Intensity Models, 2D/3D Anatomy Reconstruction, Pelvic Parameters Measurement, Total Hip Arthroplasty Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-53707 SN - 1438-0064 ER - TY - JOUR A1 - Lemanis, Robert A1 - Zachow, Stefan A1 - Fusseis, Florian A1 - Hoffmann, René T1 - A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells JF - Paleobiology N2 - The chambered shell of modern cephalopods functions as a buoyancy apparatus, allowing the animal to enter the water column without expending a large amount of energy to overcome its own weight. Indeed, the chambered shell is largely considered a key adaptation that allowed the earliest cephalopods to leave the ocean floor and enter the water column. It has been argued by some, however, that the iconic chambered shell of Paleozoic and Mesozoic ammonoids did not provide a sufficiently buoyant force to compensate for the weight of the entire animal, thus restricting ammonoids to a largely benthic lifestyle reminiscent of some octopods. Here we develop a technique using high-resolution computed tomography to quantify the buoyant properties of chambered shells without reducing the shell to ideal spirals or eliminating inherent biological variability by using mathematical models that characterize past work in this area. This technique has been tested on Nautilus pompilius and is now extended to the extant deep-sea squid Spirula spirula and the Jurassic ammonite Cadoceras sp. hatchling. Cadoceras is found to have possessed near-neutral to positive buoyancy if hatched when the shell possessed between three and five chambers. However, we show that the animal could also overcome degrees of negative buoyancy through swimming, similar to the paralarvae of modern squids. These calculations challenge past inferences of benthic life habits based solely on calculations of negative buoyancy. The calculated buoyancy of Cadoceras supports the possibility of planktonic dispersal of ammonite hatchlings. This information is essential to understanding ammonoid ecology as well as biotic interactions and has implications for the interpretation of geochemical data gained from the isotopic analysis of the shell. Y1 - 2015 U6 - https://doi.org/10.1017/pab.2014.17 VL - 41 IS - 2 SP - 313 EP - 329 PB - Cambridge University Press CY - Cambridge ER - TY - GEN A1 - Wilson, David A1 - Bücher, Pia A1 - Grewe, Carl Martin A1 - Anglin, Carolyn A1 - Zachow, Stefan A1 - Michael, Dunbar T1 - Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Point Cloud Data T2 - 15th Annual Meeting of the International Society for Computer Assisted Orthopaedic Surgery (CAOS) Y1 - 2015 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 - Wilson, David A1 - Bücher, Pia A1 - Grewe, Carl Martin A1 - Mocanu, Valentin A1 - Anglin, Carolyn A1 - Zachow, Stefan A1 - Dunbar, Michael T1 - Validation of Three Dimensional Models of the Distal Femur Created from Surgical Navigation Data T2 - Orthopedic Research Society Annual Meeting Y1 - 2015 CY - Las Vegas, Nevada ER - TY - GEN A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - Assessing the Relative Positioning of an Osteosynthesis Plate to the Patient-Specific Femoral Shape from Plain 2D Radiographs N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient­specific surface of the distal femur based on 2D X­ray images. Our goal is to study from clinical data, how the plate­to­bone distance affects bone healing. The patient­specific 3D shape of the femur is, however, seldom recorded for cases of femoral osteosynthesis since this typically requires Computed Tomography (CT), which comes at high cost and radiation dose. Our method instead utilizes two postoperative X­ray images to derive the femoral shape and thus can be applied on radiographs that are taken in clinical routine for follow­up. First, the implant geometry is used as a calibration object to relate the implant and the individual X­ray images spatially in a virtual X­ray setup. In a second step, the patient­specific femoral shape and pose are reconstructed in the virtual setup by fitting a deformable statistical shape and intensity model (SSIM) to the images. The relative positioning between femur and implant is then assessed in terms of displacement between the reconstructed 3D shape of the femur and the plate. A preliminary evaluation based on 4 cadaver datasets shows that the method derives the plate­to­bone distance with a mean absolute error of less than 1mm and a maximum error of 4.7 mm compared to ground truth from CT. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing. T3 - ZIB-Report - 15-21 KW - 3d-­reconstruction from 2d X­rays KW - statistical shape and intensity models KW - fracture fixation of the distal femur KW - pose estimation Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54268 SN - 1438-0064 ER - TY - GEN A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - 3D Assessment of Osteosynthesis based on 2D Radiographs N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient-specific surface of the distal femur based on postoperative 2D radiographs. In a first step, the implant geometry is used as a calibration object to relate the implant and the individual X-ray images spatially in a virtual X-ray setup. Second, the patient-specific femoral shape and pose are reconstructed by fitting a deformable statistical shape and intensity model (SSIM) to the X-rays. The relative positioning between femur and implant is then assessed in terms of the displacement between the reconstructed 3D shape of the femur and the plate. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing and, ultimately, to derive load recommendations after surgery. T3 - ZIB-Report - 15-47 KW - 3d-reconstruction from 2d X-rays KW - statistical shape and intensity models KW - osteosynthesis follow-up Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-56217 SN - 1438-0064 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 - CHAP A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - Assessing the relative positioning of an osteosynthesis plate to the patient-specific femoral shape from plain 2D radiographs T2 - Proceedings of the 15th Annual Meeting of CAOS-International (CAOS) N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient­specific surface of the distal femur based on 2D X­ray images. Our goal is to study from clinical data, how the plate­to­bone distance affects bone healing. The patient­specific 3D shape of the femur is, however, seldom recorded for cases of femoral osteosynthesis since this typically requires Computed Tomography (CT), which comes at high cost and radiation dose. Our method instead utilizes two postoperative X­ray images to derive the femoral shape and thus can be applied on radiographs that are taken in clinical routine for follow­up. First, the implant geometry is used as a calibration object to relate the implant and the individual X­ray images spatially in a virtual X­ray setup. In a second step, the patient­specific femoral shape and pose are reconstructed in the virtual setup by fitting a deformable statistical shape and intensity model (SSIM) to the images. The relative positioning between femur and implant is then assessed in terms of displacement between the reconstructed 3D shape of the femur and the plate. A preliminary evaluation based on 4 cadaver datasets shows that the method derives the plate­to­bone distance with a mean absolute error of less than 1mm and a maximum error of 4.7 mm compared to ground truth from CT. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing. KW - 3d-­reconstruction from 2d X­rays KW - statistical shape and intensity models KW - fracture fixation of the distal femur KW - pose estimation Y1 - 2015 ER - TY - CHAP A1 - Ehlke, Moritz A1 - Heyland, Mark A1 - Märdian, Sven A1 - Duda, Georg A1 - Zachow, Stefan T1 - 3D Assessment of Osteosynthesis based on 2D Radiographs T2 - Proceedings of the Jahrestagung der Deutschen Gesellschaft für Computer- und Roboterassistierte Chirurgie (CURAC) N2 - We present a novel method to derive the surface distance of an osteosynthesis plate w.r.t. the patient-specific surface of the distal femur based on postoperative 2D radiographs. In a first step, the implant geometry is used as a calibration object to relate the implant and the individual X-ray images spatially in a virtual X-ray setup. Second, the patient- specific femoral shape and pose are reconstructed by fitting a deformable statistical shape and intensity model (SSIM) to the X-rays. The relative positioning between femur and implant is then assessed in terms of the displacement between the reconstructed 3D shape of the femur and the plate. We believe that the approach presented in this paper constitutes a meaningful tool to elucidate the effect of implant positioning on fracture healing and, ultimately, to derive load recommendations after surgery. KW - 3d-reconstruction from 2d X-rays KW - osteosynthesis follow-up KW - statistical shape and intensity models Y1 - 2015 SP - 317 EP - 321 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 - 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 - Baum, Daniel A1 - Mahlow, Kristin A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Müller, Johannes A1 - Hege, Hans-Christian T1 - The Potential of Surface-based Geometric Morphometrics for Evolutionary Studies: An Example using Dwarf Snakes (Eirenis) T2 - Abstract in DigitalSpecimen 2014 N2 - Geometric morphometrics plays an important role in evolutionary studies. The state-of-the-art in this field are landmark-based methods. Since the landmarks usually need to be placed manually, only a limited number of landmarks are generally used to represent the shape of an anatomical structure. As a result, shape characteristics that cannot be properly represented by small sets of landmarks are disregarded. In this study, we present a method that is free of this limitation. The method takes into account the whole shape of an anatomical structure, which is represented as a surface, hence the term ‘surface-based morphometrics’. Correspondence between two surfaces is established by defining a partitioning of the surfaces into homologous surface patches. The first step for the generation of a surface partitioning is to place landmarks on the surface. Subsequently, the landmarks are connected by curves lying on the surface. The curves, called ‘surface paths’, might either follow specific anatomical features or they can be geodesics, that is, shortest paths on the surface. One important requirement, however, is that the resulting surface path networks are topologically equivalent across all surfaces. Once the surface path networks have been defined, the surfaces are decomposed into patches according to the path networks. This approach has several advantages. One of them is that we can discretize the surface by as many points as desired. Thus, even fine shape details can be resolved if this is of interest for the study. Since a point discretization is used, another advantage is that well-established analysis methods for landmark-based morphometrics can be utilized. Finally, the shapes can be easily morphed into one another, thereby greatly supporting the understanding of shape changes across all considered specimens. To show the potential of the described method for evolutionary studies of biological specimens, we applied the method to the para-basisphenoid complex of the snake genus Eirenis. By using this anatomical structure as example, we present all the steps that are necessary for surface-based morphometrics, including the segmentation of the para-basisphenoid complex from micro-CT data sets. We also show some first results using statistical analysis as well as classification methods based on the presented technique. Y1 - 2014 ER - TY - 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 - 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 - 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 - JOUR A1 - Zinser, Max A1 - Zachow, Stefan A1 - Sailer, Hermann T1 - Bimaxillary "rotation advancement" procedures in patients with obstructive sleep apnea: A 3-dimensional airway analysis of morphological changes JF - International Journal of Oral & Maxillofacial Surgery Y1 - 2013 U6 - https://doi.org/10.1016/j.ijom.2012.08.002 VL - 42 IS - 5 SP - 569 EP - 578 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 - Galloway, Francis A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Worsley, Peter A1 - Zachow, Stefan A1 - Nair, Prasanth A1 - Taylor, Mark T1 - A large scale finite element study of a cementless osseointegrated tibial tray JF - Journal of Biomechanics Y1 - 2013 U6 - https://doi.org//10.1016/j.jbiomech.2013.04.021 VL - 46 IS - 11 SP - 1900 EP - 1906 ER - TY - JOUR A1 - 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 - 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 - Ramm, Heiko A1 - Victoria Morillo, Oscar Salvador A1 - Todt, Ingo A1 - Schirmacher, Hartmut A1 - Ernst, Arneborg A1 - Zachow, Stefan A1 - Lamecker, Hans ED - Freysinger, Wolfgang T1 - Visual Support for Positioning Hearing Implants T2 - Proceedings of the 12th annual meeting of the CURAC society Y1 - 2013 SP - 116 EP - 120 ER - TY - JOUR A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Heller, Markus O. A1 - Weber, Britta A1 - Hege, Hans-Christian A1 - Zachow, Stefan T1 - Omnidirectional Displacements for Deformable Surfaces JF - Medical Image Analysis Y1 - 2013 U6 - https://doi.org/10.1016/j.media.2012.11.006 VL - 17 IS - 4 SP - 429 EP - 441 PB - Elsevier ER - TY - JOUR A1 - Lamas-Rodríguez, Julián A1 - Heras, Dora Blanco A1 - Argüello, Francisco A1 - Kainmüller, Dagmar A1 - Zachow, Stefan A1 - Bóo, Montserrat T1 - GPU-accelerated level-set segmentation JF - Journal of Real-Time Image Processing Y1 - 2013 UR - http://dx.doi.org/10.1007/s11554-013-0378-6 U6 - https://doi.org/10.1007/s11554-013-0378-6 SN - 1861-8200 SP - 1 EP - 15 PB - Springer Berlin Heidelberg ER - TY - 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 - GEN A1 - Ramm, Heiko A1 - Morillo Victoria, Oscar Salvador A1 - Todt, Ingo A1 - Schirmacher, Hartmut A1 - Ernst, Arneborg A1 - Zachow, Stefan A1 - Lamecker, Hans T1 - Visual Support for Positioning Hearing Implants N2 - We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit. T3 - ZIB-Report - 13-53 KW - bone anchored hearing implant KW - surgery planning KW - segmentation KW - visualization Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42495 SN - 1438-0064 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 - 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 - 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 - GEN A1 - Bindernagel, Matthias A1 - Kainmüller, Dagmar A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Analysis of inter-individual anatomical shape variations of joint structures T2 - Proc. Int. Society of Computer Assisted Orthopaedic Surgery (CAOS) Y1 - 2012 IS - 210 ER - TY - CHAP A1 - Nguyen, The Duy A1 - Lamecker, Hans A1 - Kainmüller, Dagmar A1 - Zachow, Stefan ED - Ayache, Nicholas ED - Delingette, Hervé ED - Golland, Polina ED - Mori, Kensaku T1 - Automatic Detection and Classification of Teeth in CT Data T2 - Proc. Medical Image Computing and Computer Assisted Intervention (MICCAI) Y1 - 2012 VL - 7510 SP - 609 EP - 616 ER - TY - JOUR A1 - Nguyen, The Duy A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Automatic bone and tooth detection for CT-based dental implant planning JF - Int. J. Computer Assisted Radiology and Surgery Y1 - 2012 VL - 7, Supplement 1 IS - 1 SP - 293 EP - 294 PB - Springer 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 - 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 - 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 - JOUR A1 - Ho, Karen A1 - Saevarsson, Stefan A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - Sharma, Gulshan A1 - Rex, Erica A1 - Amiri, Shahram A1 - Wu, Barnabas A1 - Leumann, Andre A1 - Anglin, Carolyn T1 - Computed tomography analysis of knee pose and geometry before and after total knee arthroplasty JF - Journal of biomechanics Y1 - 2012 UR - http://www.ncbi.nlm.nih.gov/pubmed/22796002 U6 - https://doi.org/10.1016/j.jbiomech.2012.06.004 VL - 45 IS - 13 SP - 2215 EP - 21 ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric shape and intensity models for accurate simulation of X-ray images T2 - Eurographics Workshop on Visual Computing for Biomedicine (NVIDIA best poster award) Y1 - 2012 ER - TY - JOUR A1 - Ramm, Heiko A1 - Kahnt, Max A1 - Zachow, Stefan T1 - Patientenspezifische Simulationsmodelle für die funktionelle Analyse von künstlichem Gelenkersatz JF - Computer Aided Medical Engineering (CaMe) Y1 - 2012 VL - 3 IS - 2 SP - 30 EP - 36 ER - TY - CHAP A1 - Kahnt, Max A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan ED - Levine, Joshua A. ED - Paulsen, Rasmus R. ED - Zhang, Yongjie T1 - Feature-Preserving, Multi-Material Mesh Generation using Hierarchical Oracles T2 - Proc. MICCAI Workshop on Mesh Processing in Medical Image Analysis (MeshMed) Y1 - 2012 VL - 7599 SP - 101 EP - 111 ER - TY - CHAP A1 - Ramm, Heiko A1 - Zachow, Stefan ED - Niederlag, Wolfgang ED - Lemke, Heinz ED - Peitgen, Heinz-Otto ED - Lehrach, Hans T1 - Computergestützte Planung für die individuelle Implantatversorgung T2 - Health Academy Y1 - 2012 VL - 16 SP - 145 EP - 158 ER - TY - GEN A1 - Ehlke, Moritz A1 - Ramm, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Efficient projection and deformation of volumetric intensity models for accurate simulation of X-ray images N2 - We present an efficient GPU-based method to generate virtual X-ray images from tetrahedral meshes which are associated with attenuation values. In addition, a novel approach is proposed that performs the model deformation on the GPU. The tetrahedral grids are derived from volumetric statistical shape and intensity models (SSIMs) and describe anatomical structures. Our research targets at reconstructing 3D anatomical shapes by comparing virtual X-ray images generated using our novel approach with clinical data while varying the shape and density of the SSIM in an optimization process. We assume that a deformed SSIM adequately represents an anatomy of interest when the similarity between the virtual and the clinical X-ray image is maximized. The OpenGL implementation presented here generates accurate (virtual) X-ray images at interactive rates, thus qualifying it for its use in the reconstruction process. T3 - ZIB-Report - 12-40 KW - Digitally Reconstructed Radiograph (DRR), Anatomy Reconstruction, Statistical Shape and Intensity Model (SSIM), GPU acceleration Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-16580 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 - von Berg, Jens A1 - Dworzak, Jalda A1 - Klinder, Tobias A1 - Manke, Dirk A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Lorenz, Cristian T1 - Temporal Subtraction of Chest Radiographs Compensating Pose Differences T2 - SPIE Medical Imaging Y1 - 2011 ER - TY - CHAP A1 - Bindernagel, Matthias A1 - Kainmüller, Dagmar A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian T1 - An Articulated Statistical Shape Model of the Human Knee T2 - Bildverarbeitung für die Medizin 2011 Y1 - 2011 U6 - https://doi.org/10.1007/978-3-642-19335-4_14 SP - 59 EP - 63 PB - Springer ER - TY - CHAP A1 - Kahnt, Max A1 - Galloway, Francis A1 - Seim, Heiko A1 - Lamecker, Hans A1 - Taylor, Mark A1 - Zachow, Stefan T1 - Robust and Intuitive Meshing of Bone-Implant Compounds T2 - CURAC Y1 - 2011 SP - 71 EP - 74 CY - Magdeburg ER - TY - GEN A1 - SK, Saevarsson A1 - GB, Sharma A1 - S, Montgomery A1 - KCT, Ho A1 - Ramm, Heiko A1 - Lieck, Robert A1 - Zachow, Stefan A1 - C, Anglin T1 - Kinematic Comparison Between Gender Specific and Traditional Femoral Implants T2 - Proceedings of the 11th Alberta Biomedical Engineering (BME) Conference (Poster) Y1 - 2011 SP - 80 ER - TY - GEN A1 - Grewe, Carl Martin A1 - Lamecker, Hans A1 - Zachow, Stefan T1 - Digital morphometry: The Potential of Statistical Shape Models T2 - Anthropologischer Anzeiger. Journal of Biological and Clinical Anthropology Y1 - 2011 SP - 506 EP - 506 ER - TY - JOUR A1 - Taylor, William R. A1 - Pöpplau, Berry M. A1 - König, Christian A1 - Ehrig, Rainald A1 - Zachow, Stefan A1 - Duda, Georg A1 - Heller, Markus O. T1 - The medial-lateral force distribution in the ovine stifle joint during walking JF - Journal of Orthopaedic Research Y1 - 2011 U6 - https://doi.org/10.1002/jor.21254 VL - 29 IS - 4 SP - 567 EP - 571 ER - TY - JOUR A1 - Rybak, Jürgen A1 - Kuß, Anja A1 - Lamecker, Hans A1 - Zachow, Stefan A1 - Hege, Hans-Christian A1 - Lienhard, Matthias A1 - Singer, Jochen A1 - Neubert, Kerstin A1 - Menzel, Randolf T1 - The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System JF - Front. Syst. Neurosci. Y1 - 2010 U6 - https://doi.org/10.3389/fnsys.2010.00030 VL - 4 IS - 30 ER - TY - CHAP A1 - Deuflhard, Peter A1 - Dössel, Olaf A1 - Louis, Alfred A1 - Zachow, Stefan T1 - More Mathematics into Medicine! T2 - Production Factor Mathematics Y1 - 2010 UR - http://www.springer.com/mathematics/book/978-3-642-11247-8 SP - 357 EP - 378 PB - Springer ER - TY - CHAP A1 - Seim, Heiko A1 - Kainmüller, Dagmar A1 - Lamecker, Hans A1 - Bindernagel, Matthias A1 - Malinowski, Jana A1 - Zachow, Stefan ED - v. Ginneken, B. T1 - Model-based Auto-Segmentation of Knee Bones and Cartilage in MRI Data T2 - Proc. MICCAI Workshop Medical Image Analysis for the Clinic Y1 - 2010 SP - 215 EP - 223 ER -