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Oyarzun Laura, Cristina; Drechsler, Klaus; Wesarg, Stefan; Bale, Reto

Accurate Physics-Based Registration for the Outcome Validation of Minimal Invasive Interventions and Open Liver Surgeries

2017

IEEE Transactions on Biomedical Engineering, Vol.64 (2017), 2, pp. 362-371

The purpose of this paper is to present an outcome validation tool for tumor radiofrequency (RF) ablation and resection. Methods: Intervention assessment tools require an accurate registration of both pre- and postoperative computed tomographies able to handle big deformations. Therefore, a physics-based method is proposed with that purpose. To increase the accuracy both automatically detected internal and surface physical landmarks are incorporated in the registration process. Results: The algorithm has been evaluated in 25 clinical datasets containing RF ablations, resections, and patients with recurrent tumors. The achieved accuracy is 1.2 mm measured as mean internal distance between vessel landmarks and a positive predictive value of 0.95. The quantitative and qualitative results of the outcome validation tool show that in 50% of the cases tumors were only partially covered by the treatment. Conclusion: The use of internal and surface landmarks combined with a physics-based registration method increases the accuracy of the results compared to the accuracy of state of the art methods. An accurate outcome validation tool is important in order to certify that the tumor and its safety margin were fully covered by the treatment. Significance: An accurate outcome validation tool can result in a decrease of the tumor recurrence rate.

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Shekhar, Raj; Wesarg, Stefan; González Ballester, Miguel Angel; Drechsler, Klaus; Sato, Yoshinobu; Erdt, Marius; Linguraru, Marius George; Oyarzun Laura, Cristina

Clinical Image-Based Procedures. Translational Research in Medical Imaging: 5th International Workshop, CLIP 2016. Held in Conjunction with MICCAI 2016

2016

Berlin, Heidelberg, New York : Springer, 2016

International Workshop on Clinical Image-based Procedures (CLIP) <5, 2016, Athens, Greece>

Lecture Notes in Computer Science (LNCS) 9958

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Oyarzun Laura, Cristina; Oelmann, Simon; Drechsler, Klaus; Wesarg, Stefan

Reducing Over- and Undersegmentations of the Liver in Computed Tomographies Using Anatomical Knowledge

2016

Efthyvoulos, Kyriacou (Ed.) et al.: XIV Mediterranean Conference on Medical and Biological Engineering and Computing : MEDICON 2016. Berlin, Heidelberg, New York: Springer, 2016. (IFMBE Proceedings 57), pp. 382-387

Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON) <14, 2016, Paphos, Cyprus>

In the last decades several liver segmentation methods have been proposed. The proposed methods go from region growing to the more complex statistical shape models. Despite the robustness of those algorithms, liver segmentation is still a challenging task especially in areas in which its neighboring organs have similar intensities, e.g., heart and ribcage. In addition to this, pathological organs that contain tumors near their surface present additional difficulties. This paper presents a solution to increase the accuracy of those algorithms in the aforementioned areas. The effect of the improvement using the generated heart and ribcage walls (7% and 1% respectively) is evaluated on 9 clinical computer tomographies (CT). The improvement (12 %) when tumors are near the surface, on the contrary, is tested on 7 clinical CT images.

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Oelmann, Simon; Oyarzun Laura, Cristina; Drechsler, Klaus; Wesarg, Stefan

Active Contour based Segmentation of Resected Livers in CT Images

2015

Ourselin, Sébastien (Ed.) et al.: Medical Imaging 2015: Image Processing. Bellingham: SPIE Press, 2015. (Proceedings of SPIE 9413), pp. 941316-1 - 941316-6

SPIE Medical Imaging Symposium <2015, Orlando, FL, USA>

The majority of state of the art segmentation algorithms are able to give proper results in healthy organs but not in pathological ones. However, many clinical applications require an accurate segmentation of pathological organs. The determination of the target boundaries for radiotherapy or liver volumetry calculations are examples of this. Volumetry measurements are of special interest after tumor resection for follow up of liver regrow. The segmentation of resected livers presents additional challenges that were not addressed by state of the art algorithms. This paper presents a snakes based algorithm specially developed for the segmentation of resected livers. The algorithm is enhanced with a novel dynamic smoothing technique that allows the active contour to propagate with different speeds depending on the intensities visible in its neighborhood. The algorithm is evaluated in 6 clinical CT images as well as 18 artificial datasets generated from additional clinical CT images.

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Oyarzun Laura, Cristina; Drechsler, Klaus; Wesarg, Stefan

Anatomical Discovery: Finding Organs in the Neighborhood of the Liver

2014

Romero, Laura M. Roa (Ed.): XIII Mediterranean Conference on Medical and Biological Engineering and Computing : MEDICON 2013. Berlin, Heidelberg, New York: Springer, 2014. (IFMBE Proceedings 41), pp. 348-351

The Mediterranean Conference on Medical and Biological Engineering and Computing (MEDICON) <13, 2013, Seville, Spain>

Image segmentation and registration algorithms are fundamental to assist medical doctors for better treatment of the patients. To this end accuracy in the results given by those algorithms is crucial. The surroundings of the organ to be segmented or registered can provide additional information that at the end improves the result. In this paper a novel algorithm to detect the organs that surround the liver is introduced. Even though our work is focused on the liver, the algorithm could be extended to other parts of the body. The algorithm has been tested in 24 clinical CT datasets. In addition to this, an example application is introduced for which the detection is a useful tool.

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Erdt, Marius; Linguraru, Marius George; Oyarzun Laura, Cristina; Shekhar, Raj; Wesarg, Stefan; González Ballester, Miguel Angel; Drechsler, Klaus

Clinical Image-Based Procedures. Translational Research in Medical Imaging: Second International Workshop, CLIP 2013. Held in Conjunction with MICCAI 2013

2014

Berlin, Heidelberg, New York : Springer, 2014

International Workshop on Clinical Image-based Procedures (CLIP) <2, 2013, Nagoya, Japan>

Lecture Notes in Computer Science (LNCS) 8361

This book constitutes revised selected papers from the International Workshop on Clinical Image-Based Procedures, CLIP 2013, held in conjunction with MICCAI 2012 in Nagoya, Japan, in September 2013. The 19 papers presented in this volume were carefully reviewed and selected from 26 submissions. The workshop was a productive and exciting forum for the discussion and dissemination of clinically tested, state-of-the-art methods for image-based planning, monitoring and evaluation of medical procedures.

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Linguraru, Marius George; Oyarzun Laura, Cristina; Shekhar, Raj; Wesarg, Stefan; González Ballester, Miguel Angel; Drechsler, Klaus; Sato, Yoshinobu; Erdt, Marius

Clinical Image-Based Procedures. Translational Research in Medical Imaging: Third International Workshop, CLIP 2014. Held in Conjunction with MICCAI 2014

2014

Berlin, Heidelberg, New York : Springer, 2014

International Workshop on Clinical Image-based Procedures (CLIP) <3, 2014, Boston, MA, USA>

Lecture Notes in Computer Science (LNCS) 8680

CLIP 2014 provided a successful forum for the dissemination of emerging image-based clinical techniques. Specific topics included pre-interventional image segmentation and classification (to support diagnosis and clinical decision making), interventional and surgical planning and analysis of dynamic images, and evaluation, visualization and correction techniques for image-based procedures. Clinical applications covered the skull and the brain, cardiac defects, blood vessels, abdominal organs, and cancer in adults and children. The presentations and discussions around the meeting emphasized current challenges and emerging techniques in image-based procedures, strategies for clinical translation of image-based techniques, the role of computational anatomy and image analysis for surgical planning and interventions, and the contribution of medical image analysis to open and minimally invasive surgery.

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Knaub, Anton; Drechsler, Klaus (Betreuer)

Entwicklung eines Appearance Models zur modellbasierten Lebersegmentierung in MRT-Daten

2014

Darmstadt, Hochschule, Bachelor Thesis, 2014

Der Standard der Diagnostizierung von Lebertumoren in der Radiologie ist bis heute die Computertomographie (CT). Auf Basis dieser Daten wurden zahlreiche Segmentierungsverfahren entwickelt und erfolgreich für die automatisierte Diagnose und Planung von Interventionen eingesetzt. Die Gefahr bei CT besteht darin, dass der Patient einer erhöhten Strahlungsdosis ausgesetzt wird. Dies ist einer der Gründe, weswegen die Magnetresonanztomographie (MRT) verstärkt von Radiologen zur Diagnose eingesetzt wird. Es gibt viele Ansätze zur Segmentierung von Organen wie der Leber. Besonders gute Ergebnisse wurden mit modellbasierten Ansätzen für die automatische Segmentierung der Leber in CT-Daten entwickelt. Auf den Wunsch der Radiologen soll auch eine Lebersegmentierung auf MRT-Daten ermöglicht werden. Aus diesem Grund wird in dieser Arbeit ein bestehendes modellbasierendes Verfahren, das Probabilistic Active Shape Model von Matthias Kirschner, aufgegriffen und um ein Appearance Model für MRT-Daten erweitert und somit eine Lebersegmentierung auf MRT-Daten ermöglicht. Dazu wird eine geeignete Vorverarbeitungspipeline für MRT-Lebern gewählt. Des Weiteren werden verschiedene Trainingsmethoden des Appearance Models untersucht und die geeignetste selektiert und evaluiert. Die Ergebnisse der Evaluation der Segmentierung auf acht kontrastinjizierten Lebern liefern einen durchschnittlichen Volumenüberlappungsfehler von 13,37 % bei einer durchschnittlichen Oberflächendistanz von 2,39 mm.

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Steger, Teena; Drechsler, Klaus; Wesarg, Stefan

Image-Based Bronchoscopy Navigation System Based on CT and C-arm Fluoroscopy

2014

Erdt, Marius (Ed.) et al.: Clinical Image-Based Procedures. Translational Research in Medical Imaging : Second International Workshop, CLIP 2013. Held in Conjunction with MICCAI 2013. Berlin, Heidelberg, New York: Springer, 2014. (Lecture Notes in Computer Science (LNCS) 8361), pp. 15-22

International Workshop on Clinical Image-based Procedures (CLIP) <2, 2013, Nagoya, Japan>

Lung cancer diagnosis requires biopsy of airway tissue, which is mostly done by bronchoscopy. Although preoperative CT is available, intraoperatively only 2D information provided by the bronchoscopic camera and fluoroscopy is used. But, guidance of the bronchoscope to the target site would highly benefit from knowing the exact 3D position of the instrument inside the airways. In this paper, we present a system for preoperative planning and intraoperative navigation during bronchoscopy. The preoperative components are automatic bronchial tree segmentation and skeletonization, semi-automatic tumor segmentation and a virtual fly-through simulation for planning purposes. During the intervention, we apply C-arm pose estimation using a marker plate on the patient table to align preoperative CT and intraoperative fluoroscopy. Thus, we can calculate the current 3D position of the bronchoscope inside the bronchial tree. Evaluation of the system components on patient CT and phantom fluoroscopy images showed promising results with high accuracy and robustness.

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Drechsler, Klaus; Knaub, Anton; Oyarzun Laura, Cristina; Wesarg, Stefan

Liver Segmentation in Contrast Enhanced MR Datasets Using a Probabilistic Active Shape and Appearance Model

2014

IEEE Computer Society: IEEE 27th International Symposium on Computer-Based Medical Systems : CBMS 2014. Los Alamitos, Calif.: IEEE Computer Society Conference Publishing Services (CPS), 2014, pp. 523-524

IEEE Symposium on Computer-Based Medical Systems (CBMS) <27, 2014, New York, NY, USA>

The current standard for diagnosing liver tumors is contrast-enhanced multiphase computed tomography. On this basis, several software tools have been developed by different research groups worldwide to support physicians for example in measuring remnant liver volume, analyzing tumors, and planning resections. Several algorithms have been developed to perform these tasks. Most of the time, the segmentation of the liver is at the beginning of the processing chain. Therefore, a vast amount of CT-based liver segmentation algorithms have been developed. However, clinics slowly move from CT as the current gold standard for diagnosing liver diseases towards magnetic resonance imaging. In this work, we utilize a Probabilistic Active Shape Model with an MR specific preprocessing and appearance model to segment the liver in contrast enhanced MR images. Evaluation is based on 8 clinical datasets.

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Hammon, Matthias; Cavallaro, Alexander; Erdt, Marius; Dankerl, Peter; Kirschner, Matthias; Drechsler, Klaus; Wesarg, Stefan; Uder, Michael; Janka, Rolf

Model-Based Pancreas Segmentation in Portal Venous Phase Contrast-Enhanced CT Images

2014

Journal of Digital Imaging, Vol.26 (2014), 6, pp. 1082-1090. First published online 08 March 2013

This study aims to automatically detect and segment the pancreas in portal venous phase contrast-enhanced computed tomography (CT) images. The institutional review board of the University of Erlangen-Nuremberg approved this study and waived the need for informed consent. Discriminative learning is used to build a pancreas tissue classifier incorporating spatial relationships between the pancreas and surrounding organs and vessels. Furthermore, discrete cosine and wavelet transforms are used to build texture features to describe local tissue appearance. Classification is used to guide a constrained statistical shape model to fit the data. The algorithm to detect and segment the pancreas was evaluated on 40 consecutive CT data that were acquired in the portal venous contrast agent phase. Manual segmentation of the pancreas was carried out by experienced radiologists and served as reference standard. Threefold cross validation was performed. The algorithm-based detection and segmentation yielded an average surface distance of 1.7 mm and an average overlap of 61.2 % compared with the reference standard. The overall runtime of the system was 20.4 min. The presented novel approach enables automatic pancreas segmentation in portal venous phase contrast-enhanced CT images which are included in almost every clinical routine abdominal CT examination. Reliable pancreatic segmentation is crucial for computer-aided detection systems and an organ-specific decision support.

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Oyarzun Laura, Cristina; Drechsler, Klaus; Wesarg, Stefan

Two-Step FEM-Based Liver-CT Registration: Improving Internal and External Accuracy

2014

Ourselin, Sébastien (Ed.) et al.: Medical Imaging 2014: Image Processing : Progress in Biomedical Optics and Imaging Vol. 15 No. 35. Bellingham: SPIE Press, 2014. (Proceedings of SPIE 9034), 7 p.

SPIE Medical Imaging Symposium <2014, San Diego, CA, USA>

To know the exact location of the internal structures of the organs, especially the vasculature, is of great importance for the clinicians. This information allows them to know which structures/vessels will be affected by certain therapy and therefore to better treat the patients. However the use of internal structures for registration is often disregarded especially in physical based registration methods. In this paper we propose an algorithm that uses finite element methods to carry out a registration of liver volumes that will not only have accuracy in the boundaries of the organ but also in the interior. Therefore a graph matching algorithm is used to find correspondences between the vessel trees of the two livers to be registered. In addition to this an adaptive volumetric mesh is generated that contains nodes in the locations in which correspondences were found. The displacements derived from those correspondences are the input for the initial deformation of the model. The first deformation brings the internal structures to their final deformed positions and the surfaces close to it. Finally, thin plate splines are used to refine the solution at the boundaries of the organ achieving an improvement in the accuracy of 71%. The algorithm has been evaluated in CT clinical images of the abdomen.

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Drechsler, Klaus; Meixner, Steven; Oyarzun Laura, Cristina; Wesarg, Stefan

A Framework for Validation of Vessel Segmentation Algorithms

2013

Rodrigues, Pedro Pereira (Ed.) et al.: Proceedings of CBMS 2013 : The 26th IEEE International Symposium on Computer-Based Medical Systems. New York: IEEE, Inc., 2013, pp. 518-519

IEEE Symposium on Computer-Based Medical Systems (CBMS) <26, 2013, Porto, Portugal>

Validation methods used in literature to evaluate vessel segmentation algorithms suffer to a great extent from objectiveness, reliability and reproducibility. This is because almost each group has its own way to evaluate an algorithms. In this paper, an extendable standardized evaluation framework for quantitative validation of vessel segmentation algorithms is presented. As ground-truth, it uses a physical vascular model to simulate the growth of vessels within organ masks extracted from clinical CT datasets. A set of image- and graph- based evaluation metrics are calculated to analyze various aspects of the algorithms under study. Using the proposed framework helps to meet the aforementioned quality criteria.

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Drechsler, Klaus; Erdt, Marius; Linguraru, Marius George; Oyarzun Laura, Cristina; Sharma, Karun; Shekhar, Raj; Wesarg, Stefan

Clinical Image-Based Procedures. From Planning to Intervention: International Workshop, CLIP 2012. Held in Conjunction with MICCAI 2012

2013

Berlin, Heidelberg, New York : Springer, 2013

International Workshop on Clinical Image-based Procedures (CLIP) <1, 2012, Nice, France>

Lecture Notes in Computer Science (LNCS) 7761

CLIP 2012 provided a successful forum for the dissemination of emerging image-based clinical techniques. Specific topics included pre-interventional image segmentation and classification (to support diagnosis and clinical decision making), interventional and surgical planning and analysis of dynamic images, and evaluation, visualization and correction techniques for image-based procedures. Clinical applications covered the skull and the brain, cardiac defects, blood vessels, abdominal organs, and cancer in adults and children. The presentations and discussions around the meeting emphasized current challenges and emerging techniques in image-based procedures, strategies for clinical translation of image-based techniques, the role of computational anatomy and image analysis for surgical planning and interventions, and the contribution of medical image analysis to open and minimally invasive surgery.

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Oyarzun Laura, Cristina; Plaza, Pablo Bueno; Drechsler, Klaus

Comparison of Rigid Registration Methods in Four Clinical Scenarios

2013

Drechsler, Klaus (Ed.) et al.: Clinical Image-Based Procedures. From Planning to Intervention : International Workshop, CLIP 2012. Held in Conjunction with MICCAI 2012. Berlin, Heidelberg, New York: Springer, 2013. (Lecture Notes in Computer Science (LNCS) 7761), pp. 114-121

International Workshop on Clinical Image-based Procedures (CLIP) <1, 2012, Nice, France>

Deformable registration algorithms need in general an appropriate initialization of the volumes that is made by rigid registration algorithms. Very often intensity based rigid registration algorithms are used which provide a good initialization for certain deformable algorithms. However when the algorithm to be used for the deformation is based on a physical approach in which forces are applied to different points of the volume those rigid registration algorithms are not the most appropriate. In this paper we present a comparison between three rigid registration approaches (distance based, curvature based and combination) which detect the areas that are highly deformed and remove them from the calculation of the initial transformation. Its usability is analyzed in four clinical scenarios, namely: livers with large deformations due to breathing, livers before and after tumor ablation, resections and open liver surgery. The results show that the combination approach performs better than the other two in cases when a tumor has been resected.

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Drechsler, Klaus; Oyarzun Laura, Cristina; Wesarg, Stefan

Hepatic Vein Segmentation Using Wavefront Propagation and Multiscale Vessel Enhancement

2013

Ourselin, Sebastien (Ed.) et al.: Medical Imaging 2013: Image Processing. Part One : Progress in Biomedical Optics and Imaging. Proceedings Issue. Vol. 14, No. 36. Bellingham: SPIE Press, 2013. (Proceedings of SPIE 8669), pp. 86691A-1 - 86691A-7

SPIE Medical Imaging Symposium <2013, Lake Buena Vista, FL, USA>

Modern volumetric imaging techniques such as CT or MRI, aid in the understanding of a patient's anatomy and pathologies. Depending on the medical use case, various anatomical structures are of interest. Blood vessels play an important role in several applications, e.g. surgical planning. Manual delineation of blood vessels in volumetric images is error prone and time consuming. Automated vessel segmentation is a challenging problem due to acquisition-dependent problems such as noise, contrast, spatial resolution, and artifacts. In this paper, a vessel segmentation method is presented that combines a wavefront propagation technique with Hessian-based vessel enhancement. The latter has proven its usefulness as a preprocessing step to detect tubular structures before the actual segmentation is carried out. The former allows for an ordered growing process, which enables topological analysis. The contribution of this work is as follows. 1. A new vessel enhancement filter for tubular structures based on the Laplacian is proposed, 2. a wavefront propagation technique is proposed that prevents leaks by imposing a threshold on the maximum number of voxels that the propagating front must contain, and 3. a volumetric hole filling method is proposed to fill holes, bays, and tunnels which are caused at locations where the tubular structure assumption is violated. The proposed method reduces approximately 50% of the necessary eigenvalue calculations for vessel enhancement and prevents leaks starting at small spots, which usually occur using standard region growing. Qualitative and quantitative evaluation based on several metrics (statistical measures, dice and symmetric average surface distance) is presented.

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Erdt, Marius; Knapp, Oliver; Drechsler, Klaus; Wesarg, Stefan

Region Detection in Medical Images Using HOG Classifiers and a Body Landmark Network

2013

Novak, Carol L. (Ed.) et al.: Medical Imaging 2013: Computer-Aided Diagnosis. Part One. Bellingham: SPIE Press, 2013. (Proceedings of SPIE 8670), pp. 867004-1 - 867004-7

SPIE Medical Imaging Symposium <2013, Lake Buena Vista, FL, USA>

Automatic detection of anatomical structures and regions in 3D medical images is important for several computer aided diagnosis tasks. In this work, a new method for simultaneous detection of multiple anatomical areas is proposed. The method consists of two steps: first, single rectangular region candidates are detected independently using 3D variants of Histograms of Oriented Gradients (HOG) features. These features are robust against small changes between regions in rotation and scale which typically occur between different individuals. In a second step, the positions of the detected candidates are refined by incorporating a body landmark network that exploits anatomical relations between different structures. The landmark network consists of a principle component based statistical modeling of the relative positions between the detected regions in training images. The method has been evaluated on thoracic/abdominal CT images of the portal venous phase. In 216 CT images, eight different structures have been trained. Results show an increase in performance using the combination of HOGs and the landmark network in comparison to using independent classifiers without anatomical relations.

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Oyarzun Laura, Cristina; Plaza, Pablo Bueno; Drechsler, Klaus; Wesarg, Stefan

Skeleton Based Refinement of Multi-Material Volumetric Meshes

2013

Ourselin, Sebastien (Ed.) et al.: Medical Imaging 2013: Image Processing. Part Two : Progress in Biomedical Optics and Imaging. Proceedings Issue. Vol. 14, No. 36. Bellingham: SPIE Press, 2013. (Proceedings of SPIE 8669), pp. 866936-1 - 866936-6

SPIE Medical Imaging Symposium <2013, Lake Buena Vista, FL, USA>

Accurate multi-material mesh generation is necessary for many applications, e.g. image-guided surgery, in which precision is important. For this application, it is necessary to enhance conventional algorithms with physiological information that adds accuracy to the results. There are several approaches working on the generation of such meshes. However, state of the art approaches show inaccuracies in the areas in which thin structures are, e.g. liver vasculature. These algorithms are not able to detect the vessels in areas in which they are narrow and they assign their elements to wrong materials, e.g., parenchyma. We propose to extend two state of the art algorithms, namely that by Boltcheva et al. and that by Pons et al. and enhance them making use of the skeleton of these structures to solve this problem. By analyzing the mesh generated by the aforementioned algorithms one can find several intersections between the mesh belonging to the vessels and the skeleton, showing that some elements must be mismatched. We evaluate the proposed algorithm in 23 clinical datasets of the liver, in which we previously segmented parenchyma and vessels. For quantitative evaluation, the meshes generated with and without skeleton information are compared. The improvements are shown by means of intersection number, volume and length differences of the vasculature mesh using the different methods. The results show an improvement of 65% for the number of intersections, 4% for the volume and 22% for the length.

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Keil, Matthias; Oyarzun Laura, Cristina; Drechsler, Klaus; Wesarg, Stefan

Combining B-Mode and Color Flow Vessel Segmentation for Registration of Hepatic CT and Ultrasound Volumes

2012

Ropinski, Timo (Ed.) et al.: Eurographics Workshop on Visual Computing for Biology and Medicine : EG VCBM 2012. Goslar: Eurographics Association, 2012, pp. 57-64

Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) <3, 2012, Norrköping, Sweden>

Multimodal registration of intraoperative ultrasound and preoperative computed tomography imaging is the basis for percutaneous hepatic interventions. Currently, a rigid registration is performed manually by the surgeon using vessel structures and other anatomical landmarks for visual guidance. In this work our approach for intraoperative vessel segmentation from two ultrasound imaging modes, namely B-Mode and color flow mode, is presented. This segmentation is an important step for automation of the intraoperative registration which relies on vessel structures visible in contrast enhanced CT and ultrasound volumes. This paper describes the problems that arise when using B-mode ultrasound for segmentation of vessels and how they can be solved by introducing additional vessel information from color flow imaging. On a total number of 21 patients, our system was applied successfully in 15 cases. For nine randomly chosen patients studied in this paper, our system achieves a 3.45 mm accuracy at points used for registration and 5.01 mm for other landmarks which were not used for the registration process.

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Drechsler, Klaus; Sakas, Georgios (Betreuer); Fellner, Dieter W. (Betreuer); Mönch, Christian (Betreuer)

Extraction of Hepatic Veins in Contrast Enhanced CT with Application to Interventional Planning

2012

Darmstadt, TU, Diss., 2012

The Liver performs several important tasks that are essential for survival. However, liver cancer, the third most common type of cancer, affects these functions significantly. Different treatment options are available, but a surgical resection, if possible, offers the best prognosis for the patient. Thus, the decision, whether a surgical resection is feasible, is important and must be taken with care in a pre-interventional planning stage. Modern volumetric imaging techniques such as CT or magnetic resonance imaging (MRI) are utilized to decide which treatment is best for the patient and to plan the intervention. However, the amount of anatomical details visible in the acquired volumes is steadily increasing. This comes along with an increasing amount of data per patient. Manual examination is time consuming and prone to errors. As a matter of fact, several software systems were proposed to support the surgeon during the planning phase. The extraction of blood vessels plays an important role in these applications. The segmentation of vessels is a challenging problem that has to deal with acquisition-dependent problems such as noise, contrast, spatial resolution, and artifacts. Furthermore, blood vessel specific characteristics like high variability of size and curvature result in additional difficulties for segmentation algorithms. The liver, in particular, exhibits another challenge to vessel segmentation algorithms. Its supply and drain vessel systems are densely distributed within the liver, and because of partial volume effects and motion artifacts, they seem to be connected at some points. The focus of the present thesis is the robust extraction of hepatic veins in multiphase CT volumes. Therefore, an image processing pipeline is presented that covers vessel enhancement, vessel segmentation, graph creation and tree reconstruction. The pipeline was used to develop an application for interventional planning. It allows for the simulation of intraoperative hepatic vein clamping for (sub-)segment oriented liver resections and the execution of risk analysis to judge surgical risk during an atypical resection. Furthermore, results of the present thesis were also successfully used in an application for intraoperative navigation to extract liver vessels in 3D ultrasound data and matching of anatomical vessel trees and graphs of the liver for registration of 3D volumes.

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Erdt, Marius; Oyarzun Laura, Cristina; Drechsler, Klaus; De Beni, Stefano; Solbiati, Luigi

Improving Diagnosis and Intervention: A Complete Approach for Registration of Liver CT Data

2012

Yoshida, Hiroyuki (Ed.) et al.: Abdominal Imaging: Computational and Clinical Applications : Third International Workshop Held in Conjunction with MICCAI 2011. Berlin, Heidelberg, New York: Springer, 2012. (Lecture Notes in Computer Science (LNCS) 7029), pp. 108-115

International Workshop on Computational and Clinical Applications in Abdominal Imaging <3, 2011, Toronto, Canada>

Registration of liver CT scans from different points in time or different phases of contrast agent saturation is a highly demanded tool for computer aided diagnosis, operation planning and intervention. This work presents a complete registration workflow to precisely overlap scans from 4 different application scenarios including registration of pretreatment and post-treatment data as well as registration of multi-phase CT. Various state of the art techniques in shape modeling and matching, visualization as well as augmented interaction are applied to cover all of the described scenarios in a clinically usable system. Our system has been in use for clinical evaluation under real life conditions and has been tested on more than 30 patients.

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Drechsler, Klaus; Oyarzun Laura, Cristina; Wesarg, Stefan

Interventional Planning of Liver Resections: An Overview

2012

IEEE Engineering in Medicine and Biology Society (EMBS): 34th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. Proceedings : EMBC 2012. Stoughton: Printing House, 2012, pp. 3744-3747

Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) <34, 2012, San Diego, CA, USA>

Liver cancer is the third most common type of cancer. Among available treatment options, a surgical resection offers the best prognosis for long-term survival. It is important that such a surgical procedure is carefully prepared. Modern computer technology offers convenient ways to simulate different resection scenarios and help to determine the best treatment for a given case. This paper provides a non-exhaustive overview of existing computer-based systems for interventional planning of liver resections. They are reviewed according to their medical use case, e.g. if they support typical or atypical resections.

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Oyarzun Laura, Cristina; Drechsler, Klaus; Erdt, Marius; Keil, Matthias; Noll, Matthias; De Beni, Stefano; Sakas, Georgios; Solbiati, Luigi

Intraoperative Registration for Liver Tumor Ablation

2012

Yoshida, Hiroyuki (Ed.) et al.: Abdominal Imaging: Computational and Clinical Applications : Third International Workshop Held in Conjunction with MICCAI 2011. Berlin, Heidelberg, New York: Springer, 2012. (Lecture Notes in Computer Science (LNCS) 7029), pp. 133-140

International Workshop on Computational and Clinical Applications in Abdominal Imaging <3, 2011, Toronto, Canada>

Computer aided navigation augments intraoperatively gathered U/S with planning information that the doctor carries out before the intervention on a CT volume. A crucial step for the navigation is the registration between CT and U/S. Our approach consists on a landmark based registration. The correspondences between both modalities are found automatically using a graph to graph matching algorithm. Therefore, liver and vessels are previously segmented. The whole process has being tested on 15 pairs of real clinical data. The results are promising.

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Meixner, Steven; Drechsler, Klaus (Betreuer)

Konzeption und Realisierung einer Testumgebung zum standardisierten Evaluieren von Gefäßsegmentierungs-Algorithmen

2012

Darmstadt, Hochschule, Bachelor Thesis, 2012

Computersimulationen zur Unterstützung von Ärzten bei der Diagnose und Therapie (z.B. zur Navigation bei chirurgischen Eingriffen) sind im Vormarsch. Solche medizinischen Softwareapplikationen bieten ein hohes Maß an Präzision und unterstützen den Chirurgen bei der Operation. Bei der operativen Entfernung eines Tumors aus der Leber beispielsweise werden auch Teile der Leber mit entfernt. Diese operative Entfernung von Gewebe aus einem Organ wird auch als Resektion bezeichnet. Eine computergestützte Planung von Resektionsstellen in der präoperativen Phase ermöglicht eine exakte Bestimmung der Gefäße, welche den Tumor versorgen und welche Gefäße zur weiteren Durchblutung anderer Segmente der Leber benötigt werden. Diese Möglichkeit der Operationsplanung führt zu einer Minimierung von Komplikationen während der Operation und somit nicht zuletzt zu einer höheren Heilungsquote und schnelleren Genesung des Patienten. Hierzu werden in der präoperativen Phase die Gefäße aus einem durch Computertomographie (CT) gewonnenen Volumenbild der Leber segmentiert. Der verwendete Segmentierungsalgorithmus muss dabei trotz unterschiedlich starkem Kontrast und Rauschen der CT-Bilddaten möglichst präzise Ergebnisse erzielen. Es ist daher immens wichtig, bei der Erstellung einer solchen medizinischen Applikation ein geeignetes Segmentierungsverfahren zu wählen oder aber auch selbst zu entwickeln. Die Ergebnisse, die dieser Segmentierungsalgorithmus liefert, sollten frühzeitig evaluiert werden. Zwar wird in zahlreichen Publikationen für neu entwickelte Segmentierungsalgorithmen mit guten Evaluationsergebnissen geworben, jedoch wurden diese getrennt voneinander und mit unterschiedlicher Herangehensweise in der Implementierung und Wahl der Metriken evaluiert. Ein quantitativer Vergleich zwischen diesen Segmentierungsalgorithmen ist deshalb nicht möglich. Diese Arbeit zeigt nun den Weg von der Konzipierung bis hin zur Umsetzung einer Testumgebung, die eine standardisierte und somit objektive und zuverlässige Evaluierung von Segmentierungsalgorithmen ermöglicht. Diese Algorithmen werden dabei mit Hilfe derselben Evaluationsmetriken untersucht und die Ergebnisse in einen quantitativen Vergleich gesetzt. Als "Ground-Truth-Segmentierung" dienen Gefäßbäume, die auf Basis biologischer Wachstumsprozesse simuliert werden. Demonstriert wird die Funktionalität der Testumgebung in Form einer beispielhaften Evaluierung von zwei Segmentierungsalgorithmen.

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Drechsler, Klaus; Erdt, Marius; Oyarzun Laura, Cristina; Wesarg, Stefan

Multiphase Risk Assessment of Atypical Liver Resections

2012

Soda, Paolo (Ed.) et al.: 25th IEEE Symposium on Computer-Based Medical Systems and HealthGrid Conference : The 25th IEEE International Symposium on Computer-Based Medical Systems. New York: IEEE, Inc., 2012, 4 p.

IEEE Symposium on Computer-Based Medical Systems (CBMS) <25, 2012, Rome, Italy>

In this work, we present a system based on open-source toolkits that can utilize multiple phases of a liver CT dataset to plan a surgery before the patient enters the operation room. The contributions are an optimized deformable registration of arterial and venous phases of the liver and a methodology to assess surgical risk utilizing both phases. It is shown by the example of two clinical cases, how our system enables the fusion of complementary information into a 3D representation of the patient anatomy. Processing times of single processing steps on a modern machine are quite low, which allows for an integration into clinical routine.

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Drechsler, Klaus; Oyarzun Laura, Cristina

Simulation of Portal Vein Clamping and the Impact of Safety Margins for Liver Resection Planning

2012

Yoshida, Hiroyuki (Ed.) et al.: Abdominal Imaging: Computational and Clinical Applications : Third International Workshop Held in Conjunction with MICCAI 2011. Berlin, Heidelberg, New York: Springer, 2012. (Lecture Notes in Computer Science (LNCS) 7029), pp. 149-156

International Workshop on Computational and Clinical Applications in Abdominal Imaging <3, 2011, Toronto, Canada>

In this work, we present a planning tool for liver interventions. It allows for a simulation of the color change on the liver surface after clamping the portal vein at a user defined position. The result is a patient-specific approximation of the (sub-) segmental borders on the liver surface. Furthermore, the impact of different safety margins around a tumor can be simulated to assess the risk of a resection. In addition, it provides delinated portal- and hepatic vein, which can be overlapped to the 2D CT slices, and 3D visualization of the results.

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Chen, Yufei; Drechsler, Klaus; Oyarzun Laura, Cristina; Zhao, Weidong; Liu, Yanli

A Graph Description and Analysis Framework of Liver Vascular System

2011

Journal of Computational Information Systems, Vol.7 (2011), 6, pp. 1998-2005

Accurate description and analysis of liver vascular system is critical in diagnosis and treatment of liver diseases. Even though there are plenty of researches put their efforts on the acquisition of optimal visual information in liver vascular system, quite a few studies focus on the quantitatively geometrical and structural analysis on them. In this paper, we proposed a graph description and analysis framework for liver vascular structure representation. First of all, the vessels were enhanced through Hessian eigenvalue calculation in order to be conveniently segmented from the liver image. Secondly, a three dimensional thinning based skeletonization method was applied on the vessel image to obtain the topological structure of the liver vessels. The skeleton result was then represented as a graph, followed by the geometrical attributes computation. Finally, the graph was efficiently pruned to form a directed acyclic vascular tree without redundant and irrelevant branches based on a flow conservation approach. The experiments on liver CT datasets show that the proposed framework can effectively obtain the liver vascular structure and its quantitative description.

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Friedl, Sven; Drechsler, Klaus; Oyarzun Laura, Cristina; Kuleschow, Andreas; Kondruweit, Markus; Wittenberg, Thomas

A Holistic Approach Using Multimodal Image-Data for the Support of Cardiac Surgery Interventions

2011

Lemke, Heinz U. (Ed.) et al.: CARS 2011. Computer Assisted Radiology and Surgery : Proceedings of the 25st International Congress and Exhibition : International Journal of Computer Assisted Radiology and Surgery, Vol. 6 (2011), Supplement 1. Berlin, Heidelberg, New York: Springer, 2011, pp. S235-S238

Computer Assisted Radiology and Surgery (CARS) <25, 2011, Berlin, Germany>

This work addresses the exploitation of multi-modal images in the planning phase and transfer of the acquired planning data to intra-operative procedures in cardiac surgery interventions. Specifically, within this work, for intervention planning the registration of coronary angiography images with CCT data (3D/2D registration), and the transfer from the acquired images and planning data to the intra-operative use and availability during the intervention by the registration of angiography data with live optical video (or endoscopy) at the operation site (2D/2D+T registration is) are focused on.

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Chen, Yufei; Drechsler, Klaus; Zhao, Weidong; Oyarzun Laura, Cristina

A Thinning-based Liver Vessel Skeletonization Method

2011

IEEE Communications Society: 2011 International Conference on Internet Computing and Information Services : ICICIS 2011. Los Alamitos, Calif.: IEEE Computer Society Conference Publishing Services (CPS), 2011, pp. 152-155

International Conference on Internet Computing and Information Services (ICICIS) <2011, Hong Kong, China)

In the clinical practice of diagnosis and treatment of liver disease, how to effectively represent and analyze the vascular structure has been a widely studied topic for a long time. In this paper, we propose a method for the three-dimensional skeletal graph generation of liver vessels using 3D thinning algorithm and graph theory. First of all, the principal methods for skeletonization are introduced, followed by their comparative analysis. Secondly, the 3D thinning-based skeletonization method together with a filling hole pre-processing on liver vessel image is employed to form the liver skeleton. A graph-based technique is then employed on the skeleton image to efficiently form the liver vascular graph. The thinning-based liver vessel skeletonization method was evaluated on liver vessel images with other two kinds of skeletonization approaches to show its effectiveness and efficiency.

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Erdt, Marius; Kirschner, Matthias; Drechsler, Klaus; Wesarg, Stefan; Hammon, Matthias; Cavallaro, Alexander

Automatic Pancreas Segmentation in Contrast Enhanced CT Data Using Learned Spatial Anatomy and Texture Descriptors

2011

IEEE Engineering in Medicine and Biology Society (EMBS): 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro : ISBI 2011. New York: IEEE Press, 2011, pp. 2076-2082

IEEE International Symposium on Biomedical Imaging (ISBI) <8, 2011, Chicago, IL, USA>

Pancreas segmentation in 3-D computed tomography (CT) data is of high clinical relevance, but extremely difficult since the pancreas is often not visibly distinguishable from the small bowel. So far no automated approach using only single phase contrast enhancement exist. In this work, a novel fully automated algorithm to extract the pancreas from such CT images is proposed. Discriminative learning is used to build a pancreas tissue classifier that incorporates spatial relationships between the pancreas and surrounding organs and vessels. Furthermore, discrete cosine and wavelet transforms are used to build computationally inexpensive but meaningful texture features in order to describe local tissue appearance. Classification is then used to guide a constrained statistical shape model to fit the data. Cross-validation on 40 CT datasets yielded an average surface distance of 1.7 mm compared to ground truth which shows that automatic pancreas segmentation from single phase contrast enhanced CT is feasible. The method even outperforms automatic solutions using multiple-phase CT both in accuracy and computation time.

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Drechsler, Klaus; Strosche, Michael; Oyarzun Laura, Cristina

Automatic ROI Identification for Fast Liver Tumor Segmentation Using Graph-Cuts

2011

Dawant, Benoit M. (Ed.) et al.: Medical Imaging 2011: Image Processing. Part Two : Progress in Biomedical Optics and Imaging. Proceedings Issue. Vol. 12, No. 31. Bellingham: SPIE Press, 2011. (Proceedings of SPIE 7962), pp. 79622S-1 - 79622S-7

SPIE Medical Imaging Symposium <2011, Lake Buena Vista, FL, USA>

The key challenge in tumor segmentation is to determine their exact location and volume. Difficulties arise because of low intensity boundaries, varying shapes and sizes. Furthermore, tumors can be located everywhere in the liver. Interactive segmentation methods seem to be the most appropriate in terms of reliability and robustness. In this work, we use a graph-cut based method to interactively segment tumors. However, complexity of the underlying graphs is enormous for clinical 3D datasets. We propose a method to identify automatically a region of interest using a coarse resolution image, which is then used to construct a reduced graph for final segmentation in the original image in full resolution. We compared our results to ground truth segmentations done by experts. Our results suggest that accuracy is comparable to other approaches. The average overlap was 80%, the average surface distance 0.73 mm and the average maximum surface distance 5.31 mm.

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Drechsler, Klaus; Oyarzun Laura, Cristina

Closing the Gap: From Planning to Intervention in Cardiology

2011

Richard, Paul (Ed.) et al.: Computer Vision, Imaging and Computer Graphics : Theory and Applications. Berlin, Heidelberg, New York: Springer, 2011. (Communications in Computer and Information Science 229), pp. 187-200

International Joint Conference on Computer Vision and Computer Graphics Theory and Applications (VISIGRAPP) <5, 2010, Angers, France>

It is likely that in the near future the diagnostic of coronary arteries will be done using non-invasive computed tomography angiography and that only the intervention, if necessary, will be carried out using invasive techniques. Preinterventional gathered CTA data can be used to carry out an automated quantitative analysis of the arteries, which can provide complementary information during a cardiac catheterization when only coronary angiograms are available. We propose an anatomical landmark-based rigid 3D/2D registration algorithm which enables the fusion of both modalities. It has to solve for six transformation parameters (three rotation and three translation parameters). An exhaustive search in a six dimensional search space is usually computationally very expensive and algorithms using optimization strategies can get lost in local minima. We propose a method based on centroids to reduce search space from six to four dimensions and use information stored in modern C-Arm devices to further reduce the search space. With our method registration errors of < 2 mm are feasible. Execution times of < 1 sec. can be reached on a QuadCore CPU.

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Oyarzun Laura, Cristina; Drechsler, Klaus

Computer Assisted Matching of Anatomical Vessel Trees

2011

Computers & Graphics, Vol.35 (2011), 2, pp. 299-311

Many inexact automatic tree matching algorithms are available. However, they provide matches that are not completely error free. Another option is to use manually matched node-pairs, but this enormously slows down the process. Our contribution to the state of the art is to combine the advantages of both solutions. We enhance the automatic tree matching algorithm designed by Graham et al., so that it is possible to interact with it by previously selecting important matches or by subsequently fixing the provided wrong matches. We apply the tree matching algorithm to the anatomical vasculature of the liver. Furthermore, we developed several visualization features to make manual tree interaction as easy as possible. Both, the interactive and automatic part of the implemented component were evaluated. As a result, the speed of the automatic tree matching algorithm is increased. It takes 7.45 s for trees up to 192 nodes and less than 1 s if three input matches are provided. In addition to this, an in-depth evaluation of the robustness of the algorithm is presented. The results are remarkable. The average of wrong matches varies between 1.17 and 1.4 node-pairs in the worst cases. The rate of correct matches is high. The evaluation of the visualization features for interactive refinement of matches showed that the percentage of wrong matches found is increased from 56.25% to 78.43%. The mean time to find them is decreased from 227 to 122 s.

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Oyarzun Laura, Cristina; Drechsler, Klaus

Graph to Graph Matching: Facing Clinical Challenges

2011

Olive, Mark (Ed.) et al.: Twenty-Fourth IEEE Symposium on Computer-Based Medical Systems and HealthGrid Conference : CBMS 2011 + HG 2011. Los Alamitos, Calif.: IEEE Computer Society, 2011, 6 p.

IEEE Symposium on Computer-Based Medical Systems (CBMS) <24, 2011, Bristol, UK>

State of the art anatomical tree matching algorithms find correspondences between trees that contain topological differences. However there are still open problems that were not considered until now. For example, when the liver vasculature is segmented, portal and hepatic vein are not separated due to segmentation errors. Because of this reason the resulting structure is not a tree but a graph. On the other hand, inaccuracies in the generation of the graph, as well as artifacts or inhomogeneities in the contrast medium result in graphs containing gaps. In this work, we present a novel graph to graph matching algorithm. It solves the aforementioned problems by taking the whole graph structure into account and does not depend on separated trees. In addition to this it is robust against gaps in the graph. We developed our algorithm so that it does not depend on the root of the graph which is often assumed to be known. The algorithm was evaluated on real clinical data of the liver.

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Oelmann, Simon; Drechsler, Klaus (Betreuer)

Konzeption und Realisierung eines Verfahrens zur automatischen Erkennung von fehlerhaften Verbindungsstellen in einer Graphenrepräsentation des Gefäßsystems der Leber

2011

Darmstadt, TU, Bachelor Thesis, 2011

Bei der Planung von Leberoperationen ist es hilfreich, den Verlauf der Portal- sowie der Lebervene zu kennen, um bestimmte Lebersegmente sowie verschiedene Typen von Tumoren identifizieren zu können. Auch wenn die beiden Venen in der Realität vollständig voneinander getrennt sind, kommt es aufgrund der niedrigen optischen Auflösung, mit der CT-Daten gewonnen werden, in den segmentierten Volumendaten der beiden Venen zu Verschmelzungen. Diese Bachelorarbeit beschreibt ein eigenes, neues Verfahren zur Identifizierung dieser Verbindungsstellen innerhalb einer Graphenrepräsention der Portal- und der Lebervene. Nach einer Erläuterung benötigter Grundlagen folgt eine zusammenfassende Beschreibung bereits existierender Trennungsalgorithmen. Auf diesen aufbauend wird die Idee des neuen Verfahrens formuliert, das die Festlegung auf eine Trennungsstelle von dem häufigsten Zusammentreffen derjenigen Kriterien abhängig macht, die für die Trennung an dieser Stelle sprechen. Anschließend wird der neue Trennungsalgorithmus ausführlich beschrieben. Da der Algorithmus die als Wurzeln bezeichneten Eingänge in das Gefäßsystem kennen muss, wird für die Detektion der Wurzeln die Modifizierung eines bestehenden Verfahrens sowie ein weiteres, eigenes Verfahren vorgestellt. Auf Möglichkeiten zur Identifizierung von Zyklen in Graphen sowie zur Suche von wurzelverbindenden Kantenpfaden wird ebenfalls eingegangen, da diese zur Implementierung des Trennungsalgorithmus bekannt sein müssen. Abschließend werden die Ergebnisse vorgestellt, die das Trennungsverfahren bei Testdatensätzen lieferte. Hierbei wurden für 21 Verbindungsstellen 17 Trennungsvorschläge korrekt generiert.

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Chen, Yufei; Drechsler, Klaus; Zhao, Weidong; Oyarzun Laura, Cristina

Liver Vessel Tree Generation Based on Skeletonization and Graph Representation

2011

The 5th International Conference on Bioinformatics and Biomedical Engineering : iCBBE 2011. New York: The Institute of Electrical and Electronics Engineers (IEEE), 2011, 4 p.

International Conference on Bioinformatics and Biomedical Engineering (iCBBE) <5, 2011, Wuhan, China>

Liver vessel tree generation is of importance for liver disease diagnosis and surgery plan. In this paper, we propose a method for generation of the liver vessel tree based on skeletonization and graph representation. First of all, basic methodology in the proposed method is introduced. Secondly, the 3D-thinning skeletonization algorithm together with the graph-based technique are employed on the liver vasculature to form an undirected cyclic graph. Thirdly, a new flow conservation based approach is applied to efficiently prune the graph into a directed acyclic tree. Experiments on a variety of liver CT datasets show the effectiveness and efficiency of the proposed method.

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Drechsler, Klaus; Oelmann, Simon; Oyarzun Laura, Cristina

Separation of Interconnected Hepatic Veins

2011

Olive, Mark (Ed.) et al.: Twenty-Fourth IEEE Symposium on Computer-Based Medical Systems and HealthGrid Conference : CBMS 2011 + HG 2011. Los Alamitos, Calif.: IEEE Computer Society, 2011, 6 p.

IEEE Symposium on Computer-Based Medical Systems (CBMS) <24, 2011, Bristol, UK>

The proper separation of hepatic veins is crucial for discriminative visualization during surgical planning and intraoperative navigation, automated analysis and liver segment approximation. However, due to several reasons liver and portal vein may be connected at some points and may contain loops. In this work, we propose a novel graphbased method to separate interconnected hepatic veins. Furthermore, we show how to transfer the graph-based separation results back to the imaging data to improve the initial segmentation and discriminate portal and liver vein. In addition, we propose a majority voting operation to correct some segmentation imperfections. Promising qualitative and quantitative evaluation results are presented.

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Drechsler, Klaus; Oyarzun Laura, Cristina

A Novel Multiscale Integration Approach for Vessel Enhancement

2010

Dillon, Tharam et al.: Twenty-Third IEEE Symposium on Computer-Based Medical Systems : CBMS 2010. Los Alamitos, Calif.: IEEE Computer Society, 2010, pp. 92-97

IEEE Symposium on Computer-Based Medical Systems (CBMS) <23, 2010, Perth, Australia >

A novel multiscale integration method to be used for vessel enhancement, called Weighted Additive Response, is presented. It overcomes limitations of the widely used maximum response approach in terms of separation of nearby vessels and robustness to noise. Furthermore, its usefulness as a preprocessing step for a subsequent segmentation is shown. The practicability of the proposed method is quantitatively and qualitatively evaluated with public available artificial and clinical datasets.

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Drechsler, Klaus; Oyarzun Laura, Cristina

Comparison of Vesselness Functions for Multiscale Analysis of the Liver Vasculature

2010

University of Ioannina: ITAB 2010 : 10th International Conference on Information Technology and Applications in Biomedicine. New York: IEEE, Inc., 2010, 5 p.

International Conference on Information Technology and Applications in Biomedicine (ITAB) <10, 2010, Corfu, Greece>

The accurate segmentation of liver vessels is an important step for further computer assisted analysis in oncologic planning tools. Multiscale based vessel enhancement methods are very famous and many papers about this topic were published. Vesselness filters proposed by Sato et al., Frangi et al. and Erdt et al. are based on eigenvalue analysis of the Hessian matrix. They were developed using completely different approaches, namely experimental, geometrical and analytical. In this paper, their behavior at junctions and nearby vessels is systematically compared and evaluated for the enhancement of the liver vasculature. We found that the filter function proposed by Frangi et al. has problems at junctions, while the ones developed by Sato et al and Erdt et al. have problems with nearby vessels. The latter are preferred for the task of liver vessel enhancement.

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Drechsler, Klaus; Oyarzun Laura, Cristina

Dimension Reduction Based on Centroids for Multimodal Anatomical Landmark-Based 3d/2d Registration of Coronary Angiograms

2010

IMAGAPP 2010, IVAPP 2010. Proceedings. Portugal: INSTICC (Institute for Systems and Technologies of Information, Control and Communication), 2010, pp. 171-178

International Conference on Information Visualization Theory and Applications (IVAPP) <1, 2010, Angers, France>

We present an anatomical landmark-based rigid 3D/2D registration algorithm to register computed tomography angiography (CTA) datasets with coronary angiograms (CA) gathered during a cardiac catheterization. It has to solve for six transformation parameters (three rotation and three translation parameters). An exhaustive search in a six dimensional search space is usually computationally very expensive and algorithms using optimization strategies can get lost in local minima. We propose a method based on centroids to reduce search space from six to four dimensions. Modern C-Arm devices store a lot of information about the acquisition geometry that are used to further reduce the search space. We use this method to develop an efficient smart exhaustive search to solve for the six transformation parameters in a competitive time. With our method registration errors of < 2 mm are feasible. Execution times of < 1 sec. can be reached on a QuadCore CPU.

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Oyarzun Laura, Cristina; Drechsler, Klaus

Efficient Globally Optimal Matching of Anatomical Trees of the Liver

2010

Bartz, Dirk (Ed.) et al.: Eurographics Workshop on Visual Computing for Biology and Medicine : EG VCBM 2010. Goslar: Eurographics Association, 2010, pp. 75-82

Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) 2, 2010, Leipzig, Germany>

Many inexact automatic tree matching algorithms are nowadays available. However, they provide matches that are not completely error free. Another option is to use manually matched node-pairs, but this enormously slows down the process. Our contribution to the state of the art is to combine the advantages of both solutions. We enhance the automatic tree matching algorithm designed by Graham et al., so that it is possible to interact with it by previously selecting important matches or by subsequently fixing the provided wrong matches. Thanks to this enhancement the speed of the algorithm is greatly increased. It takes 7.45 seconds for trees up to 192 nodes and less than 1 second if three input matches are provided. In addition to this an in-depth evaluation of the robustness of the algorithm is presented. The results are remarkable. The average of wrong matches varies between 1.17 and 1.4 node-pairs in the worst cases. The rate of correct matches is high.

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Drechsler, Klaus; Oyarzun Laura, Cristina

Hierarchical Decomposition of Vessel Skeletons for Graph Creation and Feature Extraction

2010

Park, Taesung (Ed.) et al.: 2010 IEEE International Conference on Bioinformatics and Biomedicine. Proceedings. New York: The Institute of Electrical and Electronics Engineers (IEEE), 2010, pp. 456-461

IEEE International Conference on Bioinformatics and Biomedicine (BIBM) <4, 2010, Hong Kong, China>

Graphs are useful representations of the liver vasculature. They support tree matching algorithms in landmark based registration algorithms, they are useful to separate connected vessels from two different vessel systems and are the basis of vessel annotation tools. In this paper, we propose a hierarchical decomposition of vessel skeletons into subbranches. This simplifies the process of creating labeled graphs and extracting features. Furthermore, we propose a measure to classify voxels as branch voxels. We applied our method to several datasets with satisfying results and found that the number of sub-branches is normal distributed under rotation.

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Strosche, Michael; Drechsler, Klaus (Betreuer)

Interaktive Tumor-Segmentierung in medizinischen Volumendaten

2010

Darmstadt, TU, Bachelor Thesis, 2010

In der heutigen Medizin spielt die computergestützte Bildverarbeitung eine sehr große Rolle. Diese ist beispielsweise bei der Operationsplanung zur Resektion von Tumoren oder bei der computergestützten Diagnose sehr hilfreich. Hierbei ist, in Abhängigkeit der Fragestellung, oftmals eine Segmentierung der Bilddaten notwendig. Zur Segmentierung der Bilddaten steht eine Reihe verschiedener Pixel-, Kanten-, Regionen und modellbasierter Verfahren zur Verfügung, welche allerdings oftmals Schwächen in der Qualität des Segmentierungsergebnisses aufweisen, vor allem im Bezug auf Rauschen im Bild, und einen hohen Aufwand für die Vor- und Nachbearbeitung haben. Das Graph-Cut- Segmentierungsverfahren kann diesen Aufwand vermindern, da der Benutzer intuitiv Saatpunkte im Bilddatensatz setzen und das Ergebnis interaktiv beeinflussen kann. Des Weiteren kann es durch die Modifikation der Kostenfunktion auf individuelle Problemstellungen angepasst werden. Aufgrund des hohen Speicherbedarfs des Graph-Cut-Verfahrens wurde im Rahmen dieser Bachelorarbeit ein Verfahren zur Anwendung auf große Datensätze entwickelt, welches durch einen Multi-Resolution-Ansatz in mehreren Schritten die Segmentierung eines Bilddatensatzes zulässt. Für das Graph-Cut-Verfahren wurde des Weiteren eine auf Lebertumore optimierte Kostenfunktion entwickelt. Bei der Evaluation des implementierten Verfahrens hat sich gezeigt, dass der Speicherverbrauch durch die Anwendung eines Multi-Resolution-Ansatzes erheblich reduziert und auch die Laufzeit des Verfahrens hierdurch minimiert werden konnte.

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Drechsler, Klaus; Oyarzun Laura, Cristina; Chen, Yufei; Erdt, Marius

Semi-Automatic Anatomical Tree Matching for Landmark-Based Elastic Registration of Liver Volumes

2010

Journal of Healthcare Engineering, Vol.1 (2010), 1, pp. 101-123

One promising approach to register liver volume acquisitions is based on the branching points of the vessel trees as anatomical landmarks inherently available in the liver. Automated tree matching algorithms were proposed to automatically find pair-wise correspondences between two vessel trees. However, to the best of our knowledge, none of the existing automatic methods are completely error free. After a review of current literature and methodologies on the topic, we propose an efficient interaction method that can be employed to support tree matching algorithms with important pre-selected correspondences or after an automatic matching to manually correct wrongly matched nodes. We used this method in combination with a promising automatic tree matching algorithm also presented in this work. The proposed method was evaluated by 4 participants and a CT dataset that we used to derive multiple artificial datasets.

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Stallkamp, Jan; Drechsler, Klaus; Bergen, Tobias; Kaltenbacher, Dominik; Burisch, Michael; Kage, Andreas; Münzenmayer, Christian; Sakas, Georgios; Werner, Norman; Wechsler, Axel; Winter, Christian; Wittenberg, Thomas

Whole'O'Hand - A Holistic Intervention and Interaction System: A Novel Concept for Closed-Loop Liver Surgery

2010

Biomedizinische Technik, Vol.55 (2010), Supplement 1, pp. 27-31 in Section G Computergestützte Chirurgie

Jahrestagung der Deutschen Gesellschaft für Biomedizinische Technik im VDE (BMT) <44, 2010, Rostock, Germany>

Minimal-invasive surgery (MIS) and similar technologies are known to reduce the trauma for the patients. Nevertheless, the keyhole incisions also reduce vision, orientation and maneuverability of the surgeon. To compensate these losses, MIS interventions have always been dependent on technical equipment, as e.g. endoscopes. Within the generation of instruments currently available the increasing technological possibilities are barely used. To overcome the named disadvantages, the project Whole'O'Hand supports the surgeon's vision, orientation, and dexterity with a new concept for the integration and fusion of endoscopy, robotics, mechatronics, sensing and measuring devices, computer-assisted diagnosis, navigation, and visual computing.

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Wittenberg, Thomas; Drechsler, Klaus; Kaltenbacher, Dominik; Friedl, Sven; Rotinat-Libersa, Christine; Reis, C.; Di Betta, Marie; Sakas, Georgios; Perrot, Yann; Stallkamp, Jan; Kondruweit, Markus

'MISS Heart': Assisting Systems for Minimal Invasive Smart Suturing in Cardiac Surgery - A Conceptually Closed-Loop Approach

2009

Dössel, Olaf (Ed.) et al.: World Congress on Medical Physics and Biomedical Engineering 2009. Proceedings DVD-ROM. Berlin, Heidelberg, New York: Springer, 2009. (IFMBE Proceedings 25), IFMBE 25/IV; pp. 445-448

World Congress on Medical Physics and Biomedical Engineering (WC) <11, 2009, Munich, Germany>

The project MISS (Minimal invasive smart suture) provides solutions and concepts for several key issues within cardiac surgery. These issues include pre-operative imagebased stenosis detection and planning, intra-operative semiautomatic registration and dynamically adapting of video and angiography data, as well as the presentation of two novel concepts for bypass connection. The proposed solutions are conceptually parts of a closed-loop surgical interaction process and will in the mid-term be connected accordingly.

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Akram, Shahid; Drechsler, Klaus (Betreuer); Lacalli, Christina (Betreuer)

Coronary Tree Segmentation Using an Enhanced Corkscrew Algorithm

2009

Darmstadt, TU, Master Thesis, 2009

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Bobda, Christophe; Cheng, Kevin; Mühlbauer, Felix; Drechsler, Klaus; Schulte, Jan; Murr, Dominik; Tanougast, Camel

Enabling Self-Organization in Embedded Systems with Reconfigurable Hardware

2009

Cumplido, René (Ed.): International Journal of Reconfigurable Computing. New York, USA: Hindawi Publishing Corporation, 2009, 9 p.

We present a methodology based on self-organization to manage resources in networked embedded systems based on reconfigurable hardware. Two points are detailed in this paper, the monitoring system used to analyse the system and the Local Marketplaces Global Symbiosis (LMGS) concept defined for self-organization of dynamically reconfigurable nodes.

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Chen, Yufei; Oyarzun Laura, Cristina; Drechsler, Klaus

Generation of a Graph Representation from Three-Dimensional Skeletons of the Liver Vasculature

2009

Shi, Riyi (Ed.) et al.: Proceedings of the 2009 2nd International Conference on Biomedical Engineering and Informatics. New York: IEEE, Inc., 2009, 5 p.

International Conference on Biomedical Engineering and Informatics (BMEI) <2, 2009, Tianjin, China>

Extracting hepatic vasculature from three dimensional imagery is important for diagnosis of liver disease and planning of liver surgery. In this paper we propose a method for generation of 3D skeletal graph of liver vessels using thinning algorithm and graph theory. First of all, basic methodology in the proposed method is introduced. Secondly, the skeletonization method together with a pre-processing method on liver vessel images is employed to form liver skeleton image. Thirdly, a graphbased technique is then employed on the skeleton result to efficiently form the hepatic vessel system. The liver vessel tree generation method was evaluated on liver CT datasets to show its effectiveness and efficiency.

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Drechsler, Klaus; Oyarzun Laura, Cristina

Registration of Cardiac CT Data with Coronary Angiograms Using Digitally Reconstructed Radiographs

2009

Dössel, Olaf (Ed.) et al.: World Congress on Medical Physics and Biomedical Engineering 2009. Proceedings DVD-ROM. Berlin, Heidelberg, New York: Springer, 2009. (IFMBE Proceedings 25), IFMBE 25/IV, pp. 1431-1434

World Congress on Medical Physics and Biomedical Engineering (WC) <11, 2009, Munich, Germany>

A semi-automatic point-based 3D-2D registration approach to register computed tomography (CT) data with coronary angiograms using digitally reconstructed radiographs (DRR) is presented. It allows us to augment the coronary angiograms with pathologies (e.g. calcifications) found in CT data with an automated analysis tool that was previously developed in our department. We also present an efficient method to enable a backprojection from 2D into 3D space and to detect overlapping vessels. First qualitative results are presented.

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Kreitz, Christopher; Drechsler, Klaus (Betreuer)

Segmentvisualisierung der Leber für die intraoperative Navigation

2009

Darmstadt, TU, Diplomarbeit, 2009

Für einige Lebertumore ist die vollständige chirurgische Entfernung die derzeit einzige potentiell heilende Therapie. Die Operabilität ist von diversen Faktoren abhängig: 1. Der Tumor muß mit ausreichend Sicherheitsabstand zum gesunden Gewebe entfernt werden. 2. Das restliche Lebergewebe muß eine ausreichende Funktionsleistung erbringen, welche vom verbleibenden Lebervolumen abhängt. 3. Von der Durchblutung abgetrennte Bereiche müssen erkannt und ebenfalls entfernt werden. Drei Operationsstrategien berücksichtigen diese Faktoren: 1. Hemihepatektomie (komplette Entfernung einer Leberhälfte). 2. Tumororientierte Operation (Keilförmiges Stück der Leber wird entfernt). 3. Segmentorientierte Operation (Eins oder mehrere der Lebersegmente wird entfernt). Zur unterstützenden Operationsplanung und zur besseren Orientierung des Chirurgen während des Eingriffs wurde in dieser Arbeit ein Software-Tool entwickelt, welches patientenspezifische Leber(sub)segmente aus präoperativen CT Daten mit möglichst wenig User-Interaktion anhand von Abstraktionen der Lebergefäße berechnet und visualisiert.

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Drechsler, Klaus; Oyarzun Laura, Cristina; Sakas, Georgios

Towards Computer Assisted Cardiac Catheterization: How 3D Visualization Supports It

2009

Institute for Systems and Technologies of Information, Control and Communication (INSTICC): VISIGRAPP 2009. Proceedings : International Joint Conference on Computer Vision and Computer Graphics Theory and Applications [CD-ROM]. INSTICC Press, 2009, IMAGAPP; pp. 159-165

International Conference on Imaging Theory and Applications (IMAGAPP) <1, 2009, Lisboa, Portugal>

Although cardiac catheterization procedures take place under x-ray guidance, the doctor is almost blind. Vessels are almost invisible until he injects a contrast agent and looking only at 2D x-ray images and reconstructing a 3D image in his head makes it error prone and tedious. Only experienced doctors are able to accomplish this procedure with the expected results. This paper describes our preliminary work and work in progress to support doctors during cardiac catheterizations using 3D visualization.

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Drechsler, Klaus; Oyarzun Laura, Cristina; Sakas, Georgios

Towards Improving Cardiac Catheterizations through 3D Visualization Using CT Angiography

2009

European Heart Journal. Supplements, Vol.11 (2009), Supplement B, p. S59, Abstract 282

International Conference of Non-Invasive Cardiovascular Imaging <9, 2009, Barcelona, Spain>

Our purpose is to assist the catheterization using a preoperatively generated CT angiography to extract the heart, segment the vessels, analyse them and register it intraoperatively with the x-ray angiography to present the "scene" to the doctor in 3D and thus enabling catheterizations also for less experienced doctors.

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Drechsler, Klaus; Grimm, Matthias (Betreuer)

Realisierung einer Bluetooth-basierten Bake zur Ortserkennung mobiler Endgeräte

2003

Darmstadt, TU, Diplomarbeit, 2003

Eine der Hauptaufgaben des Mobile Computing besteht darin, den Kontext des Benutzers zu erkennen. Nur so lassen sich Context Aware Services verwirklichen, also Dienste, die dem Benutzer in Abhängigkeit seiner aktuellen Umgebung angeboten werden. Die Umgebung eines Benutzers wird durch viele Attribute beschrieben. Dazu gehört auch der aktuelle Aufenthaltsort. Zu den bedeutendsten Ansätzen der Ortserkennung im Innenbereich gehört die Verwendung von Infrarot-Baken. Diese senden ein meist statisches Signal, das vom Empfänger als Identifikation eines Ortes interpretiert werden kann. Ein wesentlicher Nachteil dieser Baken ist aber die Eigenschaft, daß die Erkennung des Signals Sichtkontakt zwischen Endgerät und Bake voraussetzt. In den letzten Jahren gewinnt die auf Funk basierende Bluetooth-Technologie immer mehr an Bedeutung und ist zunehmend in mobilen Endgeräten vorzufinden. Es liegt somit nahe diese Technologie zur Ortserkennung einzusetzen, um damit die Nachteile der Infrarot-Baken zu vermeiden. Das Ziel dieser Diplomarbeit war die Realisierung einer Bluetooth-basierten Bake als embedded system, welche zur Ortserkennung mobiler Endgeräte eingesetzt werden kann. Neben dem Hardwareentwurf bestand ein wichtiger Teil der Arbeit darin, einen minimalen Bluetooth-Protokollstack zu implementieren, welcher mit den knappen Ressourcen des Mikrocontrollers auskommt. Ausserdem musste ein Konzept für die Funktionsweise der Bake gefunden werden, da Bluetooth verbindungsorientiert arbeitet und ein Broadcast nicht möglich ist. Gelöst wurde dieses Problem durch Implementierung eines Pseudobroadcast, bei dem zu jedem gefundenen Endgerät nacheinander eine Verbindung aufgebaut wird, um Ortsinformationen zu übertragen. In Tests funktioniert diese Methode sehr zuverlässig. Ein weiterer Teil dieser Diplomarbeit galt der Konzeptionierung einer Distanz-Schätzung zwischen Sender und Empfänger auf Basis der Signalstärke. Es wird ein Modell vorgestellt, welches die Signalausbreitung mathematisch beschreibt und auf Probleme und deren mögliche Lösungen hingewiesen. Beispielsweise erreicht ein Funksignal aufgrund von Reflexionen den Empfänger üblicherweise über mehrere Wege. Wird nun die Stärke des Signals gemessen, dann ist das Ergebnis erheblich davon abhängig, welchen Weg das gemessene Signal zurückgelegt hat. Es läßt sich aber nicht feststellen, welches Signal man gemessen hat, weswegen man mit Ungenauigkeiten bei der Distanz-Berechnung rechnen muß, die sich höchstens algorithmisch verbessern lassen. Zusätzlich beschreibt diese Diplomarbeit Sicherheitsprobleme, die bei der Nutzung der Bluetooth-basierten Bake auftreten können. Dazu gehört der Täuschungsangriff, bei dem ein Angreifer Baken installiert, die einem Empfänger falsche Ortsinformationen senden, um diesen so durcheinander zu bringen. Um diesen Angriff abzuwenden wird eine Lösung beschrieben, bei der die Baken gegenüber einem Endgerät über einen sicheren Kanal "Vor-Authentifiziert" werden. Bei jedem Kontakt mit einer Bake wird dann ein Challenge-Response-Protokoll verwendet, um das Endgerät von der Echtheit der folgenden Ortsinformationen zu überzeugen.