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Noll, Matthias; Wesarg, Stefan

An Automatic Free Fluid Detection for Morrison´s-Pouch

2016

Shekhar, Raj (Ed.) et al.: Clinical Image-Based Procedures. Translational Research in Medical Imaging : 5th International Workshop, CLIP 2016. Held in Conjunction with MICCAI 2016. Berlin, Heidelberg, New York: Springer, 2016. (Lecture Notes in Computer Science (LNCS) 9958), pp. 77-84

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

Ultrasound provides a useful and readily available imaging tool to detect free fluids in blunt abdominal trauma patients. However, applying conventional 2D ultrasound to diagnose the patient requires a well trained physician. In this paper we describe a fully automatic free fluid detection pipeline for the hepathorenal recess or Morrison's pouch using 3D ultrasound acquisitions. The image data is collected using the standardized "Focused Assessment with Sonography for Trauma" (FAST) exam. Our method extracts key structures like the kidney and the liver from the image data and uses their relative positions to search and detect free fluids between the organ interfaces. To evaluate our method we have developed a free fluid simulation that allows us to generate free fluid images using acquisitions of healthy volunteers. Our intentions are to enable even untrained ultrasound operators to perform a free fluid diagnosis of an injured person. In order to do this, our method additionally provides basic image acquisition guidance information.

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Noll, Matthias; Nadolny, Anne; Wesarg, Stefan

Automated Kidney Detection for 3D Ultrasound Using Scan Line Searching

2016

The International Society for Optical Engineering (SPIE): Proceedings of SPIE, Article 9790-46, 6 p.

SPIE Medical Imaging Symposium <2016, San Diego, CA, USA>

Ultrasound (U/S) is a fast and non-expensive imaging modality that is used for the examination of various anatomical structures, e.g. the kidneys. One important task for automatic organ tracking or computer-aided diagnosis is the identification of the organ region. During this process the exact information about the transducer location and orientation is usually unavailable. This renders the implementation of such automatic methods exceedingly challenging. In this work we like to introduce a new automatic method for the detection of the kidney in 3D U/S images. This novel technique analyses the U/S image data along virtual scan lines. Here, characteristic texture changes when entering and leaving the symmetric tissue regions of the renal cortex are searched for. A subsequent feature accumulation along a second scan direction produces a 2D heat map of renal cortex candidates, from which the kidney location is extracted in two steps. First, the strongest candidate as well as its counterpart are extracted by heat map intensity ranking and renal cortex size analysis. This process exploits the heat map gap caused by the renal pelvis region. Substituting the renal pelvis detection with this combined cortex tissue feature increases the detection robustness. In contrast to model based methods that generate characteristic pattern matches, our method is simpler and therefore faster. An evaluation performed on 61 3D U/S data sets showed, that in 55 cases showing none or minor shadowing the kidney location could be correctly identified.

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Nadolny, Anne; Noll, Matthias (Advisor)

Strahlenbasierte Segmentierung der Niere in 3D Ultraschall Daten

2015

Brandenburg/Havel, FH, Master Thesis, 2015

Im Verlauf dieser Arbeit wird ein Verfahren zur vollautomatischen Segmentierung der Niere in 3D Ultraschalldaten entwickelt und die Ergebnisse präsentiert. Dafür wird zu Beginn Hintergrundwissen zusammengetragen und der Stand der Technik ermittelt. Anschließend erfolgt eine umfangreiche Vorverarbeitung der Daten, welche die Grundlage für die Detektion und Segmentierung der Niere bildet. Für diese wird auf strahlenbasierte Verfahren zurückgegriffen. Derartige Verfahren wurden bereits auf CT und MRT Daten erfolgreich für Segmentierungen verwendet und sollen nun auf ihre Übertragung auf Ultraschalldaten geprüft werden. Abschließend erfolgt eine Evaluation der Ergebnisse sowie eine Problemdefinition. Zudem werden mögliche Weiterentwicklungen vorgestellt.

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Wang, Anqi; Noll, Matthias; Wesarg, Stefan

Tumorsegmentierung in CD3/CD8-gefärbten Histopathologien

2015

Handels, H. (Ed.) et al.: Bildverarbeitung für die Medizin 2015 : Algorithmen - Systeme - Anwendungen. Proceedings des Workshops. Wiesbaden: Springer, Vieweg, 2015. (Informatik aktuell), pp. 347-352

Workshop Bildverarbeitung für die Medizin (BVM) <18, 2015, Lübeck, Germany>

Segmentierung von bestimmten Gewebetypen in Histopathologien ist eine oft untersuchte Fragestellung. Üblicherweise werden dafür Gewebeproben mit Hämatoxylin-Eosin(HE)-Färbung verwendet. CD3/CD8-F¨arbungen hingegen sind nötig zur Sichtbarmachung von Immunzellen, differenzieren aber nur wenig zwischen unterschiedlichen Gewebearten. Vorteilhaft wäre es, wenn aus nur einem Gewebeschnitt mit einer bestimmten Färbung beide Informationen extrahiert werden könnten. In dieser Arbeit stellen wir ein Segmentierungsverfahren auf CD3/CD8-gef¨arbten Gewebeproben vor, das effizient zu berechnende und gleichzeitig aussagekräftige Features als Eingabe für einen Clustering- Algorithmus verwendet. In der Evaluation wird ein durchschnittlicher Accuracy-Wert von 94,44% erzielt. Dieser Wert ist vergleichbar mit den Ergebnissen verwandter State of the Art Methoden, die HE-gefärbte Proben einsetzen.

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Noll, Matthias; Li, Xin; Wesarg, Stefan

Automated Kidney Detection and Segmentation in 3D Ultrasound

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. 83-90

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

Ultrasound provides the physical capabilities for a fast and save disease diagnosis in various medical scenarios including renal exams and patient trauma assessment. However, the experience of the ultrasound operator is the key element in performing ultrasound diagnosis. Thus, we like to introduce our automatic kidney detection and segmentation algorithm for 3D ultrasound. The approach utilizes basic kidney shape information to detect the kidney position. Following, the Level Set algorithm is applied to segment the detection result. In combination this method may help physicians and inexperienced trainees to achieve kidney detection and segmentation for diagnostic purposes.

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Jung, Florian; Steger, Sebastian; Knapp, Oliver; Noll, Matthias; Wesarg, Stefan

COSMO - Coupled Shape Model for Radiation Therapy Planning of Head and Neck Cancer

2014

Linguraru, Marius George (Ed.) et al.: Clinical Image-Based Procedures. Translational Research in Medical Imaging : Third International Workshop, CLIP 2014. Held in Conjunction with MICCAI 2014. Berlin, Heidelberg, New York: Springer, 2014. (Lecture Notes in Computer Science (LNCS) 8680), pp. 25-32

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

Radiation therapy plays a major role in head and neck cancer treatment. Segmentation of organs at risk prior to the radiation therapy helps to prevent the radiation beam from damaging healthy tissue, whereas a concentrated ray can target the cancerous regions. Unfortunately, the manual annotation of all relevant structures in the head and neck area is very time-consuming and existing atlas-based solutions don't provide sufficient segmentation accuracy. Therefore, we propose a coupled shape model (CoSMo) for the segmentation of key structures within the head and neck area. The model's adaptation to a test image is done with respect to the appearance of its items and the trained articulation space. 40 data sets labeled by clinicians containing 22 structures were used to build the CoSMo. Even on very challenging data sets with unnatural postures, which occur far more often than expected, the model adaptation algorithm succeeds. A first evaluation showed an average directed Hausdorff distance of 13.22mm and an average DICE overlap of 0.62. Furthermore, we review some of the challenges we encountered during the course of building our model from image data, taken from actual radiation therapy planing cases.

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Wang, Anqi; Sakas, Georgios (Advisor); Noll, Matthias (Advisor)

Detektion von Tumorgewebe und invasiver Tumorgrenze in CD3/CD8 gefärbten Gewebeschnitten (Histopathologien)

2014

Darmstadt, TU, Master Thesis, 2014

Konventionelle Krankheitsprognose bei Krebserkrankungen basiert auf Größe des Tumors, Auftrittsort von Krebszellen und Vorliegen von Metastasen. Diese Anzeichen lassen jedoch keine Aussage über den postoperativen Krankheitsverlauf zu. Erste Studien haben ergeben, dass in solchen Fällen die Betrachtung der Immunantwort des Körpers eine zuverlässigere Vorhersage treffen kann. Die Immunantwort drückt sich in Art und Auftrittshäufigkeit von Immunzellen (sogenannte T-Zellen) in und um den Tumor aus. Zur Validierung dieser These wird in der vorliegenden Arbeit ein Verfahren entwickelt, das automatisch auf CD3/CD8-gefärbten histopathologischen Aufnahmen den Tumor und die invasive Tumorgrenze segmentiert. In Kombination mit einer anderen Arbeit, die ein Verfahren zur Zellenzählung implementiert, sollen große Datenmengen von Patienten evaluiert werden, deren Krankheitsverlauf bekannt ist. Die größte Herausforderung dieser Arbeit besteht im verwendeten Material. Üblicherweise wird Gewebe auf HE-gefärbten Aufnahmen segmentiert. CD3/CD8 sind hingegen Färbungen, welche T-Zellen klar erkennbar darstellen, aber unterschiedliche Gewebearten nur wenig differenzieren. Eine zusätzliche Schwierigkeit ist die Entwicklung des Verfahrens bei einer kleinen Menge an verfügbaren Trainings- und Testdaten. Aus der Aufgabenstellung ergeben sich für das Verfahren die Anforderungen Geschwindigkeit (Evaluation großer Datenmengen) und Genauigkeit der Segmentierung. Die Geschwindigkeitsanforderung wird erfüllt, indem effizient zu berechnende und gleichzeitig aussagekräftige Features als Eingabe für ein Clustering-Algorithmus verwendet werden. Die Verarbeitung einer Aufnahme dauert durchschnittlich 5 Minuten. Gemessen an dem Zeitaufwand eines Pathologen für die gleiche Aufgabe ist dies eine große Zeitersparnis. Die Evaluation ergab einen durchschnittlichen Accuracy-Wert von 0,94. Dieser Wert ist vergleichbar mit den Ergebnissen verwandter State of the Art Methoden, welche auf HE-gefärbten Aufnahmen arbeiten.

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Noll, Matthias; Puhl, Julian; Wesarg, Stefan

Enhanced Shadow Detection for 3D Ultrasound

2014

Deserno, Thomas Martin (Ed.) et al.: Bildverarbeitung für die Medizin 2014 : Algorithmen, Systeme, Anwendungen. Proceedings des Workshops. Berlin, Heidelberg, New York: Springer, 2014. (Informatik aktuell), pp. 234-239

Workshop Bildverarbeitung für die Medizin (BVM) <2014, Aachen, Germany>

Ultrasound imaging offers a fast, convenient and save instrument to conduct patient examinations for various medical scenarios. However, depending on the target region, occluding bone segments and other materials cause large and undesirable shadowing artifacts. Thus, the experience of the ultrasound operator is crucial for obtaining an ultrasound without artifacts for patient diagnosis. Even more so, when applying automated image processing algorithms. We therefore like to introduce our automatic 3D ultrasound shadow detection method that employs scan line energy and local image entropy information. Applying the method can help to prevent low quality image acquisitions with large shadowing artifacts by indicating shadow occurrences.

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Hoßbach, Martin; Noll, Matthias; Wesarg, Stefan

Simplified Stereo-Optical Ultrasound Plane Calibration

2013

Bosch, Johan G. (Ed.) et al.: Medical Imaging 2013: Ultrasonic Imaging, Tomography, and Therapy : Progress in Biomedical Optics and Imaging. Proceedings Issue. Vol. 14, No. 42. Bellingham: SPIE Press, 2013. (Proceedings of SPIE 8675), pp. 86750X-1 - 86750X-7

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

Image guided therapy is a natural concept and commonly used in medicine. In anesthesia, a common task is the injection of an anesthetic close to a nerve under freehand ultrasound guidance. Several guidance systems exist using electromagnetic tracking of the ultrasound probe as well as the needle, providing the physician with a precise projection of the needle into the ultrasound image. This, however, requires additional expensive devices. We suggest using optical tracking with miniature cameras attached to a 2D ultrasound probe to achieve a higher acceptance among physicians. The purpose of this paper is to present an intuitive method to calibrate freehand ultrasound needle guidance systems employing a rigid stereo camera system. State of the art methods are based on a complex series of error prone coordinate system transformations which makes them susceptible to error accumulation. By reducing the amount of calibration steps to a single calibration procedure we provide a calibration method that is equivalent, yet not prone to error accumulation. It requires a linear calibration object and is validated on three datasets utilizing different calibration objects: a 6mm metal bar and a 1:25mm biopsy needle were used for experiments. Compared to existing calibration methods for freehand ultrasound needle guidance systems, we are able to achieve higher accuracy results while additionally reducing the overall calibration complexity.

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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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Keil, Matthias; Noll, Matthias

A Real-Time Online Video Overlay Navigation System for Minimally Invasive Laparoscopic Tumor Resection

2011

Wong, Kenneth H. (Ed.) et al.: Medical Imaging 2011: Visualization, Image-Guided Procedures, and Modeling. Part One : Progress in Biomedical Optics and Imaging. Proceedings Issue. Vol. 12, No. 33. Bellingham: SPIE Press, 2011. (Proceedings of SPIE 7964), pp. 796416-1 - 796416-8

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

The purpose of this paper is to present a detailed description of our real-time navigation system for computer assisted surgery. The system was developed with laparoscopic partial nephrectomies as a first application scenario. The main goal of the application is to enable tracking of the tumor position and orientation during a surgery. Our system is based on ultrasound to CT registration and electromagnetic tracking. The basic idea is to process tracking information to generate an augmented reality (AR) visualization of a tumor model in the camera image of a laparoscopic camera. Thereby it enhances the surgeon's view on the current scene and therefore facilitates higher safety during the surgery. So far we have applied our system in vitro during two phantom trials with a surgeon which yielded promising results.

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Keil, Matthias; Noll, Matthias

Extending MITK by a Real-Time Online Video Overlay Navigation System for Minimally Invasive Surgery: Release 2.00

2010

MIDAS Journal, (2010), 9 p.

International Workshop on Systems and Architectures for Computer Assisted Interventions (ICCAS) <3, 2010, Beijing, China>

The purpose of this paper is to present our extension of the MITK toolkit by a real-time navigation system for computer assisted surgery. The system was developed with laparoscopic partial nephrectomies as a first application scenario. The main goal of the application is to enable tracking of the tumor position and orientation during surgery. Our system is based on ultrasound to CT registration and electromagnetic tracking. The basic idea is to process tracking information to generate an augmented reality (AR) visualization of a tumor model in the camera image of a laparoscopic camera. Our system will enhance the surgeon's view on the current scene and therefore facilitates higher safety during the surgery. A key intention of the development was to use only open source toolkits such as VTK, MITK and OpenCV in order to implement the desired functionality. So far we have applied our system in vitro in two phantom trials with a surgeon which yielded promising results.

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Noll, Matthias; Keil, Matthias (Advisor)

Intraoperative Navigation für die minimalinvasive Resektion von Nierentumoren

2010

Darmstadt, TU, Diplomarbeit, 2010

The purpose of this diploma thesis is to present a detailed description of a real-time navigation system for computer assisted surgery. The system that is based on open source technology was developed with laparoscopic partial nephrectomies as a first application scenario. The main goal of the application is to enable tracking of the tumor position and orientation during a surgery. The system is based on ultrasound to CT registration and electromagnetic tracking. The basic idea is to process electromagnetic tracking information to generate an augmented reality (AR) visualization of a tumor model in a laparoscopic camera image. This way the system enhances the surgeon's view on the operating field and therefore facilitates higher safety during the surgery. So far the system was applied in vitro with two phantom trials with the aid of a surgeon which yielded promising results.