Chair for Computer Aided Medical Procedures & Augmented Reality
Lehrstuhl für Informatikanwendungen in der Medizin & Augmented Reality

Aslı Okur Kuru

Picture of me Dipl. Inf. Univ.
Aslı Okur Kuru


My status

Room 1:
MI 03.13.058
Chair for Computer Aided Medical Procedures
Technische Universität München
Boltzmannstr. 3
85748 Garching b. München Germany
+49 (89) 289-19401 (MI 03.13.058)
+49 (89) 289-17059
Room 2:
IFL (01.01.03a-c)
Klinikum rechts der Isar
Technische Universität München
Ismaninger Str. 22
81675 München Germany
+49 (89) 4140-6457 (IFL)
+49 (89) 4140-6458 (IFL)

Research Interests

  • Computer Aided Surgery / Image Guided Surgery
  • Nuclear Imaging
  • Surgical Workflow
  • Intraoperative Usability


  • 1996 - 2004
    Deutsche Schule Istanbul - Istanbul, Turkey


Student Projects


  • drop by and ask!
    detect catheter's tips and estimate the depth. , ) detect catheter's tips in real-time and 2)estimate the depth of detected electrodes, however, few things need to be improved: 1) high-resolution detection map, 2) graphical model and make it work on noisy images. , ) $IF( $AND( $FIND($GET(superMe),Matthias Wieczorek), $EXACT(open,open) ),
  • Computation of Detectability Indices for Medical Imaging (DA/MA/BA)
    Medical imaging is a well established tool for diagnosis. Most imaging modalities however have drawbacks, such as radiation exposure and long imaging times. To alleviate these drawbacks, optimized imaging protocols are an interesting topic of research. For cases where the imaging target is already known, it is often possible to compute feature descriptors enabling optimization of the acquisition protocol for this particular feature. A particular group of such feature descriptors are the detectability indices, which form the basis for this Master's thesis. , ) $IF( $AND( $FIND($GET(superMe),Patrick Wucherer, Philipp Stefan), $EXACT(finished,open) ),
  • Development of Pain Therapy Simulator (Facet joint infiltration) (DA/MA/BA)
    The facet joint infiltration is a procedure in minimally invasive surgery. It aims at pain reduction at the small vertebral joints in the area of the lumbar and thoracic spine. The procedure consists of the placement of a very fine needle in the vicinity of the small vertebral joints and the medical therapy is subsequently conducted at the location where the pain occurs. The objective of this research project is (a) the development of a procedural simulator for facet joint infiltration in close colaboration with medical partners of the Klinikum rechts der Isar (Neuro-Kopf Zentrum) and (b) to conduct a study investigating the suitability of the simulator for training. , ) $IF( $AND( $FIND($GET(superMe),P. Coan, A. Bravin, C. Ferrero, Jean-Michel Letang, Nicolas Freud), $EXACT(open,open) ),
  • A hybrid method to compute the 3D dose in tissue samples during micro-CT image acquisition (DA/MA/BA)
    The aim of the project is to develop a software platform to compute the 3D distribution of dose deposited in tissue samples during micro-CT image acquisition performed with monochromatic synchrotron radiation. The dose can be divided into two components: the primary dose deposited directly by the incident X-ray beam and the secondary dose deposited by scattered and fluorescence X-rays. Previous work carried out in the context of synchrotron stereotactic radiation therapy has shown that a deterministic algorithm can be used to compute the primary dose map [1], whereas a hybrid approach (combination of Monte Carlo and deterministic calculations) is well suited to the calculation of the secondary dose [1,2]. The aim of the master internship is to adapt this method to assess dose deposition inevitable (but optimizable) in CT image acquisition. Special care will be taken to relate optimal hybrid parameters to the geometrical/physical CT set-up. The software development will be carried out in the framework of the Geant4/GATE Monte Carlo code. The final goal is to obtain a tool which can permit to calculate doses in biological samples, but that also can be used to simulate the experiment and optimize the experimental procedure. , ) $IF( $AND( $FIND($GET(superMe),Matthias Wieczorek), $EXACT(open,open) ),
  • Detection Models for Emission Tomography (DA/MA/BA)
    Emission Tomography is a popular clinical tool in the diagnosis of diseases. Based on radioactive tracers marking suspicious targets (such as cancerous cells), emission tomography modalities like Single Photon Emission Computed Tomography (SPECT) or Positron Emission Tomography (PET) allow the non-invasive visualization of these tracers within the human body. Mathematically and algorithmically these modalities pose interesting research problems, in particular the inverse problem of tomographic reconstruction. Central for reconstruction is a suitable physical model of the detection process. , ) $IF( $AND( $FIND($GET(superMe),Patrick Wucherer; Séverine Habert), $EXACT(finished,open) ),
  • Estimation of radiation exposure (Master Thesis)
    The objective of the project is to estimate the radiation dose the hands of the surgeon receives. Using machine learing algorithms and the GEANT4 simulation framework the radiation dose is predicted. The hardware setup consists of a mobile C-arm/surgical simulator with multimodal sensors. The sensors are capable of recording depth and rgb values. Based on these values the hands of the surgeons are detected. Knowing where the surgeons hands are a predicition of applied radiation is made. , ) $IF( $AND( $FIND($GET(superMe),Ahmad Ahmadi), $EXACT(running,open) ),
  • A flexible framework for realistic convolution-based real-time ultrasound simulation (DA/MA/BA)
    Medical ultrasound imaging is receiving increasing importance, due to its versatile usability both in pre-operative diagnostics and monitoring, as well as intra-operative navigation and real-time update of the surgical plan. The simulation of medical ultrasound imaging is an important task and has several application areas, such as pre-operative planning and simulation of the surgical procedure, intra-operative registration of a multi-modal pre-operative plan to the intra-operative scene (e.g. involving CT imaging), multi-modal registration (US-CT, US-MRI) as well as visual servoing of robotic ultrasound acquisition. Ultrasound simulation approaches are prone to trade-offs between speed and realism. Very fast approaches based on ray-casting of US images from CT deliver rough approximations of US images, which are useful e.g. for registration in real-time and intra-operatively. In contrast to that, physically realistic simulations based on e.g. models of wave-propagation in human tissue yield images which match the real image closely, but these methods are typically very slow in execution. Convolution-based approaches take an in-between position between the two approaches, allowing for very fast (i.e. real-time) simulation, but offering realistic features such as speckle patterns. This thesis aims at understanding the physical process of ultrasound imaging fully and developing a flexible framework for realistic and fast convolution-based ultrasound simulation. , ) $IF( $AND( $FIND($GET(superMe),Patrick Wucherer, Philipp Stefan), $EXACT(draft,open) ),
  • Fluid Simulation - Realistic simulation of cement flow (DA/MA/BA)
    The objective of this research work is the formulation of a computational model for realistic real-time simulation of the brittle, porous material of the bone and the interaction of bone cement and instruments with it. This is achieved using a GPU-accelerated mesh-free SPH approach based on the CT imaging data. The research goal contributes to the complete simulation of a minimally invasive surgery (MIS) called “kyphoplasty”. The procedure is conducted on patients with fractured vertebrae in order to set the spine into an upright position and stabilize the vertebrae. First a cavity with a balloon catheter in the vertebra is created. Afterwards the cavity is filled up with cement. , ) $IF( $AND( $FIND($GET(superMe),Bernhard Fuerst), $EXACT(running,open) ),
  • GUI Design and Development for Angiography-Based Catheter Tracking (IDP)
    tba , ) $IF( $AND( $FIND($GET(superMe),Bernhard Fuerst, Ralf Stauder, Thomas Wendler), $EXACT(draft,open) ),
  • User Interface Design and Evaluation for Multimodal Imaging (DA/MA/BA)
    Today's medicine revolves a lot around the combination of different imaging and tracking modalities to form a new system for Image-Guided Therapy. Recent research show promising results in the field of image registration and fusion. However, when adopting these novel techniques to the clinical environment, the systems are often inappropriate in terms of usability, design and simplicity. This thesis will investigate user interfaces for medical applications, the student will participate in the development an interface for the EU project EndoTOFPET and evaluate the usability in close cooperation with clinical personal. , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni), $EXACT(draft,open) ),
  • Interactive Interface for Active Learning (Project)
    , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(finished,open) ),
  • High frequency ultrasound and micro computed tomography cochlea image fusion for intra cochlear navigation (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Christian Rupprecht, Federico Tombari), $EXACT(open,open) ),
  • Hand Pose Estimation from Depth Data (DA/MA/BA)
    A key challenge in modern robotics and biomedical engineering is to design artificial hands able to reproduce human abilities [2]. The difficulty to handle human-like manipulation problems is mainly due to the high number of Degrees of Freedom (DOFs) concentrated in a small volume. As a consequence, the control of robotic grasp and manipulation is an interesting challenges for engineers and scientists in the fields of robotics and machine learning. A possible solution consists in learning manipulation tasks from human observation. The fist step to apply learning methods to control anthropomorphic hands consists in tracking human palm and the fingertips (contact points) from a camera sensor. The objective of this Practical Work is to develop an algorithm able to robustly estimate the poses of palm and fingertips using only depth data. To this end, a deep learning technique [1] will be used. , ) $IF( $AND( $FIND($GET(superMe),Carsten Marr, Diana Mateus), $EXACT(finished,open) ),
  • Segmentation of blood stem cells in bright-field images (DA/MA/BA)
    During the analysis of single-cell time-lapse experiments of proliferating and differentiating blood stem cells, we often have to deal with two types of clumped cells. First, cells that are dividing are inherently clumped for certain time points. Second, due to the rising amount of cells over time one can observe more and more groups of clumped cells, especially in late timepoints. An additional characteristic of our data is that the experiments show cells in all differentiation states with different morphologies. In this project, we would like to develop a method that is able to split clumped cells, but also preserves the shape of all cell types. , ) $IF( $AND( $FIND($GET(superMe),Carsten Marr, Diana Mateus), $EXACT(finished,open) ),
  • Segmentation of embryonic stem cells in fluorescent images (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Carsten Marr and Diana Mateus), $EXACT(finished,open) ),
  • Stem cell tracking (DA/MA/BA)
    Develop/improve existing auto-tracking algorithms for improving and automating manual tracking and considering the biologists needs , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaHuelvesAlba][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Christian Rupprecht, Salvatore Virga, Federico Tombari), $EXACT(draft,open) ),
  • Humanlike Robot Movement (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Federico Tombari Daniel Wahrmann), $EXACT(open,open) ),
  • Perception for humanoid and agricultural robotics (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Severine Habert Pascal Fallavollita), $EXACT(finished,open) ),
  • Parallax-free Xray stitching using depth based pose estimation (Bachelor Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Dr. Igor Yakushev), $EXACT(finished,open) ),
  • Independent Component Analysis of Positron Emission Tomography Data (Master Thesis)
    Positron emission tomography (PET) is a medical technique that generates functional images of the human body including the brain. Typically, covariance in brain PET data is investigated using so called seed-based correlation approach. I.e., values from one brain region are correlated with values from other brain regions or throughout the brain. Thus, this method is limited by the need for hypothesis about regions to be correlated. Recently, we successfully applied a hypothesis-free analytical technique known as independent component analysis (ICA) to identify covariance patterns in PET data (Yakushev et al., submitted). ICA is an advanced computational method for separating a multivariate signal into additive components (Hyvärinen and Oja, 2000). In the above study, we applied software called Group ICA Toolbox (GIFT, that is actually developed for another imaging technique. However, PET provides a different kind of signal and has specific sources of variance. Thus, the ultimate aim of this work is to evaluate performance of ICA in PET data. The following research questions should be addressed in a series of simulation experiments optimal number of components, reproducibility of the algorithm. Ideally, the algorithm should be implemented in as a user-friendly image analysis tool. , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni, Stefanie Demirci), $EXACT(finished,open) ),
  • Cancer Matestasis detection in Lymph nodes (IDP)
    , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni,Stefanie Demirci), $EXACT(finished,open) ),
  • Crowdsourcing in the Medical Context (IDP)
    , ) $IF( $AND( $FIND($GET(superMe),Anca Stefanoiu), $EXACT(open,open) ),
  • Image Formation Models in Lightfield (Plenoptic) Microscopy Using Wave Optics (DA/MA/BA)
    Light field microscopy is a scanless techniques for high speed 3D imaging of fluorescent specimens. A conventional microscope can be turned into a light field microscope by placing a microlens array in front of the camera, allowing for a full spatio-angular capture of the light field in a single snapshot. The recorded information can be used to volumetrically reconstruct the imaged sample. , ) $IF( $AND( $FIND($GET(superMe),Christian Wachinger), $EXACT(open,open) ),
  • MR Image Synthesis (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Christian Rupprecht, Iro Laina, Federico Tombari), $EXACT(running,open) ),
  • Deep Intrinsic Image Decomposition (Master Thesis)
    In this project we aim at decomposing a simple photograph into layers of material properties like reflectance, albedo, materials etc. This a very challenging but important topic in bot Computer Vision and Computer Graphics as it improves tasks like scene understanding, augmented reality and object recognition. We want to tackle this problem using the human annotated OpenSurfaces? dataset and our recent advances in deep learning especially fully connected residual networks. , ) $IF( $AND( $FIND($GET(superMe),Anca Stefanoiu), $EXACT(open,open) ),
  • Evaluation of iterative solving methods for the statistical reconstruction of lightfield microscopy data (DA/MA/BA)
    Light field microscopy is a scanless techniques for high speed 3D imaging of fluorescent specimens. A conventional microscope can be turned into a light field microscope by placing a microlens array in front of the camera allowing for a full spatio-angular capture of the light field in a single snapshot. The recorded information can be used to volumetrically reconstruct the imaged sample. Once the forward light transfer is determined based on the optical system response, the reconstruction process is an inverse problem. In fluorescence microscopy, besides the read-out noise, Poisson noise is present due to the low photon count. Hence a Poisson-Gaussian mixture model would be an appropriate approach for likelihood-based statistical reconstruction. Various iteration schemes may result from different likelihoods coupled with regularization. , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni, Ali Nasseri), $EXACT(draft,open) ),
  • Automatic Early Detection of Keratoconus (DA/MA/BA)
    Keratoconus (KCN) is a bilateral, non-inflammatory, and degenerative disorder of the cornea in the eye with an incidence of approximately 1 per 2,000 in the general population [1,2], It is characterized by progressive thinning and cone-shaped bulge of the cornea (fig.1) leading to substantial distortion of the vision [2]. The early diagnosis of keratoconus is of a great importance for patients seeking eye surgery (i.e. LASIK), which can prevent the progression of pathology after surgery [3-4]. Rabinowitz [5] shows that his preliminary research using a Wavefront analysis together with Corneal topography demonstrates a good classification between early KCN subtypes and normals. Further, Jhanji et. al. [6] concluded that swept-source OCT may provide a reliable alternative for the parameters of corneal topography (fig.2). On the other hand, Pérez et. al. [3] shows that all of these surveyors including videokeratography, Orbscan, and Pentacam together with the indices can lead to early KCN detection, however, with an increase in false positive detection. Therefore, developing a highly specific diagnostic tool for KCN detection with few false positive is highly desirable. In this IDP/MA project, the objective is to analysis data from approximately 200 patients, treated at the ophthalmology department at Klinikum Rechts der Isar / TUM. Using a retrospective corneal topographic data (fig.2) collected during follow-ups, the aim is to build an early predictive model for KCN detection. , ) $IF( $AND( $FIND($GET(superMe),Federico Tombari), $EXACT(running,open) ),
  • Keypoint Learning (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Patrick Wucherer, Philipp Stefan), $EXACT(draft,open) ),
  • Kyphoplasty balloon simulation (DA/MA/BA)
    Kyphoplasty, a percutaneous, image-guided minimally invasive surgery, is a recently introduced treatment of painful vertebral fractures which is being performed extensively worldwide. The objective of kyphoplasty is to inject polymethylmethacrylate (PMMA) bone cement under radiological image guidance into the collapsed vertebral body to stabilize it. Before injecting the cement, an inflatable balloon is placed in the vertebral body and subsequently inflated in order to restore the vertebral height and correct the kyphotic deformity caused by the compression fracture. After the balloon is deflated and removed from the vertebral body, the created cavity is filled with PMMA bone cement. The goal of the project is the implementation and validation of a kyphoplasty balloon simulation. , ) $IF( $AND( $FIND($GET(superMe),Alexander Ladikos), $EXACT(draft,open) ),
  • Real-time large-scale SLAM from RGB-D data (Master Thesis)
    You will extend an existing RGB-D reconstruction system to support large-scale scenes. In a first step you will evaluate and implement state-of-the-art algorithms for tracking and reconstruction from RGB-D data. Secondly, you will also evaluate and implement algorithms for texturing the obtained reconstruction from camera images. The real-time critical components will be implemented on a GPU. , ) $IF( $AND( $FIND($GET(superMe),Philipp Matthies), $EXACT(finished,open) ),
  • Understanding and optimization of a low energy X-ray generator for intra-operative radiation therapy (IDP)
    The research activity is focused on the combination of minimal-invasive therapy techniques with diagnostic imaging and navigation modalities, e.g. application of intra-operative radiation therapy, MRI guided high focused ultrasound or intra-operative SPECT with MRI guidance. An initial development goal is to use advanced MRI imaging to find and localize small pathologies and subsequently perform minimal-invasive therapy with a small and lightweight X-ray generator and continuous intra-operative imaging for visualization and navigation. An in-vitro setup will be created to apply the low-energy X-rays to real cancer cells and study their biological effectiveness. , ) $IF( $AND( $FIND($GET(superMe),Ma Meng), $EXACT(finished,open) ),
  • Simulation of Muscle Activity for an Augmented Reality Magic Mirror (DA/MA/BA)
    We have previously shown an augmented reality (AR) magic mirror. We create the illusion that a user standing in front of the system can look inside the own body. The video of this system received a lot of attention and has been seen over 200.000 time on Youtube. We now want to build a system for education of human anatomy using augmented reality visualization. We want to use the system to visualize muscle activity. , ) $IF( $AND( $FIND($GET(superMe),Christian Rupprecht, Federico Tombari), $EXACT(finished,open) ),
  • Tracking using Autoencoders and Manifolds (DA/MA/BA)
    In this project we want to explore the possibilities of using autoencoders to perform object tracking in video sequences. The object's bounding box is given in the first frame and needs to be tracked thoughte the sequence. We would like to use autoencoders to encode the appearance of the object and to predict its future (location and appearance). , ) $IF( $AND( $FIND($GET(superMe),Philipp Matthies
    Benjamin Frisch), $EXACT(running,open) ),
  • Marker-based inside-out tracking for medical applications using a single optical camera (Master Thesis)
    Nowadays, tracking and navigation for small imaging systems are performed mainly by devices based on infrared cameras or electromagnetic fields. These systems impose some disadvantages for the use with freehand devices such as gamma cameras or ultrasound probes: a separate system for “Outside-in” tracking is needed, which causes the main issue of a required line-of-sight between the tracking system and the tool to be tracked in the surgical environment. To solve this problem, the idea is to have a small add-on system attached to the devices being tracked. The add-on system contains of an optical camera to track several markers that are attached to the patient and calculate the inverse trajectory, i.e. the movement of the device. The idea of this project is to develop a tracking software, the “inside-out” tracking technique, with the required data set to have more accurate tracking and image fusion process. An algorithm for multi marker tracking and calculation of "best pose” will be implemented and the problems of illumination, occlusion, and stability will be addressed. Finally, the accuracy will be evaluated and compared to other tracking modalities, especially optical and electro-magnetical tracking. , ) $IF( $AND( $FIND($GET(superMe),Federico Tombari, Ulrich Eck), $EXACT(open,open) ),
  • Medical Augmented Reality with SLAM-based perception (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni), $EXACT(open,open) ),
  • Medical Image Synthesis using Generative Adversarial Networks (GANs) (DA/MA/BA)
    Magnetic resonance imaging (MRI) enables the acquisition of the underlying anatomy with different protocols, i.e. T1-weighted and T2-weighted, PD and FLAIR. Recent studies [5] show the importance of enhanced contrast image, namely double inversion recovery (DIR), which can be used for MS Lesion Segmentation. In this project, we will investigate the Medical Image Synthesis of DIR using other proptocols (might be few of them [4]). , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni), $EXACT(finished,open) ),
  • Creating Diagnostic Model for Assessing the Success of Treatment for Eye Melanoma (Project)
    An eye melanoma, also called ocular melanoma, is a type of cancer occurring in the eye. Patients having an eye melanoma typically remain free of symptoms in early states. In addition, it is not visible from the outside, which makes early diagnosis difficult. The choroidal melanoma, which is located in the choroid layer of the eye, is the most common primary malignant intra-ocular tumor in adults. At the same time, intra-ocular cancer is relatively rare – only an estimated 2,500 - 3,000 adults were diagnosed in the United States in 2015. Treatment usually consists of radiotherapy or surgery if radiotherapy was unsuccessful. For larger tumors, radiation therapy maybe associated with some loss of vision. Currently, it is unknown which factors lead to the development of such cancer and which factors determine whether a patient is responding to radiotherapy In this master thesis project, the objective is to analyze data from approximately 200 patients, treated at the ophthalmology department at Ludwig-Maximilians University hospital. Treatment consisted of a single-session, frameless outpatient procedure with the Cyberknife System by Accuray. Using pre-procedural data and information collected during follow-up, the aim is to identify factors predictive of a patient's response to treatment and the impact on a patient's visual acuity, measured by the so-called Visus. , ) $IF( $AND( $FIND($GET(superMe),Dr. Igor Yakushev & Dr. Kuangyu Shi), $EXACT(open,open) ),
  • Modeling brain connectivity from multi-modal imaging data (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Philipp Matthies), $EXACT(open,open) ),
  • MR integration of an intra-operative gamma detector and evaluation of its potential for radiation therapy (DA/MA/BA)
    , ) $IF( $AND( $FIND($GET(superMe),Christoph Hennersperger, Julia Rackerseder, Dr. Benjamin Frisch), $EXACT(running,open) ),
  • Multi-modal Deformable Registration in the Context of Neurosurgical Brain Shift (DA/MA/BA)
    Registration of medical images is crucial for bringing data obtained by different sources or at a different time into a common reference frame. Adding real-time requirements to 3D multi-modal registration allows physicians to analyze the combination of medical data both preoperatively as well as intraoperatively, providing additional benefits for the patient and helping to achieve a desirable procedure outcome. Different applications usually induce several underlying geometrical transformations ranging from global rigid movements to local nonlinear deformations such as brain shift in neurosurgery or compression of liver tissue during respiratory motion. Using a deformable registration to correct local tissue distortions allows for a transformation of preoperative data into an intraoperatively acquired local reference frame. The integration of intrinsic tissue properties and biomechanical constraints can further extend the registration framework. This thesis concentrates on real-time multi-modal deformable registration between Ultrasound (US) and X-ray Computed Tomography (CT) as well as respective Magnetic Resonance Imaging (MRI). Existing registration techniques will be analyzed and a framework to register between preoperative X-ray CT or MRI data and intraoperative US images with a particular focus on brain shift will be developed. Furthermore, the transformed preoperative data are to be visualized alongside with surgical tools, e.g. for guidance of a surgical procedure. , ) $IF( $AND( $FIND($GET(superMe),Bernhard Fuerst, Wolfgang Wein, Ahmad Ahmadi), $EXACT(running,open) ),
  • Registration of Multi-View Ultrasound with Magnetic Resonance Images (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Ralf Stauder, Mathias Magg (MITI)), $EXACT(draft,open) ),
  • Multiple Screen Detection for Eye-Tracking Based Monitor Interaction (DA/MA/BA)
    A modern operating room usually offers multiple different monitors to present various information to the surgical staff. With the trend to go from highly invasive open surgery to minimally invasive techniques such as laparoscopic surgery, Single-Port surgery or even NOTES, the amount of additional monitors is likely to increase. Knowing which monitor the surgeon is looking at, and on which part of the monitor they are focused allows for a wide variety of supporting systems, such as automatic adjustments of the endoscopic camera position through a robotic system. The goal of this work is to develop a method to recognize monitors with changing content through the cameras of head-mounted eye-tracking systems and translate the detected gaze point to the coordinate frame of the detection monitor. The work will be based on an existing framework (developed in C#) that is able to detect a single monitor, which should be extended to an arbitrary number of monitors and distinguish between them. , ) $IF( $AND( $FIND($GET(superMe),Diana Mateus), $EXACT(open,open) ),
  • New Mole Detection (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni, Slobodan Ilic), $EXACT(finished,open) ),
  • Siemens AG: X-ray PoseNet - Recovering the Poses of Portable X-Ray Device with Deep Learning (Master Thesis)
    For most CT setups usually the systems geometric parameters are known. This is necessary to compute an accurate reconstruction of the scanned object. Unfortunately for a Mobile CT this might not be the case. However to enable the reconstruction of an object given its projections from unknown geometric parameters, this master thesis explores the possibility of using Convolutional Neural Networks to train a model and estimate the necessary geometric parameters needed for tomographic reconstruction. , ) $IF( $AND( $FIND($GET(superMe),Christian Schulte zu Berge? Benjamin Frisch), $EXACT(running,open) ),
  • Predicate-based PET-MR visualization (Master Thesis)
    The combined visualization of multi-modal data such as PET-MR is a challenging task. The recently introduced predicate paradigm for visualization offers a promising approach to reduce the dimensionality and complexity of the classification (transfer function) domain and provides the clinician with an intuitive user interface. The goal of this project is to extend this technique to multi-modal visualization and apply it to for instance to PET-MR scans of prostate. , ) $IF( $AND( $FIND($GET(superMe),Christian Rupprecht, Federico Tombari), $EXACT(draft,open) ),
  • Extrinsics calibration of multiple 3D sensors (DA/MA/BA)
    Multiple 3D sensor setups are now increasingly used for a variety of computer vision applications, including rapid prototyping, reverse engineering, body scanning, automatic measurements. This project aims at developing a new approach for the calibration of the extrinsic parameters of multiple 3D sensors. The goal is to devise a technique which is simple, fast but also accurate in the estimation of the 3D pose of each sensor. The project will include study of the state of the art in the field, software development of the calibration technique (in C++) and experimental validation. , ) $IF( $AND( $FIND($GET(superMe),Séverine Habert, Ulrich Eck), $EXACT(open,open) ),
  • Radiation Exposure Estimation of full surgical procedures using CamC (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Matthias Wieczorek), $EXACT(open,open) ),
  • Manifold-based regularization of spherical functions in anisotropic X-ray dark-field tomography (Master Thesis)
    X-ray grating interferometry enables the simultaneous acquisition of absorption contrast, phase contrast and dark-field contrast. The directionally dependent dark-field data allows the tomographic reconstruction of anisotropic scattering coefficients inside the sample. This allows the recovery of structural orientations without the need to explicitly resolve them in the X-ray detector. The anisotropic scattering coefficients can be represented as spherical functions, such as spherical harmonics. Based on a closed-form spherical harmonics based forward model, the anisotropic dark-field data can be reconstructed in three dimensions. We refer to this technique as "Anisotropic X-ray Dark-field Tomography", or in short AXDT. , ) $IF( $AND( $FIND($GET(superMe),Dr. Abouzar Eslami, Ali Nasseri), $EXACT(running,open) ),
  • Robot-Assisted Vitreo-retinal Surgery (Master Thesis)
    Pars Plana Vitrectomy surgery is a minimal invasive intra- retinal surgery that has revolutionized retinal surgery since it was rst proposed in the 1970's. This sutureless technique involves the use of smaller surgical instruments (25 gauge, 51mm in diameter) and was used in the cure of conditions not treatable before. Moreover, it proved to have lower complication rate and shorter healing period than standard vitreo- retinal surgery. The barrier towards an improvement of the outcomes of this technique lies, however, in the surgeon's abilities and dexterity. In this line, an assisting robotic master-slave device could enhance the surgeon's skills when manipulating the surgical tools. The slave device is in charge of manipulating the tools whereas the master device is ma- nipulated by the surgeon to control the master device. A master input device for the controlling of the existing master robot is to be designed. Several aspects concerning the operating room environment, surgery req- uisites, surgeon's manipulation intuition and compatibility with slave device should be taken into account when nding the optimal solution. , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaRoboticCatheterUS][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaSchwarzmann][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Dr. Abouzar Eslami, Dr. Jan Bauer, Dr. Peter Noël), $EXACT(running,open) ),
  • Segmentation of Fractured Bones (Master Thesis)
    With the advent of computer aided surgery and planning, automatic post-processing of the acquired imaging data becomes more and more important but also challenging. Image segmentation is in many cases the first, very important but difficult step. A fully automatic method for segmenting bones would be highly desirable. However a few factors hamper the development of such a fully automated segmentation method. The quality of the datasets differs to a large extent in terms of contrast and resolution. The voxel intensity of the bones varies according to scan parameters and condition of the bone. The intensity of cortical and trabecular bone may be very similar in some cases. The density of osteoporotic bones is low and thus the contrast between osteoporotic bones and soft tissues is very small, in particular in fractured bones, where the trabecular bone directly adjoins to the soft tissues. In addition, it is very time consuming, inconsistent and hard to do a complete manual segmentation of the fractured bones. We look forward to propose a fast and efficient segmentation tool that effectively segments the fractures and at the same time is robust for using the output model in FEM analysis. Though the objective is to develop a segmentation tool that is as fully automated as possible, the idea is also to have the following features incorporated into the segmentation tool: semi-automatic segmentation, manual correction and output generation. The evaluation is done on CT datasets of various types of fractures in Department of Diagnostic and Interventional Radiology of Klinikum rechts der Isar in Munich. , ) $IF( $AND( $FIND($GET(superMe),Guillaume Potdevin, Dieter Hahn and Tobias Lasser), $EXACT(finished,open) ),
  • Development and implementation of 3D parallelized series expansion methods for differential phase contrast tomography (Master Thesis)
    Advances in imaging hardware have enabled differential phase contrast tomography with conventional X-ray tube sources. So far, iterative series expansion methods have been applied in a weighted maximum likelihood framework to reconstruct absorption and phase contrast data jointly in 2D slices. However, the available hardware easily generates fully 3D cone-beam data sets with full projections. The expansion of this reconstruction approach to full 3D poses challenges both in terms of memory and computational power. This thesis project comprises the development and implementation of parallelized (multi- core) or massively parallelized (GPU) variants of the fully 3D reconstruction pipeline, including generation of the system equation and the implementation of several standard iterative solvers. , ) $IF( $AND( $FIND($GET(superMe),Guillaume Potdevin, Dieter Hahn and Tobias Lasser), $EXACT(finished,open) ),
  • Development and implementation of a regularization framework for differential phase contrast tomography (Master Thesis)
    Advances in imaging hardware have enabled differential phase contrast tomography with conventional X-ray tube sources. Here, iterative series expansion methods are applied in a weighted maximum likelihood framework to reconstruct absorption and phase contrast data jointly. To fully utilize the additional information content provided by the hardware setup, which measures absorption, phase contrast and darkfield information all at once, regularization terms incorporating this information have to be introduced in the maximum likelihood framework. The aim of this thesis is the development and implementation of several regularizers integrated into the existing reconstruction pipeline, as well as an evaluation of the different strategies in terms of imaging performance. , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni, Stefanie Demirci), $EXACT(running,open) ),
  • Siemens AG: Detection of Complex Stents in Live Fluoroscopic Images for Endovascular Aneurysm Repair (Master Thesis)
    The abdominal aortic aneurysm (AAA) is a dilation of the aorta that may result in rupture, and is one of the most common aortic diseases. An AAA may be repaired by open surgery or by endovascular aneurysm repair (EVAR) to prevent rupture, and in recent years EVAR has become predominant. During the EVAR procedure, a stent is placed at the position of the aneurysm to exclude it from direct blood flow. The accuracy of stent placement is critical to prevent occlusion of the branching arteries, e.g., renal arteries. This master thesis implements methods to detect complex deployed stents in live 2D fluoroscopic images during EVAR. The proposed learning-based method trains fully convolutional neural network (FCN) models [1, 2, 3] to detect the stent. The training set consists of labelled 2D fluoroscopic image patches that contain the stent. The detection result can be further improved by integrating prior knowledge, e.g., the overlay of the registered pre-operative CT segmentation. Possible evaluation metrics include DICE coefficient (to measure repeatability), true positive rate (sensitivity), positive predictive value (precision) and Hausdorff distance. Previous research [4, 5, 6] has improved the accuracy of stent detection for EVAR. However, the methods are limited to infra-renal, abdominal EVAR cases. In contrast, stents with fenestrations/scallops are necessary for supra-renal cases and for complex AAA anatomy. Methods of this work aim to detect the complexity of the stent. The expected result qualitatively and quantitatively describes which portion/branch of the stent corresponds to which artery. For example, in a supra-renal case, the result describes whether a portion/branch of the stent covers the aorta, the left/right external iliac artery, the left/right renal artery, etc. , ) $IF( $AND( $FIND($GET(superMe),Stefanie Demirci), $EXACT(open,open) ),
  • Interventional Stent Deformation Tracking (Master Thesis)
    Despite the incredible improvement of treating abdominal aortic aneurysms (AAA), the minimally invasive deployment of a stent graft within a diseased vessel may cause comorbidities induced by the stent itself or a malfunction. So far, only ex-vivo or in-vitro experiments analyzing the interaction between stent graft and weakened vessel wall have been performed. This project aims at finding a solution for the extraction of in-vivo stent graft deformation that is to be further used for quantitaive analysis of vessel wall deformation. , ) $IF( $AND( $FIND($GET(superMe),Christian Rupprecht, Federico Tombari), $EXACT(draft,open) ),
  • Super Resolution Depth Maps (DA/MA/BA)
    This project aims at single image super-resolution applied to depth maps. Many available depth sensors have a relatively low resolution compared to the accompanied color image. We would like to recover a high-resolution depth map from the combination of low-res depth and high-res RGB image. This problem is inherently ill-posed since a multiplicity of solutions exist for any given input. Nonetheless it is a highly studies topic in computer vision. Starting with the work of Dong et. al. "Image Super-Resolution Using Deep Convolutional Networks" (TPAMI 2015) we would like to expore the application of deep neural networks to this field of study. , ) $IF( $AND( $FIND($GET(superMe),Ralf Stauder, Daniel Ostler (MITI)), $EXACT(draft,open) ),
  • Surgical Workflow Software Infrastructure Based on Business Workflow Modeling Standards (IDP)
    Surgical procedures can be described and structured by their workflow, phases, and hierarchical order of tasks and activities. This enables further analysis and comparison both of ongoing surgeries as well as for recorded datasets. Several methods for modeling of business processes have already been established, though due to the different methodical approach in this case, the available methods are not necessarily directly applicable to surgical process modeling. The aim of this work is to implement a common class structure suitable for surgical workflows and develop import and export functions to and from several known languages describing business process models (e.g. YAWL and BPMN). During the course of the implementation these languages should be evaluated for their fitness to describe surgical workflows with their specific requirements (e.g. variability in the process and probabilistic phase transitions). , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaTRUSMROrganMotion][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Dr. Armin Schneider (MITI), Ralf Stauder), $EXACT(draft,open) ),
  • Mobile Telephony Management in the Surgery Room (DA/MA/BA)
    DECT phones usually increase the reachability of the surgeons and assistants. However they introduce noise and disturbance in the operating room. To solve this problem, the "situational awareness" of the system is to be used. With a system that analyzes the current situation in the surgery and aware of what’s happening can reduce the disturbance while handling phones more effectively. MITI research group is willing to get a student to research and implement a solution for a system that take the responsibility to reply on the phones while the surgeon is performing a surgical operation. The system should be intelligent enough to categorize the received phone calls according to their importance and prioritize them according to the analysis of the current situation in the operating room – and forward the call to the surgeon if it is really needed. Also it’s important that the system store all the information needed to recognize the call (e.g. phone number, importance, and maybe the subject of the call). Project includes research opportunities in selecting the most appropriate technology and intelligent algorithm to reduce disturbance while not missing the important information of the caller. Student has the opportunity to include his or her creative ideas in how to solve and implement the solution. , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaThompson][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Philipp Matthies), $EXACT(open,open) ),
  • Tracking Add-On Camera System for gamma and ultrasound probes (DA/MA/BA)
    Tracking and Navigation of instruments / systems and small imaging systems is performed using commercially available systems based on infrared cameras or electromagnetic fields. Both have advantages and drawbacks for use with handheld gamma cameras or ultrasound probes. Main disadvantage is that you require a separate system. In this work a small system ADD-ON is developed that is directly attached to the device that is being tracked. , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaTrackGamUs][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Philipp Matthies), $EXACT(running,open) ),
  • Tracking and Visualization in ioRT (IDP/Klinisches Anwendungsprojekt)
    , ) $IF( $AND( $FIND($GET(superMe),Christoph Hennersperger), $EXACT(open,open) ),
  • Automatic acoustic coupling for robotic ultrasound imaging (Master Thesis)
    Medical ultrasound (US) is already used today as the primary modality of choice for many clinical indications. Robotic ultrasound systems could potentially provide an automation of current ultrasound acquisitions, which would be especially helpful for interventional and screening applications. While the feasibility of automatized ultrasound imaging systems was shown by various research groups up to now, the application of ultrasound gel still needs to be performed manually today. This project focuses on ultrasound coupling and aims at overcoming this issue based on developments in other research areas to allow for automatic robotic ultrasound acquisitions. , ) $IF( $AND( $FIND($GET(superMe),M.Sc.-Inf Frieder Pankratz), $EXACT(open,open) ),
  • Parallel Tracking and Mapping in UbiTrack (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Dr. Abouzar Eslami from CAMP
    affil. Prof. Dr. Michael Friebe as liasion from CAMP and TUM-IAS), $EXACT(running,open) ),
  • Calculation of signal intensity-time curves from MR images of the beating heart (Master Thesis)
    In order to assess whether a patient with a narrowing of a coronary artery has an increased risk for a heart at-tack, one is interested in quantitative parameters of the blood supply to the heart muscle. Currently those parameters could be judged only semi quantitative by visual analysis of a sequence of MRI im-ages: For that approximately 300 consecutive dynamic images are acquired by a MRI (magnetic resonance imaging) scanner. During the acquisition an intravasal CM (contrast medium) is injected and the distribution of the signal intensity increase caused by the CM is visually observed by a radiologist. The higher the increase of the observed signal intensity, the lower the risk of the patient is to suffer a hard attack in the future. To derive reliable statistical data from these measurements, the increase of the signal intensity must be measured quantitatively in each pixel of the image. That means that the signal intensity-time curves must be derived automatically for each pixel for a time period of approximately 1 minute. Due to the breathing and small movements of the patients during the acquisition period, the measured images could not be evaluated directly. The main objective of this work is to develop a mathematical method to “freeze” the movement of the heart. The second object should be to calculate the signal intensity-time curve in each pixel of the frozen sequence and visualize the result as a parameter image of the signal intensity peak. , ) $IF( $AND( $FIND($GET(superMe),Sailesh Conjeti, Kuangyu Shi, Shadi Albarqouni), $EXACT(running,open) ),
  • A Deep Learning Approach to Synthesize Virtual CT based on Transmission Scan in hybrid PET/MR (Master Thesis)
    Computed Tomography (CT) is a mandatory imaging modality for radiation treatment planning while magnetic resonance imaging (MRI) and positron emission tomography (PET) have advantages in tumor delineation and dose prescriptions. With the advent of PET/MRI, this hybrid imaging modality has advantages of simultaneous acquisition of soft tissue morphological imaging and molecular imaging, which provides advanced information supporting clinical diagnosis and therapy planning (1). To avoid multiple scanning and additional high radiation doses, a new concept was proposed to integrate low dose transmission scan (TX) into a PET/MRI machine for the synthesis of virtual CT (VCT) for treatment planning (2). However, TX is usually extremely noisy with artifact spots and it is necessary to smooth the sinogram to obtain interpretable images. This leads to consequently blurred low-resolution images. The proposed Master thesis project will aim to synthesize high-resolution virtual CT planning based on low-resolution transmission scan in integrated PET/MRI. This VCT is aimed to substitute CT scans in several applications such as radiotherapy treatment planning and attenuation correction. In particular, this project will develop advanced deep learning approach to achieve imaging super-resolution. , ) $IF( $AND( $FIND($GET(superMe),Federico Tombari, Lamberto Ballan; Christian Rupprecht), $EXACT(finished,open) ),
  • Webly supervised human activity recognition (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.MaWesemann][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Shadi Albarqouni), $EXACT(open,open) ),
  • X-ray In-Depth Decomposition (DA/MA/BA)
    In this project, we would like to work further on X-ray In-Depth decomposition presented in [1] modelling the physics of X-ray to recover the depth information. , ) $IF( $AND( $FIND($GET(superMe),Stefanie Demirci), $EXACT(running,open) ),
  • X-ray Depth Map Reconstruction for Improved Interventional Visualization (Master Thesis)
    Most minimally-invasive interventions are performed under continuous 2D X-ray imaging. However, recovering the 3D information is crucial for physicians to perform safer navigation and precise surgical instrument positioning. In the current clinical workflow, this requirement yields an increase in radiation and use of contrast agent whenever vessels need to be made visible. Improved and adapted visualization of X-Ray images has mostly been addressed in terms of 2D-3D image registration. Yet, the output of such algorithms is a projection matrix that, by itself, does not yield any meaningful visualization. It is the major aim of this master project to yield depth hints for improved interventional visualization. Having training datasets containing each an X-ray image and corresponding depth map, available, an X-ray depth model is to be built that is subsequently applied to any new incoming X-ray image to reconstruct corresponding depth hints. , ) $IF( $AND( $FIND($GET(superMe),Andreas Malecki, Matthias Wieczorek, Tobias Lasser), $EXACT(finished,open) ),
  • Tomographic reconstruction and visualization of x-ray scattering tensor data (Master Thesis)
    , ) $IF( $AND( $FIND($GET(superMe),Eva Artinger), $EXACT(finished,open) ),
  • 3D augmented virtuality sketching (Master Thesis)
    Within the interdisciplinary project "Collaborative Design Platform" a large-scale multitouch table was developed to aid urban planning and prototyping. The table interacts with the user over a multitouch surface, and can also scan objects positioned on top of it in 2.5 dimensions. In order to enhance its presentation cababilities, an additional display will be added, which offers a 3D augmented virtuality perspective on the workspace, which reflects both the physical and the virtual aspect of the scene. The view can be controlled using a special 3D mouse. In addition, the user can sketch and draw directly on the virtual world presented on the new display. , ) $IF( $AND( $FIND($GET(superMe),), $EXACT(,open) ),
  • [[Students.ProjectForm][]] ()
    , ) $IF( $AND( $FIND($GET(superMe),Martin Groher), $EXACT(finished,open) ),
  • Optimization Algorithms for 3D Computer Vision: (SEP)
    Not only in Computer Vision but also in many other applications, optimization algorithms are crucial methods for error minimization in order to get good computational results. In Computer Vision these algorithms are used for estimating e.g. homographies, projection matrices, fundamental matrices, or tensors optimally. Especially non-linear optimization methods like Levenberg-Marquardt, Gradient Descent or Gauss-Newton iteration (which might be known from Konkrete Mathematik) are essential for optimal estimation. This SEP covers the implementation of these algorithms first in Matlab, a powerful and easy-to-learn tool for mathemtical computations, and in C++. Moreover, an application for testing the optimization algorithms shall be implemented, which can be chosen from the Computer Vision area, e.g. mosaicing, or 3D scene reconstruction from 2 or multiple views. Prerequisite is an advanced knowledge in C++ programming. , ) $IF( $AND( $FIND($GET(superMe),Ben Glocker), $EXACT(finished,open) ),
  • Assessment of Knee Cartilage Thickness using Magnetic Resonance Imaging (SEP)
    Degeneration of knee joint cartilage is an important and early indicator of osteoarthritis (OA) which is one of the major socio-economic burdens nowadays. Accurate quantification of the articular cartilage degeneration in an early stage using MR images is a promising approach in diagnosis and therapy for this disease. Particularly, volume and thickness measurement of cartilage tissue has been shown to deliver significant parameters in assessment of pathologies. This project was aimed at analyzing and displaying local thickness data, notably in patellar cartilage. The resulting tools have been integrated in the “PaCaSe” software. , ) $IF( $AND( $FIND($GET(superMe),Marcus Tönnis), $EXACT(finished,open) ),
  • A GUI description language for use in Distributed Applications (SEP)
    Goal of this work is to provide a software package to collect graphical user interfaces descriptions in a distributed system, so that a system administrator can manage all connected application processes from his personal authoring computer from one application window. , ) $IF( $AND( $FIND($GET(superMe),Marcus Tönnis), $EXACT(finished,open) ),
  • A User Interface for 3D Volume Rendering in Vision Space (SEP)
    Introduction of virual-reality technology into teaching and assessment of clinical skills in the undergraduate medical course through a programme of collaborative research and development between the Human Interface Technology Lab NZ, University of Canterbury and the Departments of Surgery and Radiology, Christchurch School of Medicine and Health Sciences, University of Otago. , ) $IF( $AND( $FIND($GET(superMe),Martin Groher), $EXACT(draft,open) ),
  • 2D/3D Registration using ICP and Bitangent Invariants (SEP)
    Registration of 2D medical images to 3D volumes of a patient is a crucial issue for locating injected instruments in 3D and helping an operating physician to guide a way through the patient’s anatomy. An algorithm shall be developed to register extracted blood vessels from 2D and 3D images represented as 2D and 3D curves. This can be achieved by using an Iterative Closest Point (ICP) algorithm adapted to the 2D-3D projective case. , ) $IF( $AND( $FIND($GET(superMe),Joerg Traub, Thomas Wendler), $EXACT(draft,open) ),
  • User interface design of beta-probe-guided surgery (SEP)
    In minimally invasive tumor resection, the desirable goal is to perform a minimal but complete removal of cancerous cells. In the last decades interventional nuclear medicine probes supported the detection of remaining tumor cells. However, scanning the patient with an intraoperative probe and applying the treatment are not done simultaneously. In the past we extended the one dimensional signal of a nuclear probe to a four dimensional signal including the spatial information of the distal end of the probe. This signal can be then used to guide the surgeon in the resection of residual tissue and thus increase its spatial accuracy while allowing minimal impact on the patient. The next step is to prepare clinical experiments and integrate the solution into the clinical workflow. The student in charge of this project will contribute in that step by developing an interface suitable for the surgeons and evaluate it in ex-vivo experiments. , ) $IF( $AND( $FIND($GET(superMe),Patrick Wucherer, Philipp Stefan), $EXACT(draft,open) ),
  • Haptic Billard Game (SEP)
    , ) $IF( $AND( $FIND($GET(superMe),Christian Wachinger,Tobias Blum), $EXACT(draft,open) ),
  • Patient Position Detection using Machine Learning Techniques (DA/MA/BA)
    Although magnetic resonance imaging is considered to be non-invasive, there is at least one effect on the patient which has to be monitored: The heating which is generated by absorbed radio frequency (RF) power. It is described using the specific absorption rate (SAR). In order to obey legal limits for these SAR values, the scanner's duty cycle has to be adjusted. The limiting factor depends on the patient's position with respect to the scanner. Detection of this position allows a better adjustment of the RF power resulting in an improved scan performance and image quality. In this thesis, different machine learning techniques have to be researched and evaluated. This may include PCA, ICA, neural networks, Haar features, ... but the student is also encouraged to propose own approaches. This thesis would perfect for students who are interested in medical imaging and machine learning. Previous knowledge in those domains is helpful but not mandatory. , ) $IF( $AND( $FIND($GET(superMe),Martin Groher and Hesam Najafi), $EXACT(finished,open) ),
  • Implementation of a Fast Covariant Feature Detector (SEP)
    _to be completed_ , ) $IF( $AND( $FIND($GET(superMe),Main.BjoernSchwerdtfeger), $EXACT(draft,open) ),
  • Head Mounted Laser Projector (SEP)
    As Head Mounted Displays in Augmented Reality applications are fare away from being ready for (commercial) use we are going to construct a Head Mounted Laser Projector. This work is a case study for a car manufacturer and can lead to further steps. To fulfil this work knowledge in handicrafts, java and 3D geometry is required. , ) $IF( $AND( $FIND($GET(superMe),Main.MartinWagner , Dipl.-Ing. Stephan Eelman), $EXACT(finished,open) ),
  • Entwicklung eines Systems zur dreidimensionalen Visualisierung von Lufträumen für VFR-Piloten (SEP)
    Ziel ist die Entwicklung eines Systems, welches den Piloten kleiner Maschinen im unteren Luftraum bei der Navigation unterstützt und insbesondere in kritischen Situationen (z.B. plötzlicher Wetterumbruch, der die Fortsetzung des geplanten Fluges nicht zulässt) durch sofortige intuitive Vermittlung der aktuellen Fluglage bei der Entscheidungsfindung entlastet bzw. ihm navigatorische Arbeit abnimmt. , ) $IF( $AND( $FIND($GET(superMe),Martin Bauer), $EXACT(draft,open) ),
  • Projektive Erweiterte Realität (SEP)
    Zur Unterstützung offener chirurischer Operationen sollen präoperative Planungsdaten intraoperativ mittels geeigneter Projektionsverfahren auf den Operationssitus überlagert werden. Ziel des Projekts ist weniger die konkrete Umsetzung eines speziellen klinischen Sachverhalts als vielmehr die Untersuchung der grundsätzlichen Möglichkeiten einer solchen Projektion. Die zu entwickelnde Technik soll in verschiedenen Szenarios prototypisch eingesetzt werden. Anhand eines Prototyps sollen der Nutzen und die prinzipielle Machbarkeit einer solchen Augmentierung evaluiert werden. Die hierbei zu untersuchenden Fragestellungen reichen von der Kalibrierung des Gesamtsetups über die Verwendung unterschiedlicher Trackingkonfigurationen bis hin zu Fragen der Projektion auf unregelmäßige Oberflächen und der Kalibrierung eines solchen Systems. , ) $IF( $AND( $FIND($GET(superMe),Martin Groher), $EXACT(finished,open) ),
  • Segmentation, Centerline Extraction, and Graph Creation of Angiographic Vessels in 2D (SEP)
    _to be completed_ , ) $IF( $AND( $FIND($GET(superMe),Björn Schwerdtfeger, Simon Nestler), $EXACT(finished,open) ),
  • Systementwicklungsprojekt: Intermittent synchronisation of mobile devices using regional available communication channels (SEP)
    Nowadays in mobile scenarios different kind of data is generated locally on PDAs , mobile phones, and so on. Depending on the application it is necessary to synchronise or share this data with others and therefore a communication channel is needed. At the moment UMTS/GPRS is the favorite technique and it should be shown that it is possible to cope with limited coverage in specific situations. In order to demonstrate the usability a location based multiplayer game will be developed where it is essential to synchronise data intermittently. The game is called "Munich Hunt". It is an adoption of the well known board game “"Scotland Yard" and will be playable here in Munich as a location based multiplayer game. , ) $IF( $AND( $FIND($GET(superMe),Gaspar Delso), $EXACT(draft,open) ),
  • Optimization of a Positron Emission Tomography (PET) reconstruction algorithm (SEP)
    Iterative expectation-maximization algorithms are nowadays the most widespread choice of image reconstruction for tomographic medical scanners. However, due to the exceptional requirements in terms of memory and computation, these algorithms have often been implemented using certain simplifications in the underlying system model. Within the context of our MR/PET research project, our group is currently developing a modified version of the popular OSEM algorithm which does not rely on a simplified system model. This implementation should provide us with the required flexibility to perform an interesting set of experiments on dynamic, motion-compensated image reconstruction. The student will be in charge of analyzing the proposed reconstruction algorithm (C++) and writing an optimized version that minimizes convergence time. In a first stage the code must be studied and modified to reduce memory usage and improve cache reutilization. In a second stage, vectorization and/or GPU programming must be used to accelerate the algorithm. The resulting code will be benchmarked with real clinical data from PET/CT studies. , ) $IF( $AND( $FIND($GET(superMe),Martin Bauer), $EXACT(draft,open) ),
  • Augmented Reality Visualisation and Calibration of Medical Instruments (SEP)
    , ) $IF( $AND( $FIND($GET(superMe),Christian Wachinger), $EXACT(draft,open) ),
  • Phase-based Registration of Ultrasound Images (DA/MA/BA)
    The registration of ultrasound images is a complex task. There are several ways how to perform the registration. Feature- and intensity-based registration approaches have both their advantages and inconvenients. Recently, phase-based approaches have been published, which combine advantages from intensity- and feature-based approaches. In this work, we will implement a phase based registration method and compare its results to standard registration approaches. , ) $IF( $AND( $FIND($GET(superMe),Martin Groher), $EXACT(finished,open) ),
  • 2D / 3D Pose Estimation (SEP)
    "By pose we mean the transformation needed to map an object model from its inherent coordinate system into agreement with the sensory data."[1] In other words: given a world object in the object coordinate system (OCS) and a camera taking an image in the camera coordinate system (CCS) we want to determine a rotation and a translation from OCS to CCS by only using information from model and camera image.
    Determining the pose from 2D image and 3D model information is used in many fields of Computer Science, like robotics, Augmented Reality, etc. There are numerous ways to estimate the pose with, e.g. line or point correspondences, or even without any corresponding information given. , ) $IF( $AND( $FIND($GET(superMe),Martin Groher), $EXACT(draft,open) ),
  • Comparison of different volume renderers for 2D/3D registration (SEP)
    2D/3D or volume-to-image registration needs to compare data of different dimensions. By projecting the volume and comparing the resulting 2D image with the real 2D image using some similarity measure the quality of a registration can be evaluated. Then, the viewpoint is slightly changed, another projection is performed, and the two images are compared again, etc. The process stops once the best viewpoint (with highest similarity between projected and 2D image) is found. Different projection techniques can be used for this first step including purely software-based renderers modeling a raycasting through the volume and hardware-accelerated renderers using textures. This SEP compares these different techniques in terms of speed and accuracy , ) $IF( $AND( $FIND($GET(superMe),Dr. Asa MacWilliams), $EXACT(draft,open) ),
  • Smart Home Showroom (SEP)
    Das Smart Home Showroom bei Siemens Corporate Technology wird als voll ausgestattete intelligente Wohnung direkt neben normalen Büros und Labors eingerichtet. Es dient als zentrale Stelle für die Integration von aktuellen und zukünftigen Siemens-Technologien im häuslichen Umfeld, um neue Produkte und Dienstleistungen für Komfort, Sicherheit, Gesundheit, Unterhaltung und Umweltschutz zu ermöglichen. Die Ergebnisse verschiedener F&E-Projekte bei Corporate Technology werden in gemeinsamen Demonstratoren präsentiert. , ) $IF( $AND( $FIND($GET(superMe),Stefanie Demirci, Ali Bigdelou), $EXACT(finished,open) ),
  • Stent Graft Detection in 2D Xray Images (SEP)
    In the current clinical workflow of endovascular abdominal aortic repairs (EVAR) a stent graft is inserted via an introducer system through one femoral artery into the aneurysmatic aorta under 2D angiographic imaging. Due to the missing depth information in the X-ray visualization, it is highly difficult in particular for junior physicians to place the stent graft in the preoperatively defined position within the aorta. Therefore, methods for accurate stent graft recognition or segmentation in fluoroscopy images are highly required. , ) $IF( $AND( $FIND($GET(superMe),Tobias Sielhorst), $EXACT(finished,open) ),
  • Building a New Video See-Through AR System (SEP)
    Based on a video seethrough HMD (head mounted display) and an infra red camera for tracking a new AR system is build. The student has to care for intrinsic and extrinsic calibration of the cameras. , ) $IF( $AND( $FIND($GET(superMe),Pierre Georgel), $EXACT(draft,open) ),
  • High-Level User Interface for an Augmented Factory Navigator (SEP)
    In a project sponsored by Siemens Corporate Technology, we are developing a software to check the correctness of the building’s structure knowing the CAD model (3D model). Given pictures of the building, the software augments with the virtual model. You will need to create new and innovative user interactions which could be used on a Tablet PC and on a desktop computer, in order to navigate in this complex dataset. , ) $IF( $AND( $FIND($GET(superMe),Patrick Wucherer, Philipp Stefan), $EXACT(finished,open) ),
  • Vascular Simulator (Project)
    , ) $IF( $AND( $FIND($GET(superMe),Nicolas Padoy Tobias Blum), $EXACT(draft,open) ),
  • Design of a GUI for Definition and Manipulation of Hidden Markov Models (Bachelor Thesis)
    , )




B. Frisch, T. Maurer, A. Okur, T. Weineisen, , H. Kübler, N. Navab, HP Wester, M. Schwaiger, M. Eiber
Freehand SPECT for 111In-PSMA-I&T radioguided lymphadenectomy in prostate cancer patients
Society of Nucler Medicine and Medical Imaging Annual Meeting, Baltimore, USA, 2015 (bib)
T. Maurer, T. Weineisen, HP Wester, , A. Okur, G. Weirich, H. Kübler, M. Schwaiger, J. Gschwend, B. Frisch, M. Eiber
PSMA-radioguided surgery: Introducing molecular surgery in patients with recurrent prostate cancer
2015 Annual Meeting of the American Urological Association, New Orleans, USA, 2015 (bib)
T. Maurer, G. Weirich, , T. Weineisen, B. Frisch, A. Okur, N. Navab, M. Schwaiger, HP Wester, J. Gschwend, M. Eiber
PSMA-radioguided surgery for metastatic lymph nodes in prostate cancer
European Urology, in press, available online 6 May 2015 (bib)
T. Maurer, T. Weineisen, HP Wester, , A. Okur, G. Weirich, H. Kübler, M. Schwaiger, J. Gschwend, B. Frisch, M. Eiber
Introduction of PSMA-radioguided surgery in patients with recurrent prostate cancer: taking salvage lymphadenectomy to the next level?
Annual Congress of European Association of Urology (EAU), Madrid, March 2015 (bib)
C. Vetter, T. Lasser, A. Okur, N. Navab
1D-3D Registration for Intra-operative Nuclear Imaging in Radio-guided Surgery
IEEE Transactions on Medical Imaging 34(2):608-617, 2015 (bib)
T. Maurer, G. Weirich, T. Weineisen, HP Wester, B. Frisch, A. Okur, H. Kübler, M. Schwaiger, J. Gschwend, M. Eiber
Initial experience with PSMA-radioguided surgery in prostate cancer patients
3rd Meeting of the EAU Section of Urological Imaging, Lisbon, Portugal, 2014 (bib)
B. Frisch, M. Eiber, J. Gardiazabal, P. Matthies, T. Maurer, A. Okur, T. Lasser, N. Navab
Challenges for Intra-Operative SPECT
IEEE Nuclear Science Symposium and Medical Imaging Conference, Seattle, USA, November 2014 (bib)
A. Okur, C. Hennersperger, J.B. Runyan, J. Gardiazabal, M. Keicher, S. Paepke, T. Wendler, N. Navab
fhSPECT-US Guided Needle Biopsy of Sentinel Lymph Nodes in the Axilla: Is it Feasible?
Medical Image Computing and Computer-Assisted Intervention, MICCAI 2014, Lecture Notes in Computer Science Volume 8673, 2014, pp 577-584 (bib)
J. Gardiazabal, M. Esposito, P. Matthies, A. Okur, J. Vogel, S. Kraft, B. Frisch, T. Lasser, N. Navab
Towards personalized interventional SPECT-CT imaging
Proceedings of the 17th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Boston, USA, September 2014 (bib)
I. Einspieler, A.R. Novotny, A. Okur, M. Essler, M. E. Martignoni
First Experience With Image-guided Resection of Paraganglioma
Clinical Nuclear Medicine, Volume 39, Issue:8, August 2014. (bib)
R. Stauder, A. Okur, N. Navab
Detecting and Analyzing the Surgical Workflow to Aid Human and Robotic Scrub Nurses
The 7th Hamlyn Symposium on Medical Robotics, London, UK, July 2014 (bib)
A. Okur, R. Voigt, R. Stauder, N. Navab
Investigation of performance log files of freehand SPECT acquisitions for usage characteristics and surgical phase determination
The 7th Hamlyn Symposium on Medical Robotics, London, UK, July 2014 (bib)
P. Matthies, J. Gardiazabal, A. Okur, T. Lasser, N. Navab
Accuracy evaluation of interventional nuclear tomographic reconstruction using mini gamma cameras
The 7th Hamlyn Symposium on Medical Robotics, London, UK, July 2014 (bib)
R. Stauder, A. Okur, L. Peter, A. Schneider, M. Kranzfelder, H. Feußner, N. Navab
Random Forests for Phase Detection in Surgical Workflow Analysis
The 5th International Conference on Information Processing in Computer-Assisted Interventions (IPCAI), Fukuoka, Japan, June 2014 (bib)
P. Matthies, J. Gardiazabal, A. Okur, J. Vogel, T. Lasser, N. Navab
Mini Gamma Cameras for Intra-operative Nuclear Tomographic Reconstruction
Medical Image Analysis 18(8):1329-1336, 2014 (bib)
A. Okur, C. Gerngross, A. Schnelzer, A. Ehlerding, M. Keicher, S. Wiesner, S. Paepke, K. Scheidhauer, T. Wendler
First experience with fused ultrasound / freehand SPECT system for hybrid lymphatic mapping in breast cancer patients
52. Jahrestagung der Deutschen Gesellschaft fuer Nuklearmedizin, Hannover, Germany, Mar. 26 - 29, 2014. (bib)
A.L. Mihaljevic, A. Rieger, B. Belloni, R. Hein, A. Okur, K. Scheidhauer, T. Schuster, H. Friess, M. E. Martignoni
Transferring innovative freehand SPECT to the operating room: First experiences with sentinel lymph node biopsy in malignant melanoma
European Journal of Surgical Oncology (EJSO), Volume 40, Issue 1, January 2014. (bib)
P. Matthies, K. Sharma, A. Okur, J. Gardiazabal, J. Vogel, T. Lasser, N. Navab
First use of mini gamma cameras for intra-operative robotic SPECT reconstruction
Proceedings of the 16th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Nagoya, Japan, September 2013 (bib)
P. Matthies, A. Okur, T. Wendler, N. Navab, M. Friebe
Combination of intra-operative freehand SPECT imaging with MR images for guidance and navigation
IEEE Engineering in Medicine and Biology (EMBC), Osaka, Japan, July 2013. (bib)
J. Gardiazabal, T. Reichl, A. Okur, T. Lasser, N. Navab
First flexible robotic intra-operative nuclear imaging for image-guided surgery
Information Processing in Computer Assisted Interventions (IPCAI), Heidelberg, Germany, June 26, 2013 (bib)
C. Bluemel, A. Schnelzer, A. Okur, A. Ehlerding, S. Paepke, K. Scheidhauer, M. Kiechle
Freehand SPECT for image-guided sentinel lymph node biopsy in breast cancer
European Journal of Nuclear Medicine and Molecular Imaging.
The original publication is available online at
A. Okur, D. I. Shakir, P. Matthies, A. Hartl, M. Essler, S. I. Ziegler, T. Lasser, N. Navab
Freehand Tomographic Nuclear Imaging Using Tracked High-Energy Gamma Probes
Bildverarbeitung für die Medizin 2013 (BVM), Heidelberg, Germany, March 2013.
The original publication is available online at
A. Schnelzer, A. Ehlerding, C. Bluemel, A. Okur, K. Scheidhauer, S. Paepke, M. Kiechle
Showcase of Intraoperative 3D Imaging of the Sentinel Lymph Node in a Breast Cancer Patient using the New Freehand SPECT Technology
Breast Care 2012;7:484-486 (bib)
D. I. Shakir, A. Okur, A. Hartl, P. Matthies, M. Essler, S. I. Ziegler, T. Lasser, N. Navab
Towards Intra-operative PET for Head and Neck Cancer: Lymph Node Localization Using High-energy Probes
Proceedings of the 15th International Conference on Medical Image Computing and Computer Assisted Interventions (MICCAI), Nice, France, October 2012 (bib)
A. Bigdelou, R. Stauder, T. Benz, A. Okur, T. Blum, R. Ghotbi, N. Navab
HCI Design in the OR: A Gesturing Case-study
MICCAI 2012 Workshop on Modeling and Monitoring of Computer Assisted Interventions (M2CAI), Nice, France, October 2012 (bib)
I. Einspieler, A. Okur, A.R. Novotny, M. E. Martignoni, K. Scheidhauer
Case Report - Image-guided Resection of Paraganglioma
32nd Congress of the European Society of Surgical Oncology, Valencia, Spain, September 2012 (bib)
A. Rieger, J. Saeckl, R. Hein, A. Okur, T. Wendler, K. Scheidhauer, T. Schuster, H. Friess, M. E. Martignoni
Transferring Innovative Freehand SPECT to the Operating Room - First Experiences with Sentinel Lymphonodectomy in Malignant Melanoma
32nd Congress of the European Society of Surgical Oncology, Valencia, Spain, September 2012 (bib)
N. Navab, T. Blum, L. Wang, A. Okur, T. Wendler
First Deployments of Augmented Reality in Operating Rooms
IEEE Computer, Volume 45, Issue 7, pp. 48-55 (bib)
A. Bigdelou, A. Okur, M.-E. Hoffmann, B. Azizi, N. Navab
Towards systematic usability evaluations for the OR: an introduction to OR-Use framework
Information Processing in Computer Assisted Interventions (IPCAI), Pisa, Italy, June 27, 2012 (bib)
C. Bluemel, A. Schnelzer, A. Rieger, A. Ehlerding, A. Okur, C. Gerngross, M. E. Martignoni, K. Scheidhauer, M. Schwaiger
3D navigated (radio-guided) sentinel lymph node biopsy using freehand SPECT : final evaluation of Munich's pilot experience in the operating room
50. Jahrestagung der Deutschen Gesellschaft für Nuklearmedizin, Messe Bremen, Germany, April 2012 (bib)
A. Okur, A. Ahmadi, A. Bigdelou, T. Wendler, N. Navab
MR in OR: First analysis of AR/VR visualization in 100 intra-operative Freehand SPECT acquisitions
The 10th IEEE and ACM International Symposium on Mixed and Augmented Reality (ISMAR), Basel, Switzerland, Oct. 26 - 29, 2011. (bib)
C. Bluemel, A. Schnelzer, A. Ehlerding, A. Okur, K. Scheidhauer, M. Kiechle, M. Schwaiger
Evaluation of freehand SPECT in sentinel lymph node biopsy of breast cancer
Proceedings of the Annual Congress of the European Association of Nuclear Medicine (EANM), Birmingham, UK, October 2011 (bib)
A. Rieger, J. Saeckl, B. Belloni, R. Hein, A. Okur, K. Scheidhauer, T. Wendler, J. Traub, H. Friess, M. E. Martignoni
First Experiences with Navigated Radio-Guided Surgery Using Freehand SPECT
Case Reports in Oncology, August 2011 (bib)
A. Okur, C. Bluemel, A. Ehlerding, K. Scheidhauer, A. Schnelzer
Meme kanseri cerrahisinde freehandSPECT ile ilk tecrube: Aksiller sentinel lenf nodu biyopsisinde uc boyutlu navigasyon ve kalite guvencesi
XI. Ulusal Meme Hastaliklari Kongresi, Antalya, Turkey, Oct. 5 - 9, 2011. (bib)
C. Lapa, J. Saeckl, A. Rieger, C. Bluemel, A. Okur, T. Wendler, M. E. Martignoni, K. Scheidhauer
Investigating added value of freehand SPECT in sentinel node biopsy of melanomas
Proceedings of the Annual Meeting of the Society of Nuclear Medicine (SNM), San Antonio, Texas, USA, June 2011 (bib)
C. Bluemel, A. Ehlerding, C. Lapa, A. Okur, T. Wendler, A. Schnelzer, K. Scheidhauer
Improvements in sentinel node biopsy of breast cancer using freehand SPECT
Proceedings of the Annual Meeting of the Society of Nuclear Medicine (SNM), San Antonio, Texas, USA, June 2011 (bib)
M. C. Kreissl, A. Okur, M. Chen, A. Bartel, T. Wendler, K. Scheidhauer
Pilot study of freehand SPECT for lymphatic mapping in melanoma in upper body
Proceedings of the Annual Meeting of the Society of Nuclear Medicine (SNM), Salt Lake City, Utah, USA, June 2010 (bib)


Intra-operative Human Computer Interaction and Usability Evaluations

Intra-operative Human Computer Interaction and Usability Evaluations

Computerized medical systems play a vital role in the operating room, yet surgeons often face challenges when interacting with these systems during surgery. In this project we are aiming at analyzing and understanding the Operating Room specific aspects which affect the end user experience. Beside operating room specific usability evaluation approaches in this project we also try to improve the preliminary intra-operative user interaction methodologies.
Advanced Robotics for Multi-Modal Interventional Imaging (RoBildOR)

Advanced Robotics for Multi-Modal Interventional Imaging (RoBildOR)

This project aims at developing advanced methods for robotic image acquisitions, enabling more flexible, patient- and process-specific functional and anatomical imaging with the operating theater. Using robotic manipulations, co-registered and dynamic imaging can be provided to the surgeon, allowing for optimal implementation of preoperative planning. In particular, this projects is the first one developing concepts for intraoperative SPECT-CT, and introduces intraoperative robotic Ultrasound imaging based on CT trajectory planning, enabling registration with angiographic data. With distinguished partners from Bavarian industry, this project has a fundamental contribution in developing safe, reliable, flexible, and multi-modal imaging technologies for the operating room of the future.
Freehand SPECT for Sentinel Lymph Node Localization

Freehand SPECT for Sentinel Lymph Node Localization

Nuclear medicine imaging modalities assist commonly in surgical guidance given their functional nature. However, when used in the operating room they present limitations. Pre-operative tomographic 3D imaging can only serve as a vague guidance intra-operatively, due to movement, deformation and changes in anatomy since the time of imaging, while standard intra-operative nuclear measurements are limited to 1D or (in some cases) 2D images with no depth information. To resolve this problem we propose the synchronized acquisition of position, orientation and readings of gamma probes intra-operatively to reconstruct a 3D activity volume. In contrast to conventional emission tomography, here, in a first proof-of-concept, the reconstruction succeeds without requiring symmetry in the positions and angles of acquisition, which allows greater flexibility and thus opens doors towards 3D intra-operative nuclear imaging.
In-PSMA Radioguided Surgery

In-PSMA Radioguided Surgery

With the advent of 68Ga-HBED-PSMA PET hybrid imaging techniques, even small and atypical localized metastatic lesions of prostate cancer can be visualized. However, these lesions might not be easy to localize intraoperatively. The aim of project is to evaluate intraoperative detection of metastatic lesions using a gamma probe and freehand SPECT after injection of radioactive-labelled PSMA-ligands in correlation with postoperative histological findings.

Title: Dipl.-Inf. Univ.
Circumference of your head (in cm):  
Firstname: Aslı
Lastname: Okur Kuru
Picture: asli1b.jpg
Birthday: 1985/05/09
Nationality: Turkey
Languages: English, German, Turkish
Groups: Surgical Workflow, Reconstruction, Medical Imaging, Molecular Imaging, Computer-Aided Surgery, Medical Augmented Reality, IFL
Expertise: Surgical Workflow, Medical Imaging, Molecular Imaging, Computer-Aided Surgery, Medical Augmented Reality
Position: Scientific Staff
Status: Active
Emailbefore: okur
Room: MI 03.13.058
Telephone: +49 89 289 19401

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