@article {482, title = {Cellular correlates of gray matter volume changes in magnetic resonance morphometry identified by two-photon microscopy.}, journal = {Sci Rep}, volume = {11}, year = {2021}, month = {2021 Feb 19}, pages = {4234}, abstract = {

Magnetic resonance imaging (MRI) of the brain combined with voxel-based morphometry (VBM) revealed changes in gray matter volume (GMV) in various disorders. However, the cellular basis of GMV changes has remained largely unclear. We correlated changes in GMV with cellular metrics by imaging mice with MRI and two-photon in vivo microscopy at three time points within 12\ weeks, taking advantage of age-dependent changes in brain structure. Imaging fluorescent cell nuclei allowed inferences on (i) physical tissue volume as determined from reference spaces outlined by nuclei, (ii) cell density, (iii) the extent of cell clustering, and (iv) the volume of cell nuclei. Our data indicate that physical tissue volume alterations only account for 13.0\% of the variance in GMV change. However, when including comprehensive measurements of nucleus volume and cell density, 35.6\% of the GMV variance could be explained, highlighting the influence of distinct cellular mechanisms on VBM results.

}, issn = {2045-2322}, doi = {10.1038/s41598-021-83491-8}, author = {Asan, Livia and Falf{\'a}n-Melgoza, Claudia and Beretta, Carlo A and Sack, Markus and Lei Zheng and Weber-Fahr, Wolfgang and Kuner, Thomas and Knabbe, Johannes} } @conference {scherl_augmented_2020, title = {Augmented Reality in der Chirurgie der Ohrspeicheldr{\"u}se mittels HoloLensR}, booktitle = {Laryngo-Rhino-Otologie}, volume = {99}, year = {2020}, note = {ISSN: 0935-8943, 1438-8685 Issue: S 2 Journal Abbreviation: Laryngorhinootologie}, publisher = {{\textcopyright} Georg Thieme Verlag KG}, organization = {{\textcopyright} Georg Thieme Verlag KG}, abstract = {Thieme E-Books \& E-Journals}, keywords = {2005-23052020Abstract- und Posterband {\textendash} 91. Jahresversammlung der Deutschen Gesellschaft f{\"u}r HNO-Heilkunde, Bonn {\textendash} Welche Qualit{\"a}t macht den UnterschiedEstrel Congress Center BerlinDeutsche Gesellschaft f{\"u}r Hals-Nasen-Ohren-Heilkunde, BonnPr{\"a}sident: Prof. Dr. med. Andreas Dietz, Kopf- und Hals-Chirurgie e.V.}, doi = {10.1055/s-0040-1711515}, url = {http://www.thieme-connect.de/DOI/DOI?10.1055/s-0040-1711515}, author = {Scherl, C. and Stratemeier, J. and Hesser, J{\"u}rgen and Sch{\"o}nberg, S. and Lammert, A. and Servais, J{\'e}r{\^o}me and M{\"a}nnle, D. and Rotter, N.} } @article {scherl_augmented_2020-1, title = {Augmented reality with HoloLens in parotid surgery: how to assess and to improve accuracy}, journal = {European Archives of Oto-Rhino-Laryngology}, year = {2020}, abstract = {Augmented reality improves planning and execution of surgical procedures. The aim of this study was to evaluate the feasibility of a 3D augmented reality hologram in live parotic surgery. Another goal was to develop an accuracy measuring instrument and to determine the accuracy of the system.}, issn = {1434-4726}, doi = {10.1007/s00405-020-06351-7}, url = {https://doi.org/10.1007/s00405-020-06351-7}, author = {Scherl, Claudia and Stratemeier, Johanna and Karle, Celine and Rotter, Nicole and Hesser, J{\"u}rgen and Huber, Lena and Dias, Andre and Hoffmann, Oliver and Riffel, Philipp and Schoenberg, Stefan O. and Schell, Angela and Lammert, Anne and Affolter, Annette and M{\"a}nnle, David} } @article {jerg_diffuse_2020, title = {Diffuse domain method for needle insertion simulations}, journal = {International Journal for Numerical Methods in Biomedical Engineering}, volume = {36}, number = {9}, year = {2020}, note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cnm.3377}, pages = {e3377}, abstract = {We present a new strategy for needle insertion simulations without the necessity of meshing. A diffuse domain approach on a regular grid is applied to overcome the need for an explicit representation of organ boundaries. A phase field function captures the transition of tissue parameters and boundary conditions are imposed implicitly. Uncertainties of a volume segmentation are translated in the width of the phase field, an approach that is novel and overcomes the problem of defining an accurate segmentation boundary. We perform a convergence analysis of the diffuse elastic equation for decreasing phase field width, compare our results to deformation fields received from conforming mesh simulations and analyze the diffuse linear elastic equation for different widths of material interfaces. Then, the approach is applied to computed tomography data of a patient with liver tumors. A three-class U-Net is used to automatically generate tissue probability maps serving as phase field functions for the transition of elastic parameters between different tissues. The needle tissue interaction forces are approximated by the absolute gradient of a phase field function, which eliminates the need for explicit boundary parameterization and collision detection at the needle-tissue interface. The results show that the deformation field of the diffuse domain approach is comparable to the deformation of a conforming mesh simulation. Uncertainties of tissue boundaries are included in the model and the simulation can be directly performed on the automatically generated voxel-based probability maps. Thus, it is possible to perform easily implementable patient-specific elastomechanical simulations directly on voxel data.}, keywords = {diffuse domain, linear elastic equation, needle insertion, phase field, soft tissue}, issn = {2040-7947}, doi = {https://doi.org/10.1002/cnm.3377}, url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cnm.3377}, author = {Jerg, Katharina I. and Austerm{\"u}hl, Ren{\'e} Phillip and Roth, Karsten and Sundrup, Jonas Gro{\ss}e and Kanschat, Guido and Hesser, J{\"u}rgen W. and Wittmayer, Lisa} } @article {fotiadou2020end, title = {End-to-end trained CNN encoder-decoder network for fetal ECG signal denoising}, journal = {Physiological Measurement}, year = {2020}, publisher = {IOP Publishing}, author = {Fotiadou, Eleni and Konopczy{\'n}ski, Tomasz and Hesser, Juergen W and Vullings, Rik} } @article {ruder_feasibility_2020, title = {Feasibility of interstitial stepping-source electronic brachytherapy to locally inoperable tumors}, journal = {Journal of Contemporary Brachytherapy}, volume = {12}, number = {5}, year = {2020}, pages = {480{\textendash}486}, abstract = {Purpose Radiotherapy is the mainstay in the treatment of locally inoperable tumors. Interstitial electronic needle-based kilovoltage brachytherapy (EBT) could be an economic alternative to high-dose-rate (HDR) brachytherapy or permanent seed implantation (PSI). In this work, we evaluated if locally inoperable tumors treated with PSI at our institution may be suitable for EBT. Material and methods A total of 10 post-interventional computed tomography (CT) scans of patients, who received PSI and simulated stepping-source EBT applied with Intrabeam system and needle applicator were used. EBT treatment planning software with 3-dimensional image and projection of applicator were applied for designing trajectories and establishing dwell positions. Dwell position doses were summarized, and doses covering 90\% of the target volume (D90) achieved with stepping-source EBT were compared to those of PSI. Additionally, conformality of dose distributions and total irradiation time were assessed using conformation number (CN) or conformal index (COIN). Results In all patients, D90 of EBT exceeded the prescribed dose or D90 of PSI on average by 4.7\% or 21.3\% relative to the prescribed dose, respectively. Mean number of trajectories was 5.0 for EBT and 6.9 for PSI. Average CN/COIN for EBT was 0.69, with a mean irradiation time of 27.8 minutes for standardized dose of 13 Gy. Conclusions Stepping-source EBT allowed for a conformal treatment of inoperable interstitial tumors with similar D90. Fewer trajectories were required for EBT in majority of cases.}, issn = {1689-832X}, doi = {10.5114/jcb.2020.100381}, url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7701928/}, author = {Ruder, Arne Mathias and Inghelram, Laurens and Schneider, Frank and Sarria, Gustavo R. and Hesser, J{\"u}rgen and Bludau, Frederic and Obertacke, Udo and Wenz, Frederik and Abo-Madyan, Yasser and Giordano, Frank A.} } @mastersthesis {maur_geometrische_2020, title = {Geometrische Autokalibrierung f{\"u}r die dentale Volumentomographie}, year = {2020}, type = {phdPhD Thesis}, url = {http://www.ub.uni-heidelberg.de/archiv/28433}, author = {Maur, Susanne} } @article {mueller_imaging_2020, title = {Imaging and Characterization of Sustained Gadolinium Nanoparticle Release from Next Generation Radiotherapy Biomaterial}, journal = {Nanomaterials}, volume = {10}, number = {11}, year = {2020}, note = {Number: 11 Publisher: Multidisciplinary Digital Publishing Institute}, pages = {2249}, abstract = {Smart radiotherapy biomaterials (SRBs) present a new opportunity to enhance image-guided radiotherapy while replacing routinely used inert radiotherapy biomaterials like fiducials. In this study the potential of SRBs loaded with gadolinium-based nanoparticles (GdNPs) is investigated for magnetic resonance imaging (MRI) contrast. GdNP release from SRB is quantified and modelled for accurate prediction. SRBs were manufactured similar to fiducials, with a cylindrical shell consisting of poly(lactic-co-glycolic) acid (PLGA) and a core loaded with GdNPs. Magnetic resonance imaging (MRI) contrast was investigated at 7T in vitro (in agar) and in vivo in subcutaneous tumors grown with the LLC1 lung cancer cell line in C57/BL6 mice. GdNPs were quantified in-phantom and in tumor and their release was modelled by the Weibull distribution. Gd concentration was linearly fitted to the R1 relaxation rate with a detection limit of 0.004 mmol/L and high confidence level (R2 = 0.9843). GdNP loaded SRBs in tumor were clearly visible up to at least 14 days post-implantation. Signal decrease during this time showed GdNP release in vivo, which was calculated as 3.86 \± 0.34 \µg GdNPs release into the tumor. This study demonstrates potential and feasibility for SRBs with MRI-contrast, and sensitive GdNP quantification and release from SRBs in a preclinical animal model. The feasibility of monitoring nanoparticle (NP) concentration during treatment, allowing dynamic quantitative treatment planning, is also discussed.}, keywords = {biomaterials, gadolinium-based nanoparticles, Magnetic Resonance Imaging, quantitative magnetic resonance imaging}, doi = {10.3390/nano10112249}, url = {https://www.mdpi.com/2079-4991/10/11/2249}, author = {Mueller, Romy and Moreau, Michele and Yasmin-Karim, Sayeda and Protti, Andrea and Tillement, Olivier and Berbeco, Ross and Hesser, J{\"u}rgen and Ngwa, Wilfred} } @article {mueller_increased_2020, title = {Increased carcinoembryonic antigen expression on the surface of lung cancer cells using gold nanoparticles during radiotherapy}, journal = {Physica Medica}, volume = {76}, year = {2020}, pages = {236{\textendash}242}, abstract = {Purpose Tumor-associated antigens are a promising target of immunotherapy approaches for cancer treatments but rely on sufficient expression of the target antigen. This study investigates the expression of the carcinoembryonic antigen (CEA) on the surface of irradiated lung cancer cells in vitro using gold nanoparticles as radio-enhancer. Methods Human lung carcinoma cells A549 were irradiated and expression of CEA on the cell surface measured by flow cytometry 3~h, 24~h, and 72~h after irradiation to doses of 2~Gy, 6~Gy, 10~Gy, and 20~Gy in the presence or absence of 0.1~mg/ml or 0.5~mg/ml gold nanoparticles. CEA expression was measured as median fluorescent intensity and percentage of CEA-positive cells. Results An increase in CEA expression was observed with both increasing radiation dose and time. There was doubling in median fluorescent intensity 24~h after 20~Gy irradiation and 72~h after 6~Gy irradiation. Use of gold nanoparticles resulted in additional significant increase in CEA expression. Change in cell morphology included swelling of cells and increased internal complexity in accordance with change in CEA expression. Conclusions This study showed an increase in CEA expression on human lung carcinoma cells following irradiation. Increase in expression was observed with increasing radiation dose and in a time dependent manner up to 72~h post irradiation. The results further showed that gold nanoparticles can significantly increase CEA expression following radiotherapy.}, keywords = {Carcinoembryonic antigen, Nanoparticles, Neoantigens, Radiotherapy}, issn = {1120-1797}, doi = {10.1016/j.ejmp.2020.06.024}, url = {http://www.sciencedirect.com/science/article/pii/S1120179720301587}, author = {Mueller, Romy and Yasmin-Karim, Sayeda and DeCosmo, Kaylie and Vazquez-Pagan, Ana and Sridhar, Srinivas and Kozono, David and Hesser, Juergen and Ngwa, Wilfred} } @conference {konopczynski_instance_2020, title = {Instance Segmentation of Densely Packed Cells Using a Hybrid Model of U-Net and Mask R-CNN}, booktitle = {Artificial Intelligence and Soft Computing}, series = {Lecture Notes in Computer Science}, year = {2020}, pages = {626{\textendash}635}, publisher = {Springer International Publishing}, organization = {Springer International Publishing}, address = {Cham}, abstract = {In malignant tumors and microbial infections, cells are commonly growing under confinement due to rapid proliferation in limited space. Nonetheless, this effect is poorly documented despite influencing drug efficiency. Studying budding yeast grown in space-limited micro-environments is a great tool to investigate this effect, conditioned on a robust cell instance segmentation. Due to confinement, cells become densely packed, impairing traditional segmentation methods. To tackle that problem, we show the performance of Mask-RCNN based methods on our dataset of budding yeast populations in a space-limited environment. We compare a number of methods, which include the pure Mask R-CNN, the 1st and 2nd place solution of the 2018 Kaggle Data Science Bowl and a watershed ensemble variant of Mask R-CNN and U-Net. Additionally, we propose a Hybrid model that combines a semantic and an instance segmentation module in a sequential way. In the latter, the encoder-decoder architecture used for semantic segmentation produces a segmentation probability map, which is concatenated with the input image and then fed into the Mask R-CNN network in order to achieve the final instance segmentation result. Consequently, this model is able to efficiently share and reuse information at different levels between the two network modules. Our experiments demonstrate that the proposed model performs best and achieves a mean Average Precision (mAP) of 0.724 and a Dice coefficient of 0.9284 on our dataset.}, keywords = {Cell segmentation, Instance segmentation, Mask R-CNN, U-Net}, isbn = {978-3-030-61401-0}, doi = {10.1007/978-3-030-61401-0_58}, author = {Konopczy{\'n}ski, Tomasz and Heiman, Ron and Wo{\'z}nicki, Piotr and Gniewek, Pawe{\l} and Duvernoy, Marie-C{\'e}cilia and Hallatschek, Oskar and Hesser, J{\"u}rgen}, editor = {Rutkowski, Leszek and Scherer, Rafa{\l} and Korytkowski, Marcin and Pedrycz, Witold and Tadeusiewicz, Ryszard and Zurada, Jacek M.} } @article {sack2020interactive, title = {Interactive tool to create adjustable anatomical atlases for mouse brain imaging}, journal = {Magnetic Resonance Materials in Physics, Biology and Medicine}, year = {2020}, pages = {1{\textendash}5}, publisher = {Springer}, author = {Sack, Markus and Lei Zheng and Gass, Natalia and Ende, Gabriele and Sartorius, Alexander and Weber-Fahr, Wolfgang} } @article {rathore2020investigation, title = {Investigation on tomographic based NDT characterization of short glass fiber reinforced composites as obtained from micro injection molding}, journal = {Journal of Nondestructive Evaluation, Diagnostics and Prognostics of Engineering Systems}, year = {2020}, pages = {1{\textendash}15}, author = {Rathore, Jitendra Singh and Konopczy{\'n}ski, Tomasz and Hesser, J{\"u}rgen and Lucchetta, Giovanni and Carmignato, Simone} } @conference {roth_mask_2020, title = {Mask Mining for Improved Liver Lesion Segmentation}, booktitle = {2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI)}, year = {2020}, note = {ISSN: 1945-8452}, month = {apr}, pages = {943{\textendash}947}, abstract = {We propose a novel procedure to improve liver and lesion segmentation from CT scans for U-Net based models. Our method extends standard segmentation pipelines to focus on higher target recall or reduction of noisy false-positive predictions, boosting overall segmentation performance. To achieve this, we include segmentation errors into a new learning process appended to the main training setup, allowing the model to find features which explain away previous errors. We evaluate this on semantically distinct architectures: cascaded two-and three-dimensional as well as combined learning setups for multitask segmentation. Liver and lesion segmentation data are provided by the Liver Tumor Segmentation challenge (LiTS), with an increase in dice score of up to 2 points.}, keywords = {Biomedical imaging, combined learning setups, computerised tomography, CT scans, Data Mining, false-positive predictions, image segmentation, improved Liver lesion Segmentation, learning (artificial intelligence), learning process, lesion segmentation data, Lesions, Liver, Liver Lesion Segmentation, Liver Tumor Segmentation challenge, mask mining, medical image processing, Medical Imaging, multitask segmentation, Pipelines, segmentation errors, segmentation performance, standard segmentation pipelines, Three-dimensional displays, Training, tumours, U-Net, U-Net based models}, doi = {10.1109/ISBI45749.2020.9098460}, author = {Roth, K. and Hesser, J. and Konopczy{\'n}ski, T.} } @conference {fan_mi-net_2020, title = {MI-Net: A Deep Network for Non-linear Ultrasound Computed Tomography Reconstruction}, booktitle = {2020 IEEE International Ultrasonics Symposium (IUS)}, year = {2020}, note = {ISSN: 1948-5727}, month = {sep}, pages = {1{\textendash}3}, abstract = {Ultrasound Computed Tomography (USCT) is a new high resolution imaging method with high potential for breast cancer detection. USCT image reconstruction requires the iterative solution of a wave equation and its adjoint, being very time-consuming. To address this time consumption problem, a convolutional neural network with frequency pressure field as input is presented, outperforming classical iterative optimization strategies to solve the inverse problem. The Optical and Acoustic Breast Phantom Database (OA-Breast) is used to generate simulated USCT data using paraxial approximation forward model both for training and testing. Extensive experiments demonstrate that our neural network outperforms the classical strategies both in reconstruction time and quality.}, keywords = {acoustic tomography, Acoustics, biomedical ultrasonics, breast cancer detection, cancer, classical iterative optimization strategies, Computed tomography, convolutional neural nets, convolutional neural network, deep network, frequency pressure field, high-resolution imaging method, image reconstruction, image resolution, inverse problem, inverse problems, iterative methods, iterative solution, medical image processing, MI-net, non-linear forward model, nonlinear ultrasound computed tomography reconstruction, OA-Breast, Optical and Acoustic Breast Phantom Database, Phantoms, reconstruction time, Three-dimensional displays, time consumption problem, Time-frequency analysis, Training, ultrasonic imaging, USCT, USCT data, USCT image reconstruction, wave equation}, doi = {10.1109/IUS46767.2020.9251441}, author = {Fan, Y. and Wang, H. and Gemmeke, H. and Hesser, J.} } @article {cancers12071767, title = {Multiparametric MRI for Prostate Cancer Characterization: Combined Use of Radiomics Model with PI-RADS and Clinical Parameters}, journal = {Cancers}, volume = {12}, number = {7}, year = {2020}, pages = {1767}, abstract = {Radiomics is an emerging field of image analysis with potential applications in patient risk stratification. This study developed and evaluated machine learning models using quantitative radiomic features extracted from multiparametric magnetic resonance imaging (mpMRI) to detect and classify prostate cancer (PCa). In total, 191 patients that underwent prostatic mpMRI and combined targeted and systematic fusion biopsy were retrospectively included. Segmentations of the whole prostate glands and index lesions were performed manually in apparent diffusion coefficient (ADC) maps and T2-weighted MRI. Radiomic features were extracted from regions corresponding to the whole prostate gland and index lesion. The best performing combination of feature setup and classifier was selected to compare its predictive ability of the radiologist\’s evaluation (PI-RADS), mean ADC, prostate specific antigen density (PSAD) and digital rectal examination (DRE) using receiver operating characteristic (ROC) analysis. Models were evaluated using repeated 5-fold cross-validation and a separate independent test cohort. In the test cohort, an ensemble model combining a radiomics model, with models for PI-RADS, PSAD and DRE achieved high predictive AUCs for the differentiation of (i) malignant from benign prostatic lesions (AUC = 0.889) and of (ii) clinically significant (csPCa) from clinically insignificant PCa (cisPCa) (AUC = 0.844). Our combined model was numerically superior to PI-RADS for cancer detection (AUC = 0.779; p = 0.054) as well as for clinical significance prediction (AUC = 0.688; p = 0.209) and showed a significantly better performance compared to mADC for csPCa prediction (AUC = 0.571; p = 0.022). In our study, radiomics accurately characterizes prostatic index lesions and shows performance comparable to radiologists for PCa characterization. Quantitative image data represent a potential biomarker, which, when combined with PI-RADS, PSAD and DRE, predicts csPCa more accurately than mADC. Prognostic machine learning models could assist in csPCa detection and patient selection for MRI-guided biopsy.}, issn = {2072-6694}, doi = {10.3390/cancers12071767}, url = {https://www.mdpi.com/2072-6694/12/7/1767}, author = {Wo{\'z}nicki, Piotr and Westhoff, Niklas and Huber, Thomas and Riffel, Philipp and Froelich, Matthias F. and Gresser, Eva and von Hardenberg, Jost and M{\"u}hlberg, Alexander and Michel, Maurice Stephan and Schoenberg, Stefan O. and N{\"o}renberg, Dominik} } @mastersthesis {low_multiple_2020, title = {Multiple Retrieval Case-based Reasoning-Klinisches Entscheidungsunterst{\"u}tzungssystem auf unvollst{\"a}ndigen Datenbanken in Anwendung f{\"u}r das Tumorboard}, year = {2020}, type = {phdPhD Thesis}, url = {http://www.ub.uni-heidelberg.de/archiv/27788}, author = {L{\"o}w, Nikolas Immanuel} } @inbook {mueller_nanoparticle_2020, title = {Nanoparticle detection using photoacoustic imaging (PAI)}, booktitle = {Nanoparticle Enhanced Radiation Therapy}, series = {2053-2563}, year = {2020}, note = {Type: Book Chapter}, pages = {14{\textendash}1 to 14{\textendash}8}, publisher = {IOP Publishing}, organization = {IOP Publishing}, abstract = {Chapter 14 provides a review of photo-acoustic imaging methods for macroscopic mapping of nanoparticles in patients or animals.}, isbn = {978-0-7503-2396-3}, doi = {10.1088/978-0-7503-2396-3ch14}, url = {http://dx.doi.org/10.1088/978-0-7503-2396-3ch14}, author = {Mueller, Romy and Ngwa, Wilfred and Hesser, Juergen} } @inbook {hausmann_super-resolution_2020, title = {Super-resolution microscopy of nanogold-labelling}, booktitle = {Nanoparticle Enhanced Radiation Therapy}, series = {2053-2563}, year = {2020}, note = {Type: Book Chapter}, pages = {11{\textendash}1 to 11{\textendash}10}, publisher = {IOP Publishing}, organization = {IOP Publishing}, abstract = {Microscopic image-based modeling of nanoparticle distribution and the resulting biological damage are presented in chapter 11.}, isbn = {978-0-7503-2396-3}, doi = {10.1088/978-0-7503-2396-3ch11}, url = {http://dx.doi.org/10.1088/978-0-7503-2396-3ch11}, author = {Hausmann, Michael and Pilarczyk, G{\"o}tz and Maus, Emanuel and Hesser, J{\"u}rgen and Hildenbrand, Georg} } @article {albert_towards_2020, title = {Towards customizable thin-panel low-Z detector arrays: electrode design for increased spatial resolution ion chamber arrays}, journal = {Physics in Medicine \& Biology}, volume = {65}, number = {8}, year = {2020}, note = {Publisher: IOP Publishing}, pages = {08NT02}, abstract = {The purpose of the present development is to employ 3D printing to prototype an ion chamber array with a scalable design potentially allowing increased spatial resolution and a larger active area. An additional goal is to design and fabricate a custom size thin-panel detector array with low-Z components. As a proof of principle demonstration, a medium size detector array with 30 {\texttimes} 30 air-vented ion chambers was 3D-printed using PLA as frame for the electrodes. The active-area is 122 mm {\texttimes} 120 mm with 4 {\texttimes} 4 mm2 spatial resolution. External electrodes are cylindrical and made from conductive PLA. Internal electrodes are made from microwire. The array is symmetric with respect to the central plane and its thickness is 10 mm including build-up/-down plates of 2.5 mm thickness. Data acquisition is realized by biasing only selected chamber rows and reading only 30 chambers at a time. To test the device for potential clinical applications, 1D dose profiles and 2D dose maps with various square and irregular fields were measured. The overall agreement with the reference doses (film and treatment planning system) was satisfactory, but the measured dose differs in the penumbra region and in the field size dependence. Both of these features are related to the thin walls between neighboring ion chambers and different lateral phantom scatter in the detector panel vs homogeneous material. We demonstrated feasibility of radiation detector arrays with minimal number of readout channels and low-cost electronics. The acquisition scheme based on selected row or column {\textquoteleft}activation{\textquoteright} by bias voltage is not practical for 2D dosimetry but it allows for rapid turn-around when testing of custom arrays with the aid of multiple 1D dose profiles. Future progress in this area includes overcoming the limitations due high chamber packing ratio, which leads to the lateral scattering effects.}, issn = {0031-9155}, doi = {10.1088/1361-6560/ab8109}, url = {https://doi.org/10.1088/1361-6560/ab8109}, author = {Albert, Steffen and Brivio, Davide and Aldelaijan, Saad and Sajo, Erno and Hesser, J{\"u}rgen and Zygmanski, Piotr} } @booklet {gretz_transcutaneous_2020, title = {Transcutaneous organ function measurement}, number = {US10765354B2}, year = {2020}, month = {sep}, keywords = {detector, kit, light, sensor, sensor plaster}, url = {https://patents.google.com/patent/US10765354B2/en}, author = {Gretz, Norbert and Pill, Johannes and Schock-Kusch, Daniel and Walter, Thomas and Hesser, J{\"u}rgen and Sadick, Maliha and Eickemeyer, Felix and Hwang, Jae Hyung and Schildknecht, Christian and Watanabe, Soichi and Wach, Wolfgang and Rose, Thomas} } @article {zhao_ultrasound_2020, title = {Ultrasound transmission tomography image reconstruction with a fully convolutional neural network}, journal = {Physics in Medicine \& Biology}, volume = {65}, number = {23}, year = {2020}, note = {Publisher: IOP Publishing}, month = {nov}, pages = {235021}, abstract = {Image reconstruction of ultrasound computed tomography based on the wave equation is able to show much more structural details than simpler ray-based image reconstruction methods. However, to invert the wave-based forward model is computationally demanding. To address this problem, we develop an efficient fully learned image reconstruction method based on a convolutional neural network. The image is reconstructed via one forward propagation of the network given input sensor data, which is much faster than the reconstruction using conventional iterative optimization methods. To transform the ultrasound measured data in the sensor domain into the reconstructed image in the image domain, we apply multiple down-scaling and up-scaling convolutional units to efficiently increase the number of hidden layers with a large receptive and projective field that can cover all elements in inputs and outputs, respectively. For dataset generation, a paraxial approximation forward model is used to simulate ultrasound measurement data. The neural network is trained with a dataset derived from natural images in ImageNet and tested with a dataset derived from medical images in OA-Breast Phantom dataset. Test results show the superior efficiency of the proposed neural network to other reconstruction algorithms including popular neural networks. When compared with conventional iterative optimization algorithms, our neural network can reconstruct a 110 {\texttimes} 86 image more than 20 times faster on a CPU and 1000 times faster on a GPU with comparable image quality and is also more robust to noise.}, issn = {0031-9155}, doi = {10.1088/1361-6560/abb5c3}, url = {https://doi.org/10.1088/1361-6560/abb5c3}, author = {Zhao, Wenzhao and Wang, Hongjian and Gemmeke, Hartmut and Dongen, Koen W. A. van and Hopp, Torsten and Hesser, J{\"u}rgen} } @inbook {hesser_x-ray_2020, title = {X-ray based nanoparticle imaging}, booktitle = {Nanoparticle Enhanced Radiation Therapy}, series = {2053-2563}, year = {2020}, note = {Type: Book Chapter}, pages = {12{\textendash}1 to 12{\textendash}18}, publisher = {IOP Publishing}, organization = {IOP Publishing}, abstract = {Chapter 12 provides a review of x-ray imaging methods for macroscopic mapping of nanoparticles in patients or animals.}, isbn = {978-0-7503-2396-3}, doi = {10.1088/978-0-7503-2396-3ch12}, url = {http://dx.doi.org/10.1088/978-0-7503-2396-3ch12}, author = {Hesser, Juergen and Brivio, Davide} } @conference {wang2019accelerating, title = {Accelerating image reconstruction in ultrasound transmission tomography using L-BFGS algorithm}, booktitle = {Medical Imaging 2019: Ultrasonic Imaging and Tomography}, volume = {10955}, year = {2019}, pages = {109550B}, publisher = {International Society for Optics and Photonics}, organization = {International Society for Optics and Photonics}, author = {Wang, Hongjian and Gemmeke, Hartmut and Hopp, Torsten and Hesser, J{\"u}rgen} } @article {verma2019analysis, title = {Analysis of Impact of Humidity and Temperature on Excimer Laser Ablation of Polyethylene Terephthalate, Polymethylmethacrylate, and Porcine Corneal Tissue}, journal = {Lasers in surgery and medicine}, year = {2019}, author = {Verma, Shwetabh and Kehrer, Tobias and Hesser, J{\"u}rgen and Arba Mosquera, Samuel} } @article {roth2019boosting, title = {Boosting Liver and Lesion Segmentation from CT Scans by Mask Mining}, journal = {arXiv preprint arXiv:1908.05062}, year = {2019}, author = {Roth, Karsten and Hesser, J{\"u}rgen and Konopczy{\'n}ski, Tomasz} } @conference {maur2019cbct, title = {CBCT auto-calibration by contour registration}, booktitle = {Medical Imaging 2019: Physics of Medical Imaging}, volume = {10948}, year = {2019}, pages = {109481N}, publisher = {International Society for Optics and Photonics}, organization = {International Society for Optics and Photonics}, author = {Maur, Susanne and Stsepankou, Dzmitry and Hesser, J{\"u}rgen} } @article {jerg2019conditional, title = {Conditional random fields for phase-based lung feature tracking with ultra-low-dose x-rays}, journal = {Medical physics}, volume = {46}, number = {5}, year = {2019}, pages = {2337{\textendash}2346}, author = {Jerg, Katharina I and Lyatskaya, Yulia and Stratemeier, Johanna and Hesser, J{\"u}rgen W and Aschenbrenner, Katharina P} } @conference {fotiadou2019deep, title = {Deep convolutional encoder-decoder framework for fetal ECG signal denoising}, booktitle = {Computing in Cardiology (CinC 2019)}, year = {2019}, author = {Fotiadou, Eleni and Konopczy{\'n}ski, Tomasz and Hesser, J{\"u}rgen and Vullings, Rik} } @article {krammer2019evaluation, title = {Evaluation of a new image reconstruction method for digital breast tomosynthesis: effects on the visibility of breast lesions and breast density}, journal = {The British journal of radiology}, volume = {92}, number = {1103}, year = {2019}, pages = {20190345}, publisher = {The British Institute of Radiology.}, author = {Krammer, Julia and Zolotarev, Sergei and Hillman, Inge and Karalis, Konstantinos and Stsepankou, Dzmitry and Vengrinovich, Valeriy and Hesser, J{\"u}rgen and M. Svahn, Tony} } @article {krammer_evaluation_2019, title = {Evaluation of a new image reconstruction method for digital breast tomosynthesis: effects on the visibility of breast lesions and breast density}, journal = {The British Journal of Radiology}, volume = {92}, number = {1103}, year = {2019}, note = {Publisher: The British Institute of Radiology}, month = {sep}, pages = {20190345}, abstract = {{Objective:To compare image quality and breast density of two reconstruction methods, the widely-used filtered-back projection (FBP) reconstruction and the iterative heuristic Bayesian inference reconstruction (Bayesian inference reconstruction plus the method of total variation applied, HBI).Methods:Thirty-two clinical DBT data sets with malignant and benign findings}, issn = {0007-1285}, doi = {10.1259/bjr.20190345}, url = {https://www.birpublications.org/doi/full/10.1259/bjr.20190345}, author = {Krammer, Julia and Zolotarev, Sergei and Hillman, Inge and Karalis, Konstantinos and Stsepankou, Dzmitry and Vengrinovich, Valeriy and Hesser, J{\"u}rgen and M. Svahn, Tony} } @conference {wang2019gpu, title = {GPU Acceleration of Wave Based Transmission Tomography}, booktitle = {2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)}, year = {2019}, pages = {1753{\textendash}1756}, publisher = {IEEE}, organization = {IEEE}, author = {Wang, Hongjian and Huynh, Thai Hoa and Gemmeke, Hartmut and Hopp, Torsten and Hesser, Juergen} } @conference {ruder2019interstitial, title = {Interstitial electronic Stepping Source kV Brachytherapy: A Feasibility Study}, booktitle = {STRAHLENTHERAPIE UND ONKOLOGIE}, volume = {195}, year = {2019}, pages = {S197{\textendash}S197}, publisher = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, organization = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, author = {Ruder, AM and Inghelram, L and Schneider, F and Abo-Madyan, Y and Ehmann, M and Hesser, J and Wenz, F and Giordano, FA} } @article {roth2019liver, title = {Liver Lesion Segmentation with slice-wise 2D Tiramisu and Tversky loss function}, journal = {arXiv preprint arXiv:1905.03639}, year = {2019}, author = {Roth, Karsten and Konopczy{\'n}ski, Tomasz and Hesser, J{\"u}rgen} } @article {bilic2019liver, title = {The liver tumor segmentation benchmark (lits)}, journal = {arXiv preprint arXiv:1901.04056}, year = {2019}, author = {Bilic, Patrick and Christ, Patrick Ferdinand and Vorontsov, Eugene and Chlebus, Grzegorz and Chen, Hao and Dou, Qi and Fu, Chi-Wing and Han, Xiao and Heng, Pheng-Ann and Hesser, J{\"u}rgen and others} } @article {Kretz2018, title = {Modeling sphere dynamics in blood vessels for SIRT pre-planning {\textendash} To fathom the potential and limitations}, journal = {Z Med Phys.}, volume = {29}, year = {2019}, month = {02/2019}, pages = {15}, chapter = {5}, abstract = {

For selective internal radiation therapy (SIRT) the calculation of the 3D distribution of spheres based on individual blood flow properties is still an open and relevant research question. The purpose of this work is to develop and analyze a new treatment planning method for SIRT to calculate the absorbed dose distribution. For this intention, flow dynamics of the SIRT-spheres inside the blood vessels was simulated. The challenge is treatment planning solely using high-resolution imaging data available before treatment. The resolution required to reliably predict the sphere distribution and hence the dose was investigated. For this purpose, arteries of the liver were segmented from a contrast-enhanced angiographic CT. Due to the limited resolution of the given CT, smaller vessels were generated via a vessel model. A combined 1D/3D-flow simulation model was implemented to simulate the final 3D distribution of spheres and dose. Results were evaluated against experimental data from Y90-PET. Analysis showed that the resolution of the vessels within the angiographic CT of about 0.5mm should be improved to a limit of about 150μm to reach a reliable prediction.

}, keywords = {-PET, Blood flow simulation, Constrained constructive optimization, Smoothed particle hydrodynamics, Treatment planning, Vessel segmentation}, issn = {09393889}, doi = {10.1016/j.zemedi.2018.05.006}, url = {http://www.sciencedirect.com/science/article/pii/S0939388917301605}, author = {Kretz, D. and Hesser, J. and Glatting, G. and Diehl, S. and Wenz, F. and He, W. and Lei Zheng} } @article {Loew2019, title = {Multiple retrieval case-based reasoning for incomplete datasets}, journal = {Journal of Biomedical Informatics}, volume = {In Press, Accepted Manuscript}, year = {2019}, doi = {10.1016/j.jbi.2019.103127}, url = {https://doi.org/10.1016/j.jbi.2019.103127}, author = {Loew, Nikolas and Hesser, Juergen and Blessing, Manuel} } @conference {mueller2019nanoparticle, title = {Nanoparticle Drones to Label, Kill and Track Circulating Tumor Cells During Radiotherapy}, booktitle = {MEDICAL PHYSICS}, volume = {46}, number = {6}, year = {2019}, pages = {E191{\textendash}E191}, publisher = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, organization = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, author = {Mueller, R and Yasmin-Karim, S and Hesser, J and Ngwa, W} } @conference {ruder2019needle, title = {Needle-based stepping source electronic brachytherapy{\textendash}a feasibility study}, booktitle = {Radiotherapy and Oncology}, volume = {133}, year = {2019}, pages = {S1192{\textendash}S1193}, publisher = {ELSEVIER IRELAND LTD ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO {\textellipsis}}, organization = {ELSEVIER IRELAND LTD ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO {\textellipsis}}, author = {Ruder, Arne Mathias and Inghelram, Laurens and Schneider, Frank and Abo-Madyan, Yasser and Ehmann, Michael and Hesser, J{\"u}rgen and Wenz, Frederik and Giordano, Frank Anton} } @conference {mueller2019priming, title = {Priming the Abscopal Effect-A Lung Cancer Study}, booktitle = {MEDICAL PHYSICS}, volume = {46}, number = {6}, year = {2019}, pages = {E459{\textendash}E459}, publisher = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, organization = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, author = {Mueller, R and Yasmin-Karim, S and Moreau, M and Hesser, J and Ngwa, W} } @article {buergy2019prospective, title = {Prospective trial on telemonitoring of geriatric cancer patients using handheld devices}, journal = {Strahlentherapie und Onkologie}, year = {2019}, pages = {1{\textendash}8}, publisher = {Springer Berlin Heidelberg}, author = {Buergy, Daniel and Siefert, Victor and Neumaier, Christian and Ganslandt, Thomas and Sperk, Elena and Blessing, Manuel and Hesser, J{\"u}rgen and Welzel, Grit and Wenz, Frederik and Giordano, Frank Anton} } @article {Gass_2018, title = {Antagonism at the NR2B subunit of NMDA receptors induces increased connectivity of the prefrontal and subcortical regions regulating reward behavior}, journal = {Psychopharmacology}, year = {2018}, pages = {1{\textendash}14}, issn = {0033-3158, 1432-2072}, doi = {10.1007/s00213-017-4823-2}, url = {https://link.springer.com/article/10.1007/s00213-017-4823-2}, author = {Gass, Natalia and Becker, Robert and Sack, Markus and Schwarz, Adam J. and Reinwald, Jonathan and Cosa-Linan, Alejandro and Lei Zheng and Hohenberg, Christian Clemm von and Inta, Dragos and Meyer-Lindenberg, Andreas and Weber-Fahr, Wolfgang and Gass, Peter and Sartorius, Alexander} } @article {giordano2018app, title = {App-Based PRO Monitoring in Geriatric Patients Undergoing Radiation Therapy{\textendash}An Initial Analysis of the Prospective TeleGraPH Trial}, journal = {International Journal of Radiation Oncology{\textbullet} Biology{\textbullet} Physics}, volume = {102}, number = {3}, year = {2018}, pages = {e254}, publisher = {Elsevier}, author = {Giordano, FA and Siefert, V and Welzel, G and Blessing, M and Neumaier, C and Jahnke, L and Hesser, J and Wenz, F} } @article {Maur2018, title = {Auto-calibration by locally consistent contours for dental CBCT.}, journal = {Phys Med Biol.}, year = {2018}, month = {10/2018}, pages = {215018}, abstract = {The image quality of dental cone-beam computed tomography (CBCT) is limited by the accuracy of device calibration. Inaccurate calibration introduces errors in the reconstruction process, which may lead to severe artifacts in the reconstructed volume. Patient motion during scan acquisition induces similar effects. This paper introduces a novel auto-calibration approach calculating geometrical projection parameters from unknown patient geometry. We formulate consistency conditions linking the information of consecutive projection images and a regularization technique to prevent overall distortions. Implemented as a global optimization problem we present an efficient greedy optimizer as well. Our strategy turns out to be robust towards inaccurate initialization. As our method does not rely on consistency between projection data and tomography reconstruction it is robust towards reconstruction artifacts such as e.g. truncation. Applying our approach for auto-calibration shows a relative improvement of sharpness up to [Formula: see text] of in a standard dental CBCT setup. Evaluation is performed on digital reconstructed radiographs (DRRs) of a CT head-scan. In particular different motion types are considered and the number of anatomical structures used for calibration is varied to achieve an understanding of the behavior of the approach.}, author = {Maur, Susanne and Stsepankou, Dzmitry and Hesser, J.} } @conference {maur2018auto, title = {Auto-calibration for CBCT}, booktitle = {STRAHLENTHERAPIE UND ONKOLOGIE}, volume = {194}, year = {2018}, pages = {S151{\textendash}S152}, publisher = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, organization = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, author = {Maur, S and Stsepankou, D and Hesser, J} } @article {blessing2018automated, title = {Automated ultrafast kilovoltage{\textendash}megavoltage cone-beam CT for image guided radiotherapy of lung cancer: System description and real-time results}, journal = {Zeitschrift f{\"u}r Medizinische Physik}, volume = {28}, number = {2}, year = {2018}, pages = {110{\textendash}120}, publisher = {Elsevier}, author = {Blessing, Manuel and Arns, Anna and Wertz, Hansjoerg and Stsepankou, Dzmitry and Boda-Heggemann, Judit and Hesser, Juergen and Wenz, Frederik and Lohr, Frank} } @article {brehmer2018combined, title = {Combined stereotactic biopsy and stepping-source interstitial irradiation of glioblastoma multiforme.}, journal = {Journal of neurosurgical sciences}, volume = {62}, number = {2}, year = {2018}, pages = {214{\textendash}220}, author = {Brehmer, Stefanie and Guthier, CV and Clausen, Sven and Schneider, Frank and Schulte, Dirk-Michael and Benker, Matthias and Bludau, Frederic and Glatting, Gerhard and Marx, Alexander and Schmiedek, Peter and others} } @article {Blessing2018_4, title = {Finalized implementation of ultrafast kilovoltage-megavoltage CBCT for Image Guided Radiotherapy of lung cancer: system description and real-time results.}, journal = {Z Med Phys}, volume = {28}, year = {2018}, pages = {110-120}, doi = {10.1016/j.zemedi.2018.01.002}, url = {https://doi.org/10.1016/j.zemedi.2018.01.002}, author = {Blessing, M. and Arns, A. and Wertz , H. and Stsepankou , D. and Boda-Heggemann, J. and Hesser, J. and Wenz, F and Lohr , F.} } @conference {Konopczynski_2018, title = {Fully Convolutional Deep Network Architectures for Automatic Short Glass Fiber Semantic Segmentation from CT scans}, booktitle = {8th Conference on Industrial Computed Tomography (iCT 2018)}, year = {2018}, address = {Wels, Austria}, url = {http://www.ndt.net/article/ctc2018/papers/ICT2018_paper_id120.pdf}, author = {Konopczy{\'n}ski, Tomasz and Rathore, Danish and Rathore, Jitendra and Kr{\"o}ger, Thorben and Lei Zheng and Garbe, Christoph S. and Carmignato, Simone and Hesser, J{\"u}rgen} } @conference {shmarlouski_improvement_2018, title = {Improvement of human motion tracking by Kalman Filter}, booktitle = {STRAHLENTHERAPIE UND ONKOLOGIE}, volume = {194}, year = {2018}, pages = {S88{\textendash}S88}, publisher = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, organization = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, author = {Shmarlouski, A. and Huynh, T. H. and Hesser, J. and Lei Zheng} } @conference {mueller2018increased, title = {Increased Carcinoembryonic Antigen Expression On the Surface of Lung Cancer Cells During Radiotherapy}, booktitle = {MEDICAL PHYSICS}, volume = {45}, number = {6}, year = {2018}, pages = {E353{\textendash}E353}, publisher = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, organization = {WILEY 111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, author = {Mueller, R and Yasmin-Karim, S and Hesser, J and Ngwa, W} } @conference {konopczynski_instance_2018, title = {Instance Segmentation of Fibers from Low Resolution CT Scans via 3D Deep Embedding Learning}, booktitle = {The proceedings of BMVC 2018}, year = {2018}, address = {Northumbria University}, url = {http://bmvc2018.org/}, author = {Konopczynski, Tomasz K and Kr{\"o}ger, Thorben and Lei Zheng and Hesser, J{\"u}rgen} } @conference {426, title = {Interactive Tool to Create Adjustable Anatomical Atlases for Mouse Brain Imaging}, booktitle = {Proc. Intl. Soc. Mag. Reson. Med. 26}, year = {2018}, url = {http://indexsmart.mirasmart.com/ISMRM2018/PDFfiles/2843.html}, author = {Sack, Markus and Lei Zheng and Gass, Natalia and Sartorius, Alexander and Ende, Gabriele and Weber-Fahr, Wolfgang} } @article {Blessing_2018_2, title = {Intra-breath-hold residual motion of image-guided DIBH liver-SBRT: An estimation by ultrasound-based monitoring correlated with diaphragm position in CBCT}, journal = {Radiotherapy and Oncology}, volume = {129}, year = {2018}, month = {12/2018}, pages = {441-448}, author = {Vogel,L and Sihono, DSK and Weiss, C and Lohr, F and Stieler , F. and Wertz , H. and von Swietochowsky, S and Simeonova-Chergou, A and Wenz, F and Boda-Heggemann, J and Blessing, M.} } @article {verma2018method, title = {Method for assessing the impact of residual roughness after corneal ablation in polychromatic vision}, journal = {Investigative Ophthalmology \& Visual Science}, volume = {59}, number = {9}, year = {2018}, pages = {5806{\textendash}5806}, publisher = {The Association for Research in Vision and Ophthalmology}, author = {Verma, Shwetabh and Hesser, Juergen and Mosquera, Samuel Arba} } @article {430, title = {MIRACUM: Medical Informatics in Research and Care in University Medicine.}, journal = {Methods Inf Med.}, volume = {57}, year = {2018}, month = {07/2018}, pages = {e91}, chapter = {e82}, doi = {10.3414/ME17-02-0025}, author = {Prokosch, HU and Till, A. and Bernarding, J. and Binder, H. and Boeker, M. and Boerries, M. and Daumke, P. and Ganslandt, T. and Hesser, J. and H{\"o}ning, G. and Neumaier, M. and Marquardt, K. and Renz, H. and Rothk{\"o}tter, H-J. and Schade-Brittinger, C. and Schm{\"u}cker, P. and Sch{\"u}ttler, J. and Sedlmayr, M. and Serve, H. and Sohrabi, K. and Storf, H.} } @conference {wang2018multigrid, title = {Multigrid Method for Solving Linearized Systems in Ultrasound Transmission Tomography}, booktitle = {2018 IEEE Nuclear Science Symposium and Medical Imaging Conference Proceedings (NSS/MIC)}, year = {2018}, pages = {1{\textendash}3}, publisher = {IEEE}, organization = {IEEE}, author = {Wang, Hongjian and Gemmeke, Hartmut and Hopp, Torsten and Hesser, J{\"u}rgen} } @article {Blessing2018_3, title = {An offline technique to evaluate residual motion of the diaphragm during deep inspiratory breath-hold from cone-beam CT datasets}, journal = {Strahlentherapie und Onkologie}, volume = {194}, year = {2018}, month = {09/2018}, pages = {855{\textendash}860}, doi = {10.1007/s00066-018-1313-3}, url = {https://doi.org/10.1007/s00066-018-1313-3}, author = {Blessing, M. and Hofmann, J. and Vogel,L and Boda-Heggemann, J. and Lohr , F. and Wenz, F and Stieler , F. and Simeonova-Chergou, A.} } @article {Glodeck_2018, title = {Potential of metric homotopy between intensity and geometry information for multi-modal 3D registration}, journal = {Z Med Phys.}, volume = {28}, year = {2018}, month = {12/2018}, pages = {334}, chapter = {325}, abstract = {

This paper focuses on a novel strategy increasing robustness with respect to local optima when using Mutual Information (MI) in multi-modal image registration. This is realized by integrating additional geometry information in the cost function. Hereby, the main innovation is a generalization of multi-metric registration approaches by means of a metric homotopy. Particularly we realize a method which automatically determines the parameters of the metric homotopy. To construct the cost function independent of the choice of the optimizer, the weighting is defined as a function of one of the metrics instead of optimizer steps. In addition, a differentiable cost function is developed. In comparison to the commonly used technique to process an intensity based registration on different resolutions, the proposed method is three times faster with unchanged accuracy. It is also shown that in the presence of large landmark errors the proposed method outperforms an approach in accuracy in which both similarity functionals are applied one after the other. The method is evaluated on 3D multi-modal human brain data sets from the Retrospective Image Registration Evaluation Project (RIRE). The evaluation is performed using the evaluation website of the RIRE project to make the registration results of the proposed method easily comparable to other methods. Therefore, the presented results are also available online on the RIRE project page.

}, issn = {0939-3889}, doi = {10.1016/j.zemedi.2018.01.004}, url = {https://www.sciencedirect.com/science/article/pii/S0939388917301435}, author = {Glodeck, Daniel and Hesser, J{\"u}rgen and Lei Zheng} } @article {prabhune2018p, title = {P-PIF: a ProvONE provenance interoperability framework for analyzing heterogeneous workflow specifications and provenance traces}, journal = {Distributed and Parallel Databases}, volume = {36}, number = {1}, year = {2018}, pages = {219{\textendash}264}, publisher = {Springer}, author = {Prabhune, Ajinkya and Zweig, Aaron and Stotzka, Rainer and Hesser, J{\"u}rgen and Gertz, Michael} } @article {Arand2018, title = {Quantitative morphological analysis and digital modeling of polydisperse anisotropic carbon foam}, journal = {Carbon}, volume = {136}, year = {2018}, month = {2018}, pages = {11-20}, chapter = {11}, issn = {0008-6223}, doi = {https://doi.org/10.1016/j.carbon.2018.04.049}, url = {http://www.sciencedirect.com/science/article/pii/S000862231830410X}, author = {Frederick Arand and J{\"u}rgen Hesser} } @conference {zheng_robust_2018, title = {Robust estimation of correspondences for one-shot 3D surface reconstruction}, booktitle = {STRAHLENTHERAPIE UND ONKOLOGIE}, volume = {194}, year = {2018}, pages = {S87{\textendash}S88}, publisher = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, organization = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, author = {Lei Zheng and Shmarlouski, A. and Huynh, T. H. and Hesser, J.} } @article {424, title = {Telemedizinische Erfassung von {\quotedblbase}patient-reported outcomes{\textquotedblleft}}, journal = {Forum}, volume = {33}, year = {2018}, month = {04/2018}, pages = {94{\textendash}100}, doi = {10.1007/s12312-018-0393-4}, url = {https://doi.org/10.1007/s12312-018-0393-4}, author = {Siefert, V. and Welzel, G. and Blessing, M. and Jahnke , L. and Hesser, J. and Wenz, F and Giordano, FA} } @booklet {gretz2018transcutaneous, title = {Transcutaneous organ function measurement}, year = {2018}, note = {US Patent App. 15/861,299}, publisher = {Google Patents}, author = {Gretz, Norbert and Pill, Johannes and Schock-Kusch, Daniel and Walter, Thomas and Hesser, J{\"u}rgen and Sadick, Maliha and Eickemeyer, Felix and Hwang, Jae Hyung and Schildknecht, Christian and Watanabe, Soichi and others} } @conference {wang2018ultrasound, title = {Ultrasound Image Reconstruction Using Nesterov{\textquoteright}s Accelerated Gradient}, booktitle = {2018 IEEE Nuclear Science Symposium and Medical Imaging Conference Proceedings (NSS/MIC)}, year = {2018}, pages = {1{\textendash}3}, publisher = {IEEE}, organization = {IEEE}, author = {Wang, Hongjian and Dalkilic, Burak and Gemmeke, Hartmut and Hopp, Torsten and Hesser, J{\"u}rgen} } @conference {wang2018usct, title = {USCT image reconstruction: acceleration using Gauss-Newton preconditioned conjugate gradient}, booktitle = {Proceedings of the International Workshop on Medical Ultrasound Tomography}, year = {2018}, pages = {41{\textendash}52}, publisher = {KIT Scientific Publishing}, organization = {KIT Scientific Publishing}, author = {Wang, H and Gemmeke, H and Hopp, T and Hesser, J} } @conference {wang2018usct, title = {USCT imaging acceleration using preconditioned conjugate gradient and multigrid methods}, booktitle = {STRAHLENTHERAPIE UND ONKOLOGIE}, volume = {194}, year = {2018}, pages = {S153{\textendash}S154}, publisher = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, organization = {SPRINGER HEIDELBERG TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY}, author = {Wang, H and Gemmeke, H and Hopp, T and Hesser, J} } @article {429, title = {Using immunotherapy to boost the abscopal effect. }, journal = {Nature Reviews Cancer}, volume = {18}, year = {2018}, month = {05/2018}, pages = {322}, chapter = {313}, doi = {10.1038/nrc.2018.6.}, url = {https://www.ncbi.nlm.nih.gov/pubmed/29449659}, author = {Ngwa, W and Irabor, O. C. and Schoenfeld, D. and Hesser J. and Demaria, S. and Formenti, S. C.} } @conference {Cremer2017, title = {3D {\textquotedblright}COLOR{\textquotedblright} SIM FOR OPHTHALMOLOGIC RESEARCH}, booktitle = {Focus On Microscopy}, year = {2017}, month = {01/2017}, abstract = {

While super-resolution-microscopy (SRM) techniques have become widely available, application in the clinical context is still mostly restricted to cultivated cells. Here, we present the application of Structured Illumination Microscopy (SIM) for clinical research on extracted tissues as well as quantitative analysis of over 300 human RPE cells and their granules (intracellular particles) regarding a correlation to age related macular degeneration. So far we have shown that in human retinal tissue, SIM improves the resolution and the contrast. [1-3] In contrast to other SRM approaches, SIM can be used without modification of the specimen in all cases where conventional wide field fluorescence microscopy approaches can be applied. Since autofluorescence is a characteristic of several chorioretinal conditions, SIM offers the potential for further clinical imaging at illumination intensities that allow application to living patients. We present quantitative data, resulting from over 300 human RPE cells and over 25.000 single intracellular particles. Further we will show, that by using 3D SIM, not only automated segmentation of these granules will become statistically reliable, but also the quantitative analysis on granule density per cell for different donor ages and regions. In contrast to other SRM methods, SIM not only improves resolution, but by using autofluorescence, it is able to use excitation/emission spectra (in our case up to 3 spectral channels) to obtain information on the composition of the particles. All investigations were in accordance to the declaration of Helsinki on good clinical practice.

}, author = {Schock, Florian and Best, Gerrit and Celik, Nil and Wang, Yangyi and Bakulina, Alena and Sel, Saadettin and Birk, Udo and Heintzmann, Rainer and Hesser, J. and Dithmar, S. and Cremer , Christoph} } @article {Arand2017, title = {Accurate and efficient maximal ball algorithm for pore network extraction}, journal = {Computers \& Geosciences}, volume = {101}, year = {2017}, pages = {28{\textendash}37}, abstract = {

The maximal ball (MB) algorithm is a well established method for the morphological analysis of porous media. It extracts a network of pores and throats from volumetric data. This paper describes structural modifications to the algorithm, while the basic concepts are preserved. Substantial improvements to accuracy and efficiency are achieved as follows: First, all calculations are performed on a subvoxel accurate distance field, and no approximations to discretize balls are made. Second, data structures are simplified to keep memory usage low and improve algorithmic speed. Third, small and reasonable adjustments increase speed significantly. In volumes with high porosity, memory usage is improved compared to classic MB algorithms. Furthermore, processing is accelerated more than three times. Finally, the modified MB algorithm is verified by extracting several network properties from reference as well as real data sets. Runtimes are measured and compared to literature.

}, issn = {00983004}, doi = {10.1016/j.cageo.2017.01.004}, author = {Arand, Frederick and Hesser, J{\"u}rgen} } @article {Aschenbrenner2017, title = {Feasibility of using single photon counting X-ray for lung tumor position estimation based on 4D-CT}, journal = {Zeitschrift f{\"u}r Medizinische Physik}, volume = {27}, year = {2017}, month = {sep}, pages = {243{\textendash}254}, abstract = {

PURPOSE In stereotactic body radiation therapy of lung tumors, reliable position estimation of the tumor is necessary in order to minimize normal tissue complication rate. While kV X-ray imaging is frequently used, continuous application during radiotherapy sessions is often not possible due to concerns about the additional dose. Thus, ultra low-dose (ULD) kV X-ray imaging based on a single photon counting detector is suggested. This paper addresses the lower limit of photons to locate the tumor reliably with an accuracy in the range of state-of-the-art methods, i.e. a few millimeters. METHOD 18 patient cases with four dimensional CT (4D-CT), which serves as a-priori information, are included in the study. ULD cone beam projections are simulated from the 4D-CTs including Poisson noise. The projections from the breathing phases which correspond to different tumor positions are compared to the ULD projection by means of Poisson log-likelihood (PML) and correlation coefficient (CC), and template matching under these metrics. RESULTS The results indicate that in full thorax imaging five photons per pixel suffice for a standard deviation in tumor positions of less than half a breathing phase. Around 50 photons per pixel are needed to achieve this accuracy with the field of view restricted to the tumor region. Compared to CC, PML tends to perform better for low photon counts and shifts in patient setup. Template matching only improves the position estimation in high photon counts. The quality of the reconstruction is independent of the projection angle. CONCLUSIONS The accuracy of the proposed ULD single photon counting system is in the range of a few millimeters and therefore comparable to state-of-the-art tumor tracking methods. At the same time, a reduction in photons per pixel by three to four orders of magnitude relative to commercial systems with flatpanel detectors can be achieved. This enables continuous kV image-based position estimation during all fractions since the additional dose to the patient is negligible.

}, keywords = {Correlation coefficient, Korrelationskoeffizient, KV imaging, kV-Bildgebung, Lung tumor, Lungentumoren, Maximum Likelihood, Poisson distribution, Poisson-Verteilung, Template Matching, Ultra low dose, Ultra-niedrig-Dosis}, issn = {09393889}, doi = {10.1016/j.zemedi.2017.05.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/28595774 http://linkinghub.elsevier.com/retrieve/pii/S0939388917300843}, author = {Aschenbrenner, Katharina P. and Guthier, Christian V. and Lyatskaya, Yulia and Boda-Heggemann, Judit and Wenz, Frederik and Hesser, J{\"u}rgen W.} } @conference {healthinf17, title = {Managing Provenance for Medical Datasets - An Example Case for Documenting the Workflow for Image Processing}, booktitle = {Proceedings of the 10th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 5: HEALTHINF, (BIOSTEC 2017)}, year = {2017}, isbn = {978-989-758-213-4}, url = {http://www.scitepress.org/DigitalLibrary/PublicationsDetail.aspx?ID=l\%2f670ZzrVBo\%3d\&t=1}, author = {Ajinkya Prabhune and Rainer Stotzka and Michael Gertz and Lei Zheng and J{\"u}rgen Hesser} } @article {Prabhune2017, title = {MetaStore: an adaptive metadata management framework for heterogeneous metadata models}, journal = {Distributed and Parallel Databases}, year = {2017}, month = {oct}, pages = {1{\textendash}42}, issn = {0926-8782}, doi = {10.1007/s10619-017-7210-4}, url = {http://link.springer.com/10.1007/s10619-017-7210-4}, author = {Prabhune, Ajinkya and Stotzka, Rainer and Sakharkar, Vaibhav and Hesser, J{\"u}rgen and Gertz, Michael} } @conference {407, title = {Method to evaluate the impact of residual roughness after corneal ablation in perception and vision}, booktitle = {European Association for Vision and Eye Research}, year = {2017}, month = {09/2017}, abstract = {

Purpose: Theoretical models have also been proposed for achieving smoothness with laser systems used for ablation processes (Invest Ophthalmol Vis Sci. 2017;58:2021{\textendash}2037). However, methods do not exist for evaluating the impact of the residual roughness after corneal ablation, in perception and vision. We propose a computational method to convert wavefront aberrations with a varying degree of roughness, to a description of the human visual optical point spread function (PSF), to calculate the polychromatic retinal image.

Methods: A simulation program was developed in SCILAB (Scilab Enterprises, Versailles, France). Patient specific information like Zernike Coefficients (up to 8th Zernike order) and Pupil diameter were used to calculate the wavefront including chromatic compensation for the Red, Green and \ Blue channels (Optom Vis Sci 2003;80:6{\textendash}14). A random noise was added to the calculated wavefront to simulate the roughness in the cornea within user-defined limits. PSF of the eye was calculated for the Red, Green and Blue channels and the retinal image was determined, as a weighted combination of different color channels. Different corneal roughness conditions (Zero, Typical (X {\textmu}m) and High Roughness (X {\textmu}m)) were compared in terms of Michelson Contrast (MC) and Modulation Transfer Function (MTF).

Results: The simulated roughness in ablation reduced the perceived retinal image quality drastically (Zero Roughness MC = X, MTF = X; Typical Roughness MC = X, MTF = X; and High Roughness MC = X, MTF = X)\ 

Conclusion: The proposed model can be used for quantifying the impact of residual roughness in ablation processes at relatively low cost. This method can help compare different refractive laser platforms in terms of their associated roughness in ablation, indirectly improving the quality of results after Laser vision correction.\ 

}, keywords = {Verma2017_2}, author = {Verma, S and Hesser, J. and Arba-Mosquera, Samuel} } @article {Verma2017, title = {Optimum Laser Beam Characteristics for Achieving Smoother Ablations in Laser Vision Correction}, journal = {Investigative Opthalmology {\&} Visual Science}, volume = {58}, year = {2017}, month = {apr}, pages = {2021}, abstract = {

Purpose Controversial opinions exist regarding optimum laser beam characteristics for achieving smoother ablations in laser-based vision correction. The purpose of the study was to outline a rigorous simulation model for simulating shot-by-shot ablation process. The impact of laser beam characteristics like super Gaussian order, truncation radius, spot geometry, spot overlap, and lattice geometry were tested on ablation smoothness. Methods Given the super Gaussian order, the theoretical beam profile was determined following Lambert-Beer model. The intensity beam profile originating from an excimer laser was measured with a beam profiler camera. For both, the measured and theoretical beam profiles, two spot geometries (round and square spots) were considered, and two types of lattices (reticular and triangular) were simulated with varying spot overlaps and ablated material (cornea or polymethylmethacrylate [PMMA]). The roughness in ablation was determined by the root-mean-square per square root of layer depth. Results Truncating the beam profile increases the roughness in ablation, Gaussian profiles theoretically result in smoother ablations, round spot geometries produce lower roughness in ablation compared to square geometry, triangular lattices theoretically produce lower roughness in ablation compared to the reticular lattice, theoretically modeled beam profiles show lower roughness in ablation compared to the measured beam profile, and the simulated roughness in ablation on PMMA tends to be lower than on human cornea. For given input parameters, proper optimum parameters for minimizing the roughness have been found. Conclusions Theoretically, the proposed model can be used for achieving smoothness with laser systems used for ablation processes at relatively low cost. This model may improve the quality of results and could be directly applied for improving postoperative surface quality.

}, issn = {1552-5783}, doi = {10.1167/iovs.16-21025}, url = {http://www.ncbi.nlm.nih.gov/pubmed/28384723 http://iovs.arvojournals.org/article.aspx?doi=10.1167/iovs.16-21025}, author = {Verma, Shwetabh and Hesser, Juergen and Arba-Mosquera, Samuel} } @article {Arns2017, title = {Phantom-based evaluation of dose exposure of ultrafast combined kV-MV-CBCT towards clinical implementation for IGRT of lung cancer}, journal = {PLOS ONE}, volume = {12}, year = {2017}, month = {nov}, pages = {e0187710}, abstract = {

PURPOSE Combined ultrafast 90{\textdegree}+90{\textdegree} kV-MV-CBCT within single breath-hold of 15s has high clinical potential for accelerating imaging for lung cancer patients treated with deep inspiration breath-hold (DIBH). For clinical feasibility of kV-MV-CBCT, dose exposure has to be small compared to prescribed dose. In this study, kV-MV dose output is evaluated and compared to clinically-established kV-CBCT. METHODS Accurate dose calibration was performed for kV and MV energy; beam quality was determined. For direct comparison of MV and kV dose output, relative biological effectiveness (RBE) was considered. CT dose index (CTDI) was determined and measurements in various representative locations of an inhomogeneous thorax phantom were performed to simulate the patient situation. RESULTS A measured dose of 20.5mGE (Gray-equivalent) in the target region was comparable to kV-CBCT (31.2mGy for widely-used, and 9.1mGy for latest available preset), whereas kV-MV spared healthy tissue and reduced dose to 6.6mGE (30{\%}) due to asymmetric dose distribution. The measured weighted CTDI of 12mGE for kV-MV lay in between both clinical presets. CONCLUSIONS Dosimetric properties were in agreement with established imaging techniques, whereas exposure to healthy tissue was reduced. By reducing the imaging time to a single breath-hold of 15s, ultrafast combined kV-MV CBCT shortens patient time at the treatment couch and thus improves patient comfort. It is therefore usable for imaging of hypofractionated lung DIBH patients.

}, issn = {1932-6203}, doi = {10.1371/journal.pone.0187710}, url = {http://www.ncbi.nlm.nih.gov/pubmed/29125857 http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5681289 http://dx.plos.org/10.1371/journal.pone.0187710}, author = {Arns, Anna and Blessing, Manuel and Fleckenstein, Jens and Stsepankou, Dzmitry and Boda-Heggemann, Judit and Hesser, Juergen and Lohr, Frank and Wenz, Frederik and Wertz, Hansjoerg}, editor = {Zhang, Qinghui} } @article {Alnewaini2017, title = {Realtime, ray casting based scatter dose estimation for c-arm x-ray system}, journal = {Journal of Applied Clinical Medical Physics}, year = {2017}, keywords = {C-arm acquisition, Geant4 simulation, radiation measurements, scatter radiation}, issn = {1526-9914}, doi = {10.1002/ACM2.12036}, author = {Alnewaini, Zaid and Langer, Eric and Schaber, Philipp and David, Matthias and Kretz, Dominik and Steil, Volker and Hesser, J{\"u}rgen} } @conference {Konopczynski_2017, title = {Reference Setup for Quantitative Comparison of Segmentation Techniques for Short Glass Fiber CT Data}, booktitle = {7th Conference on Industrial Computed Tomography (iCT 2017)}, year = {2017}, address = {Leuven, Belgium}, url = {http://www.ndt.net/events/iCT2017/app/content/Paper/26_Konopczy-ski_Rev4.pdf}, author = {Konopczy{\'n}ski, Tomasz and Rathore, Jitendra and Kr{\"o}ger, Thorben and Lei Zheng and Garbe, Christoph S. and Carmignato, Simone and Hesser, J{\"u}rgen} } @conference {Hongjian2017, title = {USCT Image Reconstruction: Acceleration using Gauss-Newton Preconditioned Conjugate Gradient}, booktitle = {International Workshop on Medical Ultrasound Tomography}, year = {2017}, month = {11/2017}, address = {Speyer, Germany}, abstract = {

In this paper, we solve the inverse problem of image reconstruction in ultrasound transmission tomography, proposing a two-level strategy with an outer and an inner loop.\ At each iteration of the outer loop, the system is linearized and this linear subproblem is\ solved in the inner loop with a preconditioned conjugate gradient. A standard Cholesky\ preconditioning method based on the system matrix is compared with a matrix-free Quasi-Newton\ update approach, where a preconditioned matrix-vector product is computed at the\ beginning of every CG iteration. We also use a multigrid scheme with multi-frequency\ reconstruction to get a convergent rough reconstruction at a lower frequency and then refine\ it on a higher-resolution grid.\ 

}, author = {Hongjian Wang and Hartmut Gemmeke and Torsten Hopp and J{\"u}rgen Hesser} } @mastersthesis {389, title = {Accurate Low-Dose Iterative CT Reconstruction from Few Projections using Sparse and Non-Local Regularization Functions}, year = {2016}, month = {29.06.2016}, school = {Heidelberg}, type = {Dissertation}, abstract = {

This dissertation aims at reducing the dose and the acquisition time in medical and in industrial Computed Tomography (CT). Since X-rays carry enough energy to free electrons from atoms, they are extremely harmful to human cells and therefore the dose in X-ray CT should be as low as possible. For industrial CT, short acquisition and reconstruction times decrease the availability time of the X-ray machine and therefore increase the sales, due to a higher throughput. As a matter of principle, there are three strategies to reduce the dose, defined as the product of the tube current and the pulse length of the CT system: (1) Lowering the X-ray exposure by reducing the X-ray tube current; (2) lowering the pulse length of the industrial CT system which allows for a shorter acquisition process as well and (3) acquiring less projection views per full rotation of the source around the object, which enables both, a faster acquisition and reconstruction. However, all of these strategies have a strong negative impact on the resulting image quality, especially when they are combined. (1) and (2) introduce additional noise and (3) leads to streaking artifacts in the reconstructed images. Therefore, efficient reconstruction algorithms have to be found which can compensate the resulting image quality degradation. The X-ray model can be solved analytically by Filtered Backprojection (FBP) or iteratively by solving (regularized) objective functions. Up to now, commercial scanners still employ analytical FBP due to its fast execution times. However, the aforementioned strategies of dose reduction are not suitable for this method: The images are heavily corrupted by noise and artifacts and are therefore not suitable for medical inspection or industrial CT quality control. Total Variation (TV) is the current state of the art method for the regularization term of iterative algorithms in X-ray CT. It can remove the noise and the streaks in the images at the cost of over-smoothing of small-scaled image features and those of small intensity. Furthermore, the images suffer from a loss of contrast and spatial resolution and "stair-casing" artifacts are introduced in image regions which should be homogeneous. This dissertation presents three new regularization functions for low-dose, under-sampled, iterative CT which successively improve the reconstruction results of the current state of the art techniques: FBP and Total Variation. The first method is called the Anisotropic Total Variation (ATV). We propose a gradient re-definition so as to overcome TV{\textquoteright}s problem of over-smoothing fine structures. The re-definition is accomplished by multiplying the gradient in the definition of TV by an exponential function. We include a parameter in this function and this parameter acts like a threshold of the noise and controls which structures (noise and prominent edges) to penalize during the reconstruction. The second method focuses on the main drawbacks of TV: The production of stair-casing artifacts in regions which should be homogeneous and the over-smoothing of fine structures. To reduce the stair-casing effect of TV and at the same time to reconstruct high resolution images, we combine first and second order derivatives and we create a new regularization function. The first order Anisotropic Total Variation can separate noise and prominent edges up to a certain noise magnitude and the second order Total Variation better penalizes undesired edges than first order TV. The resulting method is called ATV+TV{\texttwosuperior}.The third method discusses a novel generalization of TV. It is called Generalized Anisotropic Total Variation (GATV). GATV uses a priori information about the Gradient Magnitude Distribution (GMD) of the underlying object for the reconstruction. By efficient parameterization, this method can separate noise and prominent image features and it can therefore overcome the problems of TV and reconstruct high quality CT images. We reconstruct real patient data and digitally simulated phantom data. We evaluate the efficiency of our proposed regularization methods based on a large experiment with 560 measurements where different numbers of projections, noise levels and 10 different realizations of the noise random variable were selected. We judge the results from a qualitative point of view by analyzing the reconstructed images in terms of edge sharpness and accuracy, image homogeneity and image details, like small structures and features. Furthermore, we apply quantitative measures to assess the image quality: The Relative Root Mean Squared Error (RRMSE), the Contrast to Noise Ratio (CNR), the Kullback-Leibler distance and a measure to rate the spatial resolution and the homogeneity of the image. The main findings of this dissertation indicate that all of the three methods successively improve the visual impression of the reconstruction results in terms of preservation of small-scaled image features and features of small intensity. Furthermore, they can improve the edge sharpness and accuracy, spatial resolution, image contrast and homogeneity and each method, ATV, ATV+TV{\texttwosuperior} and GATV, thereby improves the reconstruction results of its preceding method. In case of noise-free projections, GATV can accurately reconstruct digitally simulated data from 20 projections and it can achieve a RRMSE which is up to 1770 times smaller than the RRMSE of TV. In case of noisy projections, all of the three methods can achieve an extreme dose reduction factor of approximately 16 compared to the results of TV. Furthermore, at this reduction factor, ATV, ATV+TV{\texttwosuperior} and GATV can still lower the RRMSE by approximately 11\%, 20\% and 33\% compared to the results of TV, obtained from a high dose and many view setting. From previous publications (Xun Jia et al., Medical physics, 37:1757, 2010) we know that a 72 times dose reduction can be achieved for a TV regularized iterative reconstruction compared to FBP. Combining this information with the dose reduction potential of the proposed methods, ATV, ATV+TV{\texttwosuperior} and GATV, reveals the potential to decrease the dose and acquisition time in CT by a factor of approximately three orders of magnitude (1000), compared to conventional FBP.

}, keywords = {Compressed Sensing, CT reconstruction, Industrial CT, low-dose, Regularization, under-sampling}, url = {http://www.ub.uni-heidelberg.de/archiv/21527}, author = {Debatin, Maurice} } @proceedings {Konopczynski_2016, title = {Automated Multiscale 3D Feature Learning for Vessels Segmentation in Thorax CT Images}, year = {2016}, month = {07/2016}, abstract = {

We address the vessel segmentation problem by
building upon the multiscale feature learning method of Kiros
et al., which achieves the current top score in the VESSEL12
MICCAI challenge. Following their idea of feature learning
instead of hand-crafted filters, we have extended the method to
learn 3D features. The features are learned in an unsupervised
manner in a multi-scale scheme using dictionary learning via least
angle regression. The 3D feature kernels are further convolved
with the input volumes in order to create feature maps. Those
maps are used to train a supervised classifier with the annotated
voxels. In order to process the 3D data with a large number
of filters a parallel implementation has been developed. The
algorithm has been applied on the example scans and annotations
provided by the VESSEL12 challenge. We have compared our
setup with Kiros et al. by running their implementation. Our
current results show an improvement in accuracy over the slice
wise method from 96.661.10\% to 97.240.90\%.

}, doi = {10.1109/NSSMIC.2016.8069570}, author = {Tomasz Konopczy{\'n}ski and Thorben Kr{\"o}ger and Lei Zheng and Christoph S. Garbe and J{\"u}rgen Hesser} } @article {374, title = {Combined stereotactic biopsy and stepping-source interstitial irradiation of unresectable glioblastoma multiforme.}, journal = {J Neurosurg Sci}, year = {2016}, month = {2016 Jan 15}, abstract = {

Patients diagnosed with glioblastoma multiforme receiving stereotactic biopsy only either due to tumor localization or impaired clinical status face a devastating prognosis with very short survival times. One strategy to provide an initial cytoreductive and palliative therapy at the time of the stereotactic biopsy is interstitial irradiation through the pre-defined trajectory of the biopsy channel. We designed a novel treatment planning system and evaluated the treatment potential of a fixed-source and a stepping-source algorithm for interstitial radiosurgery on non-spherical glioblastoma in direct adjacency to risk structures. Using both setups, we show that radiation doses delivered to 100\% of the gross tumor volume shifts from sub-therapeutic (10-12 Gy) to sterilizing single doses (25-30 Gy) when using the stepping source algorithm due to improved sparing of organs-at-risk. Specifically, the maximum doses at the brain stem were 100\% of the PTV dose when a fixed central source and 38\% when a stepping-source algorithm was used. We also demonstrated precision of intracranial target points and stability of superficial and deep trajectories using both a phantom and a body donor study. Our setup now for the first time provides a basis for a clinical proof-of-concept trial and may widen palliation options for patients with limited life expectancy that should not undergo time-consuming therapies.

}, issn = {0390-5616}, author = {Brehmer, Stefanie and Guthier, Christian V and Clausen, Sven and Schneider, Frank and Schulte, Dirk M and Benker, Matthias and Bludau, Frederic and Glatting, Gerhard and Marx, Alexander and Schmiedek, Peter and Hesser, J{\"u}rgen and Wenz, Frederik and Giordano, Frank A} } @proceedings {Katha2016, title = {Compressed sensing denoising for segmentation of localization microscopy data}, year = {2016}, abstract = {

Localization microscopy (LM) allows to acquire pointillistic superresolution images of biological structures on the nanoscale. However, current structure reconstruction and segmentation approaches suffer from either exclusion of small structures or strong dependence on a-priori knowledge. We propose reconstruction methods based on compressed sensing (CS) denoising in combination with the isodata threshold for segmentation. The methods are verified on artificial test data. For the denoising, a Haar dictionary and a KSVD dictionary learning on artificial data are used. Both methods perform significantly better than the reference algorithm, a linear density filter, in terms of root-mean-square deviation from the ground truth. Furthermore, exemplary results on real LM data of irradiated cell nuclei with Heterochromatin labeling make small structures visible that are suppressed by the reference method. CS denoising demonstrates promising results for reconstruction of LM data.

}, issn = {978-1-4673-9472-7}, doi = {10.1109/CIBCB.2016.7758097}, url = {http://ieeexplore.ieee.org/document/7758097/}, author = {Katharina P. Aschenbrenner and Sebastian Butzek and Christian V. Guthier and Matthias Krufczik and Michael Hausmann and Felix Bestvater and J{\"u}rgen W. Hesser} } @proceedings {Maur2016, title = {CT Auto-calibration by Consistent Contours}, year = {2016}, month = {10/2016}, abstract = {

This paper discusses a novel strategy for estimating
projection matrices of a computed tomography using object
contours in projection images. We formulate mathematical conditions
for projection parameter consistency based on contour
detection and tracking in 2D. We derive a global optimization
problem and a greedy optimizer herein. Applying the approach
for motion detection shows an average reduction of motion error
in object space down to 0.15mm in a standard dental conebeam
CT setup. Evaluation is performed on simulated data
with different motion types and object shapes, and considers
the influence of noisy contour data. The accuracy of estimation
is linked to sample resolution, number and distinctiveness of
imaged objects, and accuracy of input data. Our strategy is robust
towards inaccurate initialization and truncated data.

}, url = {http://2016.nss-mic.org/}, author = {Maur, Susanne and Stsepankou, Dzmitry and Hesser, J.} } @article {Glodeck_2016, title = {Distortion correction of EPI data using multimodal nonrigid registration with an anisotropic regularization}, journal = {Magnetic Resonance Imaging}, volume = {34}, year = {2016}, pages = {127 - 136}, abstract = {

Abstract In this paper, a novel strategy for correcting both geometric and image intensity distortions of echo-planar imaging (EPI) MRI data is presented. To deal with small local distortions caused by rapid changes of the magnetic field, an improved multimodal registration framework using normalized mutual information (NMI) in combination with a multi-scale technique is presented to estimate a dense displacement field. To ensure the robustness of this high dimensional ill-posed inverse problem, a novel anisotropic regularization functional is used. In order to quantify geometric distortions, a new quality measure, called standardized contour distance (SCD), is introduced. It uses the outer structure shape (OSS) information as basis for the evaluation. The new registration method was evaluated with one monomodal phantom data set and two multimodal human brain data sets (BrainSuite trainings data, SPM Subject data). By comparing with recent and efficient techniques of the state of the art, in the monomodal case, the new approach achieves results comparable to the sum of squared differences as data term. In the multimodal cases, our new registration strategy improves the mean of the SCD from 0.96 {\textpm} 0.11 to 0.60 {\textpm} 0.13 in case of the SPM Subject data and from 0.92 {\textpm} 0.07 to 0.78 {\textpm} 0.11 in case of the BrainSuite trainings data.

}, issn = {0730-725X}, doi = {http://dx.doi.org/10.1016/j.mri.2015.10.032}, url = {http://www.sciencedirect.com/science/article/pii/S0730725X15002696}, author = {Daniel Glodeck and J{\"u}rgen Hesser and Lei Zheng} } @proceedings {Guthier_AAPM_2016, title = {A Fast Multi-Target Inverse Treatment Planning Strategy Optimizing Dosimetric Measures for High-Dose-Rate (HDR) Brachytherapy}, volume = {WE-DE-201-1}, year = {2016}, month = {08/2016}, author = {Guthier, C. and Damato, A. and Viswanathan, A. and Hesser, J. and Cormack , R.} } @article {Zheng_2016, title = {Influence of regional cerebral blood volume on voxel-based morphometry}, journal = {NMR Biomed}, volume = {29}, year = {2016}, month = {2016 Jun}, pages = {787-95}, abstract = {

The investigation of structural brain alterations is one focus in research of brain diseases like depression. Voxel-based morphometry (VBM) based on high-resolution 3D MRI images is a widely used non-invasive tool for such investigations. However, the result of VBM might be sensitive to local physiological parameters such as regional cerebral blood volume (rCBV) changes. In order to investigate whether rCBV changes may contribute to variation in VBM, we performed analyses in a study with the congenital learned helplessness (cLH) model for long-term findings. The 3D structural and rCBV data were acquired with T2 -weighted rapid acquisition with relaxation enhancement (RARE) pulse sequences. The group effects were determined by standard statistical parametric mapping (SPM) and biological parametric mapping (BPM) and examined further using atlas-based regions. In our genetic animal model of depression, we found co-occurrence of differences in gray matter volume and rCBV, while there was no evidence of significant interaction between both. However, the multimodal analysis showed similar gray matter differences compared with the standard VBM approach. Our data corroborate the idea that two group VBM differences might not be influenced by rCBV differences in genetically different strains. Copyright {\textcopyright} 2016 John Wiley \& Sons, Ltd.

}, issn = {1099-1492}, doi = {10.1002/nbm.3519}, author = {Lei Zheng and Cleppien, Dirk and Gass, Natalia and Falf{\'a}n-Melgoza, Claudia and Vollmayr, Barbara and Hesser, J{\"u}rgen and Weber-Fahr, Wolfgang and Sartorius, Alexander} } @conference {falfan-melgoza_longitudinal_2016, title = {Longitudinal VBM of downregulation in mice with striatum-specific D2R overexpression}, booktitle = {Proc. Intl. Soc. Mag. Reson. Med. 24}, year = {2016}, url = {http://www.ismrm.org/16/program_files/EP17.htm}, author = {Falf{\'a}n-Melgoza, Claudia and Mallien, Anne Stephanie and Lei Zheng and Sartorius, Alexander and Kellendonk, Christoph and Gass, Peter and Weber-Fahr, Wolfgang} } @conference {Prabhune2016_2, title = {MetaStore: A Metadata Framework for Scientific Data Repositories}, booktitle = {IEEE Big Data Metadata and Management}, year = {2016}, abstract = {

In this paper, we present MetaStore, a metadata management framework for scientific data repositories. Scientific experiments are generating a deluge of data and metadata. Metadata is critical for scientific research, as it enables discovering, analysing, reusing, and sharing of scientific data. Moreover, metadata produced by scientific experiments is heterogeneous and subject to frequent changes, demanding a flexible data model. Currently, there does not exist an adaptive and a generic solution that is capable of handling heterogeneous metadata models. To address this challenge, we present MetaStore, an adaptive metadata management framework based on a NoSQL database. To handle heterogeneous metadata models and standards, the MetaStore automatically generates the necessary software code (services) and extends the functionality of the framework. To leverage the functionality of NoSQL databases, the MetaStore framework allows full-text search over metadata through automated creation of indexes. Finally, a dedicated REST service is provided for efficient harvesting (sharing) of metadata using the METS metadata standard over the OAI-PMH protocol.

}, author = {Ajinkya Prabhune and Anil Keshav and Hasebullah Ansari and J{\"u}rgen Hesser} } @article {Arba-Mosquera2016, title = {Minimising residual aberration in the presence of cyclotorsion uncertainty in refractive surgery}, journal = {J Emmetropia}, volume = {3}, year = {2016}, month = {01/2016}, pages = {139{\textendash}144}, abstract = {

PURPOSE: To formulate a simple valid method to minimize the residual aberration magnitudes due to uncertainty in cyclotorsion measurement. SETTING: Optics research laboratory. METHODS: Assuming that cyclotorsion error can be estimated and compensated for with a certain level of uncertainty, we formulate a function to modify the wavefront error in order to minimize the residual aberration magnitudes due to cyclotorsion measurement uncertainty. A modal optimum nomogram factor is computed for minimization of the residual aberration for each Zernike mode. We also calculate the optimized residual aberration using the minimization factor. RESULTS: For modal optimum, the minimization factor was dependent only on Zernike meridional order and cyclotorsion uncertainty. Th e value of the minimization function ranged between {\^a}{\texteuro}{\textquotedblleft}1 and +1. CONCLUSION: In a perfectly performing system, an " overplanned " treatment will never minimize residual wavefront aberration, independent of the cyclotorsion uncertainty. An " underplanned " treatment calculated using the presented approach will minimize the residual aberration magnitude imposed by the higher order Zernike terms, and will reduce its relative orientation to the original aberration pattern. Th e gains using this method are undeniably modest, but at such low implementation costs can still be valuable.

}, issn = {2171-4703}, url = {http://www.journalofemmetropia.org/numeros/pdf/7-3/Journal-article-3.pdf}, author = {Arba-Mosquera, Samuel and De Ortueta, Diego and Verma, Shwetabh} } @article {362, title = {A novel analysis technique for transcutaneous measurement of glomerular filtration rate with ultra-low dose marker concentrations.}, journal = {IEEE Trans Biomed Eng}, year = {2016}, month = {2015 Nov 18}, abstract = {

A novel, high-precision approach (lifetime-decomposition measurement (LTDM)) for the assessment of the glomerular filtration rate (GFR) based on clearance measurements of exogenous filtration marker.

METHODS: The time-correlated single photon counting (TCSPC) acquisition in combination with a new decomposition method allows the separation of signal and background from transcutaneous measurements of GFR.

RESULTS: The performance of LTDM is compared versus the commercially available NICKidney patch-based system for transcutaneous GFR measurement. Measurements are performed in awake Sprague Dawley (SD) rats. Using the standard concentration required for the NIC-Kidney system (7mg/100g body weight (b.w.) FITCSinistrin) as reference, the mean difference (bias) of the elimination curves GFR between LTDM and NIC-Kidney was 4.8\%. On the same animal and same day, the capability of LTDM to measure GFR with a FITC-Sinistrin dose reduced by a factor of 200 (35μg/100g b.w.) was tested as well. The mean differences (half-lives with low dose using LTDM compared with those using first, the NIC-Kidney system and its standard concentration, and second, LTDM with the same concentration as for the NIC-Kidney system) were 3.4\% and 4.5\%, respectively.

CONCLUSION: We demonstrate that with the LTDM strategy substantial reductions in marker concentrations are possible at the same level of accuracy.

SIGNIFICANCE: LTDM aims to resolve the issue of the currently necessary large doses of fluorescence tracer required for transcutaneous GFR measurement. Due to substantially less influences from autofluorescence and artifacts, the proposed method outperforms other existing techniques for accurate percutaneous organ function measurement.

}, issn = {1558-2531}, doi = {10.1109/TBME.2015.2501544}, author = {Shmarlouski, Anatoli and Schock-Kusch, Daniel and Shulhevich, Yury and Buschmann, Volker and Rohlicke, Tino and Herdt, Deborah and Radle, Matthias and Hesser, J{\"u}rgen and Stsepankou, Dzmitry} } @article {357, title = {Pharmacokinetic Modeling of Intra-arterial Nimodipine Therapy for Subarachnoid Hemorrhage-Related Cerebral Vasospasm.}, journal = {Clin Neuroradiol}, year = {2016}, month = {2015 Sep 8}, abstract = {

PURPOSE: Intra-arterial (IA) administration of nimodipine has been shown to be an effective treatment for subarachnoid hemorrhage-related cerebral vasospasm. The concentrations achieved in cerebral arteries during this procedure, though, are unknown. Therefore, there are no clinical studies investigating dose-dependent effects of nimodipine. We aimed at providing a pharmacokinetic model for IA nimodipine therapy for this purpose.

METHODS: A two-compartment pharmacokinetic model for intravenous nimodipine therapy was modified and used to assess cerebral arterial nimodipine concentration during IA nimodipine infusion into the internal carotid artery (ICA).

RESULTS: According to our simulations, continuous IA nimodipine infusion at 2\ mg/h and 1\ mg/h resulted in steady-state cerebral arterial concentrations of about 200\ ng/ml and 100\ ng/ml assuming an ICA blood flow of 200\ ml/min and a clearance of 70\ l/h. About 85 \% of the maximal concentration is achieved within the first minute of IA infusion independent on the infusion dose. Within the range of physiological and pharmacokinetic data available in the literature, ICA blood flow has more impact on cerebral arterial concentration than nimodipine clearance.

CONCLUSION: The presented pharmacokinetic model is suitable for estimations of cerebral arterial nimodipine concentration during IA infusion. It may, for instance, assist in dose-dependent analyses of angiographic results.

}, issn = {1869-1447}, doi = {10.1007/s00062-015-0464-1}, author = {Seker, F and Hesser, J and Brockmann, M A and Neumaier-Probst, E and Groden, C and Schubert, R and Brockmann, C} } @inbook {Prabhune2016, title = {Prov2ONE: An Algorithm for Automatically Constructing ProvONE Provenance Graphs}, booktitle = {Provenance and Annotation of Data and Processes}, year = {2016}, pages = {204{\textendash}208}, publisher = {Springer, Cham}, organization = {Springer, Cham}, doi = {10.1007/978-3-319-40593-3_22}, url = {http://link.springer.com/10.1007/978-3-319-40593-3{\_}22}, author = {Prabhune, Ajinkya and Zweig, Aaron and Stotzka, Rainer and Gertz, Michael and Hesser, Juergen} } @article {387, title = {Real-time inverse high-dose-rate brachytherapy planning with catheter optimization by compressed sensing-inspired optimization strategies.}, journal = {Phys Med Biol}, volume = {61}, year = {2016}, month = {2016 Aug 21}, pages = {5956-72}, abstract = {

This paper demonstrates that optimization strategies derived from the field of compressed sensing (CS) improve computational performance in inverse treatment planning (ITP) for high-dose-rate (HDR) brachytherapy. Following an approach applied to low-dose-rate brachytherapy, we developed a reformulation of the ITP problem with the same mathematical structure as standard CS problems. Two greedy methods, derived from hard thresholding and subspace pursuit are presented and their performance is compared to state-of-the-art ITP solvers. Applied to clinical prostate brachytherapy plans speed-up by a factor of 56-350 compared to state-of-the-art methods. Based on a Wilcoxon signed rank-test the novel method statistically significantly decreases the final objective function value (p \< 0.01). The optimization times were below one second and thus planing can be considered as real-time capable. The novel CS inspired strategy enables real-time ITP for HDR brachytherapy including catheter optimization. The generated plans are either clinically equivalent or show a better performance with respect to dosimetric measures.

}, issn = {1361-6560}, doi = {10.1088/0031-9155/61/16/5956}, author = {Guthier, C V and Aschenbrenner, K P and M{\"u}ller, R and Polster, L and Cormack, R A and Hesser, J W} } @article {Arns2016, title = {Towards clinical implementation of ultrafast combined kV-MV CBCT for IGRT of lung cancer: Evaluation of registration accuracy based on phantom study }, journal = {Strahlentherapie und Onkologie}, volume = {192}, year = {2016}, abstract = {

{\textcopyright} 2016, Springer-Verlag Berlin Heidelberg.Purpose: Combined kV-MV cone-beam CT (CBCT) is a promising approach to accelerate imaging for patients with lung tumors treated with deep inspiration breath-hold. During a single breath-hold (15{\^A}\ s), a 3D kV-MV CBCT can be acquired, thus minimizing motion artifacts and increasing patient comfort. Prior to clinical implementation, positioning accuracy was evaluated and compared to clinically established imaging techniques. Methods and materials: An inhomogeneous thorax phantom with four tumor-mimicking inlays was imaged in 10 predefined positions and registered to a planning CT. Novel kV-MV CBCT imaging (90{\^A}{\textdegree}{\^A}\ arc) was compared to clinically established kV-chest CBCT (360{\^A}{\textdegree}) as well as nonclinical kV-CBCT and low-dose MV-CBCT (each 180{\^A}{\textdegree}). Manual{\^A}\ registration, automatic registration provided by the manufacturer and an additional in-house developed manufacturer-independent framework based on the MATLAB registration toolkit were applied. Results: Systematic setup error was reduced to 0.05{\^A}\ mm by high-precision phantom positioning with optical tracking. Stochastic mean displacement errors were 0.5 {\^A}{\textpm} 0.3{\^A}\ mm in right{\^a}{\texteuro}{\textquotedblleft}left, 0.4 {\^A}{\textpm} 0.4{\^A}\ mm in anteroposterior and 0.0 {\^A}{\textpm} 0.4{\^A}\ mm in craniocaudal directions for kV-MV CBCT with manual registration{\^A}\ (maximum errors of no more than 1.4 mm). Clinical kV-chest CBCT resulted in mean errors of 0.2{\^A}\ mm (other modalities: 0.4{\^a}{\texteuro}{\textquotedblleft}0.8{\^A}\ mm).{\^A}\ Similar results were achieved with both automatic registration methods. Conclusion: The comparison study of repositioning accuracy between novel kV-MV CBCT and clinically established volume imaging demonstrated that registration accuracy is maintained below 1{\^A}\ mm. Since imaging time is reduced to one breath-hold, kV-MV CBCT is ideal for image guidance, e.g., in lung stereotactic ablative radiotherapy.

}, keywords = {Image-guided radio, [Cone-beam computed tomography}, issn = {1439099X 01797158}, doi = {10.1007/s00066-016-0947-2}, author = {Arns, A. and Blessing, M. and Fleckenstein, J. and Stsepankou, D. and Boda-Heggemann, J. and Simeonova-Chergou, A. and Hesser, J. and Lohr, F. and Wenz, F. and Wertz, H.} } @conference {390, title = {Verwendung mehrerer Bildmerkmale mit Mutual Information in der multimodalen Bildregistrierung}, booktitle = {47. Jahrestagung der DGMP und 19. Jahrestagung der ISMRM-DS}, year = {2016}, address = {W{\"u}rzburg}, isbn = {978-3-9816508-2-2}, url = {http://www.dgmp.de/de-DE/131/dgmp-tagungsbaende}, author = {Glodeck, Daniel and Lei Zheng and Hesser, J{\"u}rgen} } @article {debatin2015, title = {Accurate low-dose iterative CT reconstruction from few projections by Generalized Anisotropic Total Variation minimization for industrial CT}, journal = {Journal of X-ray Science and Technology}, volume = {23}, year = {2015}, month = {14 August 2015 }, pages = {701{\textendash}726}, type = {Journal article}, abstract = {

BACKGROUND: Reducing the amount of time for data acquisition and reconstruction in industrial CT decreases the operation time of the X-ray machine and therefore increases the sales. This can be achieved by reducing both, the dose and the pulse length of the CT system and the number of projections for the reconstruction, respectively. OBJECTIVE: In this paper, a novel generalized Anisotropic Total Variation regularization for under-sampled, low-dose iterative CT reconstruction is discussed and compared to the standard methods, Total Variation, Adaptive weighted Total Variation and Filtered Backprojection. METHOD: The novel regularization function uses a priori information about the Gradient Magnitude Distribution of the scanned object for the reconstruction. We provide a general parameterization scheme and evaluate the efficiency of our new algorithm for different noise levels and different number of projection views. RESULTS: When noise is not present, error-free reconstructions are achievable for AwTV and GATV from 40 projections. In cases where noise is simulated, our strategy achieves a Relative Root Mean Square Error that is up to 11 times lower than Total Variation-based and up to 4 times lower than AwTV-based iterative statistical reconstruction (e.g. for a SNR of 223 and 40 projections). CONCLUSION: To obtain the same reconstruction quality as achieved by Total Variation, the projection number and the pulse length, and the acquisition time and the dose respectively can be reduced by a factor of approximately 3.5, when AwTV is used and a factor of approximately 6.7, when our proposed algorithm is used.

}, keywords = {Gradient Magnitude Distribution, iterative CT reconstruction, low-dose, under-sampling, X-ray tomography}, doi = {10.3233/XST-150522}, url = {http://content.iospress.com/articles/journal-of-x-ray-science-and-technology/xst522?resultNumber=0\&totalResults=1\&start=0\&q=author\%3A\%28\%22Debatin\%2C+Maurice\%22\%29\&resultsPageSize=10\&rows=10}, author = {Debatin, Maurice and Hesser, J{\"u}rgen} } @conference {Guthier_DEGRO_2015, title = {Compressed sensing-based LDR brachytherapy inverse treatment planning with dosimetric criteria}, booktitle = {DEGRO}, year = {2015}, publisher = {Strahlenther Onkol (2015) 191:S1{\textendash}S184}, organization = {Strahlenther Onkol (2015) 191:S1{\textendash}S184}, abstract = {

Purpose: Compressed sensing (CS)-inspired solvers for inverse treatment planning (ITP) for low-dose-rate (LDR) brachytherapy yield solutions near the global optimum in real-time. This allows investigating the role of dose volume histogram (DVH) related dosimetric criteria over dose-based objectives for the planning process.

Methods: Treatment planning aims at covering the planning target volume (PTV) with a prescribed dose while sparing organs at risks (OARs). In LDR treatment planning a dose-based objective function models this goal by minimizing the difference of prescribed and achieved dose while penalizing dose differences above and below a given threshold. However, this optimum does not imply optimality with respect to the clinically relevant dosimetric criteria. The direct usage of dosimetric criteria, earlier seen as infeasible with given optimizers, is now in reach with a new CS-based optimizer. Checking clinical usability of dosimetric criteria based objective function, ten patient cases are optimized by three different approaches, a semi-automatic manual forward planning, an inverse planning using the commercial planning system Oncentra Prostate Elekta AB with a state of the art objective function, and our own developed planning system with the CS inspired solver incorporating the criteria based objective function. For the standard dose based objective function a set of optimization parameters that are the standard at the Mannheim University Medical Center are used, whereas for the standard dosimetric criteria for clinical evaluation according to the American Society of Physicist in Medicine are selected.

Results: All three approaches return clinically acceptable plans. For V100 PTV criteria obtained values using the semi-automatic approach are 0.88{\textpm}0.06 (range: 0.77 to 0.95), 0.93{\textpm}0.03 (range: 0.84 to 0.95) with Oncentra Prostate, and 0.93{\textpm}0.02, (range: 0.91 to 0.95) using the new approach. For V150 PTV criteria almost equivalent results for the semi-automatic approach (0.55{\textpm}0.07, range: 0.43 to 0.64) and the criteria-based approach (0.55{\textpm}0.02, range: 0.52 to 0.57) are achieved, whereas it was 9.8\% lower than Oncentra Prostate solutions (0.61{\textpm}0.05, range: 0.50 to 0.68). Remaining dosimetric criteria for OARs show no statistical significance. In addition the new approach produces plans, which are more robust with respect to the standard deviation of dosimetric criteria.

Conclusion: A CS-based optimization strategy allows using dosimetric criteria based optimization for LDR treatment planning. Reducing the system complexity from sixteen to six free parameters, it yields an easier system control.

}, doi = {10.1007/s00066-015-0847-x}, url = {http://link.springer.com/article/10.1007/s00066-015-0847-x}, author = {C.V. Guthier and J.W. Hesser} } @proceedings {Guthier_2015_IFMBE, title = {Compressed Sensing-Based LDR Brachytherapy Inverse Treatment Planning with Biological Models}, volume = {51}, year = {2015}, pages = {421-424}, publisher = {Springer International Publishing}, address = {Toronto, Canada}, abstract = {

New compressed sensing-based planning algorithms allow for fast computations of optimal planning results in low-dose-rate (LDR) brachytherapy. This enables to integrate complex models in the planning process. In this paper, we develop a new strategy for including a biological model on tumor control probability (TCP) and normal tissue complication probability (NTCP) into the objective function for plan optimization. These models were tested on clinical prostate cancer cases for their effects on the planning results relative to standard physical dose constraints for planning as reference. Interestingly, with weighting treatment risks, we observe plans using biological models assign more dose to the urethra since it is less radiation sensitive than the rectum whereby the latter is spared in order to reduce side effects. At the same time, the overall TCP is comparable. We conclude that the standard plan quality evaluation based on physical dose alone does not easily allow correctly assessing treatment risks. Hence, biological models for LDR brachytherapy treatment planning are a promising approach for an optimal management of treatment outcomes of brachytherapy.

}, doi = {10.1007/978-3-319-19387-8_102}, url = {http://link.springer.com/chapter/10.1007\%2F978-3-319-19387-8_102}, author = {C. V. Guthier and K. P. Aschenbrenner and F. Wenz and J. W. Hesser} } @article {Kretz2015, title = {Discrete element method (DEM) simulation and validation of a screw feeder system}, journal = {Powder Technology}, volume = {287}, year = {2015}, pages = {131{\textendash}138}, abstract = {

A computational particle flow simulation of a feeder which transports bulk material through a horizontal cylinder by a turning screw is presented. The objective is hereby the simulation-assisted support of system design. Such systems are used in industry to either create packages of material which have a very accurately determined mass or to produce a continuous flow of the used bulk material. The well known and common problems in practical applications are the missing stability of material flux over time, throughput changes with product quality drifts and a lack in design know how based on theoretical solutions. Therefore a simulation tool is realized by Blender software (v 2.68) to foster straight forward and goal oriented screw and apparatus design. The geometrical and physical properties of the system are adjusted to a real feeder system on which the experimental measurements are performed. Simulation parameters like wall friction, internal shear forces and angle of repose are fitted to the real experimental data. Absolute deviations are smaller than 8\%. We demonstrate that a simplified particle simulation tool is able to predict properties of a real machine that progresses bulk material with different types of screws. The mass flow rate in simulation differs from the experimental mass flow rate less than 10\% for different screw types and angular velocities of the screw. Qualitative properties like the inflow and outflow behavior of the bulk are compared and the conformity is verified. It is shown that quite a simple particle simulation tool is able to verify and predict properties of a machine that progresses bulk material with different types of screws. The simulation tool allows the modeling of all relevant machine parts without expensive real manufacturing and to test their characteristics.

}, keywords = {Bulk material, DEM simulation, Granular flow, Mass flow rate, Screw feeder}, issn = {00325910}, doi = {10.1016/j.powtec.2015.09.038}, url = {http://www.sciencedirect.com/science/article/pii/S0032591015300851}, author = {Kretz, D. and Callau-Monje, S. and Hitschler, M. and Hien, A. and Raedle, M. and Hesser, J.} } @proceedings {Ortmann2015, title = {Dramatic reduction of tracer concentration in renal function monitoring through time-resolved fluorescence detection}, year = {2015}, publisher = {SPIE}, address = {San Francisco, California, United States}, url = {https://spie.org/PWB/conferencedetails/optical-diagnostics-sensing}, author = {Uwe Ortmann and Volker Buschmann and Cathleen Fichtner and Deborah Herdt and Felix Koberling and Daniel Schock-Kusch and Sabine Neudecker and Anatoli Shmarlouski and Yury Shulhevich and Dzmitry Stsepankou and J{\"u}rgen Hesser and Matthias Raedle and Rainer Erdmann} } @article {365, title = {Extension of TOPAS for the simulation of proton radiation effects considering molecular and cellular endpoints.}, journal = {Phys Med Biol}, volume = {60}, year = {2015}, month = {2015 Jul 7}, pages = {5053-70}, abstract = {

The aim of this work is to extend a widely used proton Monte Carlo tool, TOPAS, towards the modeling of relative biological effect (RBE) distributions in experimental arrangements as well as patients. TOPAS provides a software core which users configure by writing parameter files to, for instance, define application specific geometries and scoring conditions. Expert users may further extend TOPAS scoring capabilities by plugging in their own additional C++ code. This structure was utilized for the implementation of eight biophysical models suited to calculate proton RBE. As far as physics parameters are concerned, four of these models are based on the proton linear energy transfer, while the others are based on DNA double strand break induction and the frequency-mean specific energy, lineal energy, or delta electron generated track structure. The biological input parameters for all models are typically inferred from fits of the models to radiobiological experiments. The model structures have been implemented in a coherent way within the TOPAS architecture. Their performance was validated against measured experimental data on proton RBE in a spread-out Bragg peak using V79 Chinese Hamster cells. This work is an important step in bringing biologically optimized treatment planning for proton therapy closer to the clinical practice as it will allow researchers to refine and compare pre-defined as well as user-defined models.

}, issn = {1361-6560}, doi = {10.1088/0031-9155/60/13/5053}, author = {Polster, Lisa and Schuemann, Jan and Rinaldi, Ilaria and Burigo, Lucas and McNamara, Aimee L and Stewart, Robert D and Attili, Andrea and Carlson, David J and Sato, Tatsuhiko and Ramos M{\'e}ndez, Jos{\'e} and Faddegon, Bruce and Perl, Joseph and Paganetti, Harald} } @article {356, title = {Incorporation of local dependent reliability information into the Prior Image Constrained Compressed Sensing (PICCS) reconstruction algorithm.}, journal = {Z Med Phys}, volume = {25}, year = {2015}, month = {2015 Dec }, pages = {375-390}, chapter = {375}, abstract = {

PURPOSE: The reduction of dose in cone beam computer tomography (CBCT) arises from the decrease of the tube current for each projection as well as from the reduction of the number of projections. In order to maintain good image quality, sophisticated image reconstruction techniques are required. The Prior Image Constrained Compressed Sensing (PICCS) incorporates prior images into the reconstruction algorithm and outperforms the widespread used Feldkamp-Davis-Kress-algorithm (FDK) when the number of projections is reduced. However, prior images that contain major variations are not appropriately considered so far in PICCS. We therefore propose the partial-PICCS (pPICCS) algorithm. This framework is a problem-specific extension of PICCS and enables the incorporation of the reliability of the prior images additionally.

MATERIAL AND METHODS: We assumed that the prior images are composed of areas with large and small deviations. Accordingly, a weighting matrix considered the assigned areas in the objective function. We applied our algorithm to the problem of image reconstruction from few views by simulations with a computer phantom as well as on clinical CBCT projections from a head-and-neck case. All prior images contained large local variations. The reconstructed images were compared to the reconstruction results by the FDK-algorithm, by Compressed Sensing (CS) and by PICCS. To show the gain of image quality we compared image details with the reference image and used quantitative metrics (root-mean-square error (RMSE), contrast-to-noise-ratio (CNR)).

RESULTS: The pPICCS reconstruction framework yield images with substantially improved quality even when the number of projections was very small. The images contained less streaking, blurring and inaccurately reconstructed structures compared to the images reconstructed by FDK, CS and conventional PICCS. The increased image quality is also reflected in large RMSE differences.

CONCLUSIONS: We proposed a modification of the original PICCS algorithm. The pPICCS algorithm incorporates prior images as well as information about location dependent uncertainties of the prior images into the algorithm. The computer phantom and experimental data studies indicate the potential to lowering the radiation dose to the patient due to imaging while maintaining good image quality.

}, issn = {1876-4436}, doi = {10.1016/j.zemedi.2015.09.002}, author = {Vaegler, Sven and Stsepankou, Dzmitry and Hesser, J{\"u}rgen and Sauer, Otto} } @article {360, title = {A new optimization method using a compressed sensing inspired solver for real-time LDR-brachytherapy treatment planning.}, journal = {Phys Med Biol}, volume = {60}, year = {2015}, month = {2015 Mar 21}, pages = {2179-94}, abstract = {

This work discusses a novel strategy for inverse planning in low dose rate brachytherapy. It applies the idea of compressed sensing to the problem of inverse treatment planning and a new solver for this formulation is developed. An inverse planning algorithm was developed incorporating brachytherapy dose calculation methods as recommended by AAPM TG-43. For optimization of the functional a new variant of a matching pursuit type solver is presented. The results are compared with current state-of-the-art inverse treatment planning algorithms by means of real prostate cancer patient data. The novel strategy outperforms the best state-of-the-art methods in speed, while achieving comparable quality. It is able to find solutions with comparable values for the objective function and it achieves these results within a few microseconds, being up to 542 times faster than competing state-of-the-art strategies, allowing real-time treatment planning. The sparse solution of inverse brachytherapy planning achieved with methods from compressed sensing is a new paradigm for optimization in medical physics. Through the sparsity of required needles and seeds identified by this method, the cost of intervention may be reduced.

}, issn = {1361-6560}, doi = {10.1088/0031-9155/60/6/2179}, author = {Guthier, C and Aschenbrenner, K P and Buergy, D and Ehmann, M and Wenz, F and Hesser, J W} } @article {SHMAR2015, title = {A novel analysis technique for transcutaneous measurement of glomerular filtration rate with ultra-low dose marker concentrations.}, journal = {IEEE transactions on bio-medical engineering}, volume = {PP}, year = {2015}, month = {2015/11//}, pages = {1 - 1}, abstract = {

A novel, high-precision approach (lifetime-decomposition measurement (LTDM)) for the assessment of the glomerular filtration rate (GFR) based on clearance measurements of exogenous filtration marker.METHODS: The time-correlated single photon counting (TCSPC) acquisition in combination with a new decomposition method allows the separation of signal and background from transcutaneous measurements of GFR.RESULTS: The performance of LTDM is compared versus the commercially available NICKidney patch-based system for transcutaneous GFR measurement. Measurements are performed in awake Sprague Dawley (SD) rats. Using the standard concentration required for the NIC-Kidney system (7mg/100g body weight (b.w.) FITCSinistrin) as reference, the mean difference (bias) of the elimination curves GFR between LTDM and NIC-Kidney was 4.8\%. On the same animal and same day, the capability of LTDM to measure GFR with a FITC-Sinistrin dose reduced by a factor of 200 (35{\^I}{\textonequarter}g/100g b.w.) was tested as well. The mean differences (half-lives with low dose using LTDM compared with those using first, the NIC-Kidney system and its standard concentration, and second, LTDM with the same concentration as for the NIC-Kidney system) were 3.4\% and 4.5\%, respectively.CONCLUSION: We demonstrate that with the LTDM strategy substantial reductions in marker concentrations are possible at the same level of accuracy.SIGNIFICANCE: LTDM aims to resolve the issue of the currently necessary large doses of fluorescence tracer required for transcutaneous GFR measurement. Due to substantially less influences from autofluorescence and artifacts, the proposed method outperforms other existing techniques for accurate percutaneous organ function measurement.

}, keywords = {Animals, Biomedical measurement, Fluorescence, Glomerular filtration rate (GFR), Histograms, kidney function, Optical fibers, Photonics, Skin, time-correlated single photon counting (TCSPC), transcutaneous}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26595905}, author = {Shmarlouski, Anatoli and Schock-Kusch, Daniel and Shulhevich, Yury and Buschmann, Volker and Rohlicke, Tino and Herdt, Deborah and Radle, Matthias and Hesser, J{\"u}rgen and Stsepankou, Dzmitry} } @conference {Prabhune2015, title = {An Optimized Generic Client Service API for Managing Large Datasets within a Data Repository}, booktitle = {2015 IEEE First International Conference on Big Data Computing Service and Applications}, year = {2015}, publisher = {IEEE}, organization = {IEEE}, keywords = {abstract interface, application program interfaces, biological specimen datasets, biomedical optical imaging, Cache storage, client-server systems, Command Line Tool, Communities, Computer architecture, Data transfer, data warehouses, digital data repository system, download process, GCS API, Generic Client Service (GCS) API, high-resolution images, high-resolution microscopy, ingest process, KIT Data Manager, large dataset management, Large Datasets, Large Scale Data Repository, Localization Microscopy (LM), medical computing, meta data, Metadata, Metadata Management, Microscopy, Nanoscopy, nanoscopy scientific research community, optical microscopy, optimized generic client service API, scientific information systems, scientific research data, Workflow}, isbn = {978-1-4799-8128-1}, doi = {10.1109/BigDataService.2015.25}, url = {http://ieeexplore.ieee.org/articleDetails.jsp?arnumber=7184863}, author = {Prabhune, Ajinkya and Stotzka, Rainer and Jejkal, Thomas and Hartmann, Volker and Bach, Margund and Schmitt, Eberhard and Hausmann, Michael and Hesser, Juergen} } @article {jmuders03, title = {Projection-Wise Filter Optimization for Limited-Angle Cone-Beam CT Using the Approximate Inverse}, journal = {IEEE Transactions on Nuclear Science}, volume = {62}, year = {2015}, month = {02/2015}, pages = {148,163}, chapter = {1}, abstract = {

In this paper, we present a novel and efficient approach for the optimization of filters for limited-angle cone beam computed tomography (CBCT). Our method is based on the theory of approximate inverse (AI) and uses a simultaneous iterative reconstruction technique (SIRT) to estimate a view-dependent reconstruction kernel. From this kernel we then derive a set of 2-D filters that can be applied in a filtered backprojection (FBP) algorithm. By construction the resulting filters are independent of the measured data, so that they can be precomputed for a given geometric setup and be reused with different projection datasets. Our approach is the first application of the AI for 3-D limited-angle CBCT supported by iterative reconstruction, such that in comparison to existing methods, it does not rely on additional reference measurements or on the existence of an analytical inversion formula. However, our method reaches results better than standard FBP methods. Additionally, we provide a general scheme that allows the transfer of our method to other system geometries and gives us the ability to extend it with more complex filters. We will conduct several experiments with simulated and real data where we examine the image quality of our method in comparison to standard FBP and SIRT. The results will show that our angle-optimized FBP has a higher contrast-to-artifact ratio than FBP. In addition to this, we analyze the image quality perpendicular to the in-focus plane by the use of the artifact spread function and show that our technique can be employed to reduce the amount of ghosting artifacts.

}, issn = {0018-9499}, author = {Muders, Jens and Hesser, Juergen} } @article {359, title = {Robustness of sweeping-window arc therapy treatment sequences against intrafractional tumor motion.}, journal = {Med Phys}, volume = {42}, year = {2015}, month = {2015 Apr}, pages = {1538-45}, abstract = {

PURPOSE: Due to the potentially periodic collimator dynamic in volumetric modulated arc therapy (VMAT) dose deliveries with the sweeping-window arc therapy (SWAT) technique, additional manifestations of dosimetric deviations in the presence of intrafractional motion may occur. With a fast multileaf collimator (MLC), and a flattening filter free dose delivery, treatment times close to 60 s per fraction are clinical reality. For these treatment sequences, the human breathing period can be close to the collimator sweeping period. Compared to a random arrangement of the segments, this will cause a further degradation of the dose homogeneity.

METHODS: Fifty VMAT sequences of potentially moving target volumes were delivered on a two dimensional ionization chamber array. In order to detect interplay effects along all three coordinate axes, time resolved measurements were performed twice--with the detector aligned in vertical (V) or horizontal (H) orientation. All dose matrices were then moved within a simulation software by a time-dependent motion vector. The minimum relative equivalent uniform dose EUDr,m for all breathing starting phases was determined for each amplitude and period. Furthermore, an estimation of periods with minimum EUD was performed. Additionally, LINAC logfiles were recorded during plan delivery. The MLC, jaw, gantry angle, and monitor unit settings were continuously saved and used to calculate the correlation coefficient between the target motion and the dose weighed collimator motion component for each direction (CC, LR, AP) separately.

RESULTS: The resulting EUDr,m were EUDr,m(CCV) = (98.3 {\textpm} 0.6)\%, EUDr,m(CCH) = (98.6 {\textpm} 0.5)\%, EUDr,m(APV) = (97.7 {\textpm} 0.9)\%, and EUDr,m(LRH) = (97.8 {\textpm} 0.9)\%. The overall minimum relative EUD observed for 360(o) arc midventilation treatments was 94.6\%. The treatment plan with the shortest period and a minimum relative EUD of less than 97\% was found at T = 6.1 s. For a partial 120(o) arc, an EUDr,m = 92.0\% was found. In all cases, a correlation coefficient above 0.5 corresponded to a minimum in EUD.

CONCLUSIONS: With the advent of fast VMAT delivery techniques, nonrobust treatment sequences for human breathing patterns can be generated. These sequences are characterized by a large correlation coefficient between a target motion component and the corresponding collimator dynamic. By iteratively decreasing the maximum allowed dose rate, a low correlation coefficient and consequentially a robust treatment sequence are ensured.

}, issn = {0094-2405}, doi = {10.1118/1.4914166}, author = {Fleckenstein, Jens and Hesser, J{\"u}rgen and Wenz, Frederik and Lohr, Frank} } @article {358, title = {Technical Note: Nanometric organic photovoltaic thin film detectors for dose monitoring in diagnostic x-ray imaging.}, journal = {Med Phys}, volume = {42}, year = {2015}, month = {2015 Jul}, pages = {4027-32}, abstract = {

PURPOSE: To fabricate organic photovoltaic (OPV) cells with nanometric active layers sensitive to ionizing radiation and measure their dosimetric characteristics in clinical x-ray beams in the diagnostic tube potential range of 60-150 kVp.

METHODS: Experiments were designed to optimize the detector{\textquoteright}s x-ray response and find the best parameter combination by changing the active layer thickness and the area of the electrode. The OPV cell consisted of poly (3-hexylthiophene-2,5-diyl): [6,6]-phenyl C61 butyric acid methyl ester photoactive donor and acceptor semiconducting organic materials sandwiched between an aluminum electrode as an anode and an indium tin oxide electrode as a cathode. The authors measured the radiation-induced electric current at zero bias voltage in all fabricated OPV cells.

RESULTS: The net OPV current as a function of beam potential (kVp) was proportional to kVp(-0.5) when normalized to x-ray tube output, which varies with kVp. Of the tested configurations, the best combination of parameters was 270 nm active layer thicknesses with 0.7 cm(2) electrode area, which provided the highest signal per electrode area. For this cell, the measured current ranged from approximately 0.7 to 2.4 nA/cm(2) for 60-150 kVp, corresponding to about 0.09 nA-0.06 nA/mGy air kerma, respectively. When compared to commercial amorphous silicon thin film photovoltaic cells irradiated under the same conditions, this represents 2.5 times greater sensitivity. An additional 40\% signal enhancement was observed when a 1 mm layer of plastic scintillator was attached to the cells{\textquoteright} beam-facing side.

CONCLUSIONS: Since both OPVs can be produced as flexible devices and they do not require external bias voltage, they open the possibility for use as thin film in vivo detectors for dose monitoring in diagnostic x-ray imaging.

}, issn = {0094-2405}, doi = {10.1118/1.4922202}, author = {Elshahat, Bassem and Gill, Hardeep Singh and Filipyev, Ilya and Shrestha, Suman and Hesser, J{\"u}rgen and Kumar, Jayant and Karellas, Andrew and Zygmanski, Piotr and Sajo, Erno} } @article {Celik2014, title = {Automated analysis of autofluorescent human RPE cell granules using structured illumination microscopy}, journal = {Investigative Ophthalmology \& Visual Science}, volume = {55}, year = {2014}, pages = {379}, issn = {1552-5783}, url = {http://iovs.arvojournals.org/article.aspx?articleid=2269243}, author = {Celik, Nil and Best, Gerrit and Bakulina, Alena and Schock, Florian and Cremer, Christoph and Hesser, J{\"u}rgen and Dithmar, Stefan} } @article {Shmarlouski2014, title = {Automatic artifact removal from GFR measurements}, journal = {Biomedical Signal Processing and Control}, volume = {14}, year = {2014}, month = {November}, pages = {30-41}, publisher = {Elsevier}, abstract = {

Measurement of renal function in awake rats or mice can be accomplished by an intelligent plaster device that fits on the back of animals. The device performs a percutaneous measurement of the kinetics of a labeled fluorescent dye exclusively eliminated by the kidney. During the measurement, relative motion between plaster and skin leads to a variation of the illumination conditions, which emerge as artifacts in the data. In this paper, a novel strategy to detect and eliminate artifacts is suggested. The method combines cluster analysis and nonlinear regression with a priori knowledge about signal morphology to correct data. The performance of the proposed method is demonstrated on real and simulated data. Simulations were performed on data with two artifact amplitude ranges: (1) shifts in the recorded data with amplitude exceeding 3\% of the signal amplitude for a combined duration of 10\% of the total measurement time and (2) shifts greater than 3\% for approximately 30\% of the total measurement time. Prior to artifact removal, the MAE was calculated to be 10.3\% and 21.9\%, respectively. Following artifact removal using the proposed method, results showed that, when determining the half-life, the mean absolute error (MAE) was 0.88\% for range type 1 and 10.4\% for the more substantial range of the type 2 artifacts. When examining real data, the mean difference (bias) while determining the half-life was 7.5\%. Results show that novel technique outperforms a number of state-of-the-art techniques when removing artifacts from the signal recorded while an animal is allowed to move freely. In this case, the signal acquires shifts and random changes with large amplitudes, which make it impossible to use standard methods.

}, url = {http://dx.doi.org/10.1016/j.bspc.2014.06.010}, author = {Shmarlouski , A. and Shulhevich , Y. and Geraci , S. and Friedemann , J. and Gretz , N. and Neudecker , S. and Hesser , J. and Dzimitry Stsepankou} } @conference {Guthier_DEGRO2014, title = {Comparison of two different MILP optimizers for LDR brachytherapy treatment planning}, booktitle = {Jahreskongress der Deutschen Gesellschaft f{\"u}r Radioonkologie (DEGRO)}, year = {2014}, month = {08/2014}, author = {Guthier, C. and Hesser, J.} } @conference {Grunzke2014, title = {Device-Driven Metadata Management Solutions for Scientific Big Data Use Cases}, booktitle = {2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing}, year = {2014}, publisher = {IEEE}, organization = {IEEE}, keywords = {advanced processing capability, analysis capability, Apache Lucene, Apache Solr, Biology, biology computing, Communities, D, data analysis, data analysis requirements, data life cycles, data rates, data set organization, data volume, Detectors, device-driven metadata management solutions, DICOM, handling capability, innovative R\&, Light Microscopy, LSDMA project, meta data, Metadata Management, Microscopy, NeXus-ICAT, OAI-PMH, OME, open archive initiative-protocol-for-metadata harv, open microscopy environment, optical microscopy, Photon Science, Photonics, research and development, Scientific Big Data, scientific big data use cases, Standards, XML}, isbn = {978-1-4799-2729-6}, doi = {10.1109/PDP.2014.119}, url = {http://ieeexplore.ieee.org/articleDetails.jsp?arnumber=6787293}, author = {Grunzke, Richard and Hesser, J{\"u}rgen and Starek, Jurgen and Kepper, Nick and Gesing, Sandra and Hardt, Marcus and Hartmann, Volker and Kindermann, Stephan and Potthoff, Jan and Hausmann, Michael and Muller-Pfefferkorn, Ralph and Jakel, Rene} } @article {371, title = {Exercise boosts hippocampal volume by preventing early age-related gray matter loss.}, journal = {Hippocampus}, volume = {24}, year = {2014}, month = {2014 Feb}, pages = {131-4}, keywords = {Aging, Animals, Cranial Irradiation, Hippocampus, Imaging, Three-Dimensional, Longitudinal Studies, Magnetic Resonance Imaging, Male, Mice, Mice, Inbred C57BL, Physical Conditioning, Animal, Running}, issn = {1098-1063}, doi = {10.1002/hipo.22227}, author = {Fuss, Johannes and Biedermann, Sarah V and Falf{\'a}n-Melgoza, Claudia and Auer, Matthias K and Lei Zheng and Steinle, J{\"o}rg and H{\"o}rner, Felix and Sartorius, Alexander and Ende, Gabriele and Weber-Fahr, Wolfgang and Gass, Peter} } @article {372, title = {Functionally altered neurocircuits in a rat model of treatment-resistant depression show prominent role of the habenula.}, journal = {Eur Neuropsychopharmacol}, volume = {24}, year = {2014}, month = {2014 Mar}, pages = {381-90}, keywords = {Animals, Brain, Brain Mapping, Cerebrovascular Circulation, Depressive Disorder, Treatment-Resistant, Habenula, Helplessness, Learned, Magnetic Resonance Imaging, Male, Neural Pathways, Rats, Rats, Sprague-Dawley, Signal Processing, Computer-Assisted}, issn = {1873-7862}, doi = {10.1016/j.euroneuro.2013.12.004}, author = {Gass, Natalia and Cleppien, Dirk and Lei Zheng and Schwarz, Adam James and Meyer-Lindenberg, Andreas and Vollmayr, Barbara and Weber-Fahr, Wolfgang and Sartorius, Alexander} } @article {348, title = {High throughput film dosimetry in homogeneous and heterogeneous media for a small animal irradiator.}, journal = {Phys Med}, volume = {30}, year = {2014}, month = {2014 Feb}, pages = {36-46}, abstract = {

PURPOSE: We have established a high-throughput Gafchromic film dosimetry protocol for narrow kilovoltage beams in homogeneous and heterogeneous media for small-animal radiotherapy applications. The kV beam characterization is based on extensive Gafchromic film dosimetry data acquired in homogeneous and heterogeneous media. An empirical model is used for parameterization of depth and off-axis dependence of measured data.

METHODS: We have modified previously published methods of film dosimetry to suit the specific tasks of the study. Unlike film protocols used in previous studies, our protocol employs simultaneous multi-channel scanning and analysis of up to nine Gafchromic films per scan. A scanner and background correction were implemented to improve accuracy of the measurements. Measurements were taken in homogeneous and inhomogeneous phantoms at 220 kVp and a field size of 5 {\texttimes} 5 mm(2). The results were compared against Monte Carlo simulations.

RESULTS: Dose differences caused by variations in background signal were effectively removed by the corrections applied. Measurements in homogeneous phantoms were used to empirically characterize beam data in homogeneous and heterogeneous media. Film measurements in inhomogeneous phantoms and their empirical parameterization differed by about 2\%-3\%. The model differed from MC by about 1\% (water, lung) to 7\% (bone). Good agreement was found for measured and modelled off-axis ratios.

CONCLUSIONS: EBT2 films are a valuable tool for characterization of narrow kV beams, though care must be taken to eliminate disturbances caused by varying background signals. The usefulness of the empirical beam model in interpretation and parameterization of film data was demonstrated.

}, keywords = {Animals, Film Dosimetry, Models, Theoretical, Monte Carlo Method, Phantoms, Imaging, Time Factors, Water}, issn = {1724-191X}, doi = {10.1016/j.ejmp.2013.02.002}, author = {Wack, L and Ngwa, W and Tryggestad, E and Tsiamas, P and Berbeco, R and Ng, S K and Hesser, J and Zygmanski, P} } @article {MBlessing2014_ASTRO, title = {Image Guided Radiation Therapy Using Ultrafast kV-MV CBCT: End-to-End Test Results of the Finalized Implementation}, journal = {International Journal of Radiation Oncology Biology Physics}, volume = {90}, year = {2014}, pages = {S828{\textendash}S829 }, chapter = {S828}, author = {M. Blessing and A. Arns and H. Wertz and Dzimitry Stsepankou and J. Boda-Heggemann and F. Lohr and J. Hesser and F. Wenz} } @article { , title = {Image Sensor Noise Parameter Estimation by Variance Stabilization and Normality Assessment}, journal = {IEEE Transactions on Image Processing}, volume = {23}, number = {99}, year = {2014}, pages = {3990,3998}, publisher = {IEEE}, abstract = {

High-quality image denoising requires taking into account the dependence of the noise distribution on the original image. The parameters of this dependence are often unknown and we propose a new method to estimate them here. Using an optimization procedure, we find a variance-stabilizing transformation, which transforms the input image into an image with signal-independent noise. Principal component analysis of blocks of the transformed image allows estimation of the variance of the signal-independent noise so that the parameters of the original noise model can be computed. The image blocks for processing are selected in such a way that they have low stochastic texture strength but preserve the noise distribution. The algorithm does not require the original image to have homogeneous areas and can accurately process images with regular textures. It has high computational efficiency and smaller maximum estimation error compared with the state of the art. Our experiments have also shown that denoising with the noise parameters estimated by this method leads to the same results as denoising with the true noise parameters.

}, url = {http://dx.doi.org/10.1109/TIP.2014.2339194}, author = {S. Pyatykh and Hesser , Juergen} } @article {molina2014incremental, title = {Incremental Learning with SVM for Multimodal Classification of Prostatic Adenocarcinoma}, journal = {PLoS ONE}, volume = {9}, year = {2014}, author = {Molina, Jos{\'e} Fernando Garc{\'\i}a and Lei Zheng and Sertdemir, Metin and Dinter, Dietmar J and Sch{\"o}nberg, Stefan and Radle, Matthias} } @conference {Bakulina_FOM2014, title = {Investigating age-related diseases of the human retina by 3D-SIM-imaging }, booktitle = {Focus on Microscopy}, year = {2014}, month = {04/2014}, author = {Schock, F. and Best, G. and Celik, N. and Bakulina, A. and Hagmann, M. and Heintzmann, R. and Hesser, J. and Birk, U. and Dithmar, S. and Cremer, C.} } @conference {Bakulina2014, title = {Investigating deposit-crowded cells by SIM microscopy to quantify the progress of age related granule-accumulationin human RPE cells.}, booktitle = {International Microscopy Congress}, year = {2014}, month = {09/2014}, address = {Prague}, author = {Schock, F. and Best, G. and Celik, N. and Bakulina, A. and Hagmann, M. and Heintzmann, R. and Sel, S. and Birk, U. and Hesser, J. and Dithmar, S. and Cremer, C.} } @article {Arns2014_1, title = {Matching Accuracy of Ultrafast Kilovoltage-Megavoltage (kV-MV) Cone Beam CT for Image Guided Radiation Therapy}, journal = {International Journal of Radiation Oncology Biology Physics}, volume = {90}, year = {2014}, pages = {S829-S830}, chapter = {S829}, author = {A. Arns and M. Blessing and Dzimitry Stsepankou and J. Boda-Heggemann and J. Hesser and F. Wenz and F. Lohr and H. Wertz} } @conference {HartmannDGMP2014, title = {Optimisation of parameters for thermometry in deep hyperthermia treatments using MR-spectroscopy methods.}, booktitle = {DGMP Conference}, year = {2014}, month = {09/2014}, author = {Hartmann, J. and S. Pyatykh and Hesser, J. and Ott, O. and Fietkau, R. and Bert, C.} } @conference { cleppien_regional_2014, title = {Regional cerebral blood volume (rCBV) bias voxel-based morphometry (VBM) in an animal study}, booktitle = {Proceedings 22nd Scientific Meeting, International Society for Magnetic Resonance in Medicine}, year = {2014}, month = {may}, pages = {0943}, url = {http://www.ismrm.org/14/program_files/TP06.htm$\#$TP605}, author = {Cleppien , Dirk Ernst and Lei Zheng and Falf{\'a}n-Melgoza , Claudia and Vollmayr , Barbara and Weber-Fahr , Wolfgang and Sartorius , Alexander} } @article { , title = {Salt and pepper noise removal in binary images using image block prior probabilities}, journal = {Journal of Visual Communication and Image Representation}, volume = {25}, number = {5}, year = {2014}, pages = {748-754}, publisher = {Elsevier}, abstract = {During scanning and transmission, images can be corrupted by salt and pepper noise, which negatively affects the quality of subsequent graphic vectorization or text recognition. In this paper, we present a new algorithm for salt and pepper noise suppression in binary images. The algorithm consists of the computation of block prior probabilities from training noise-free images; noise level estimation; and the maximum a posteriori probability estimation of each image block. Our experiments show that the proposed method performs significantly better than the state of the art techniques.}, url = {http://dx.doi.org/10.1016/j.jvcir.2014.02.001}, author = {S. Pyatykh and Hesser , Juergen} } @article {Muders2014, title = {Stable and robust geometric self-calibration for cone-beam CT using mutual information}, journal = {IEEE Transaction on Nuclear Science}, volume = {61}, number = {1}, year = {2014}, month = {02/2014}, pages = {202,217}, author = {Muders , Jens and Hesser , J{\"u}rgen} } @article { gass_sub-anesthetic_2013, title = {Sub-Anesthetic Ketamine Modulates Intrinsic BOLD Connectivity within the Hippocampal-Prefrontal Circuit in the Rat}, journal = {Neuropsychopharmacology}, volume = {39}, year = {2014}, month = {oct}, pages = {895-906}, chapter = {895}, issn = {1740-{634X}}, doi = {10.1038/npp.2013.290}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24136293}, author = {Gass , Natalia and Schwarz , Adam J and Sartorius , Alexander and Schenker , Esther and Risterucci , Celine and Spedding , Michael and Lei Zheng and Meyer-Lindenberg , Andreas and Weber-Fahr , Wolfgang} } @article { Ng2013, title = {Automation of clip localization in Digital Tomosynthesis for setup of breast cancer patients.}, journal = {Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)}, volume = {29}, number = {1}, year = {2013}, month = {jan}, pages = {75{\textendash}82}, issn = {1724-191X}, doi = {10.1016/j.ejmp.2011.12.001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22206908}, author = {Ng , Sook Kien and Lyatskaya , Yulia and Dzimitry Stsepankou and Hesser , Juergen and Bellon , Jennifer R and Wong , Julia S and Zygmanski , Piotr} } @proceedings {Debatin2013, title = {CT Reconstruction from Few-Views by Higher Order Adaptive Weighted Total Variation Minimization}, year = {2013}, publisher = {Proc. Intl. Mtg. on Fully 3D Image Reconstruction}, abstract = {

Dose reduction in X-ray Computed Tomography (CT) is of high practical relevance. Compressed Sensing allows for efficient under-sampling while still achieving an acceptable image quality. Especially Total Variation (TV) regularization obtains accurate, robust and stable results. However, it often suffers from the loss of fine structures and stair-casing artifacts. In order to overcome these limitations, we propose a generalization of TV by higher order derivatives. We demonstrate in this paper that both stair-casing and the loss of small structures in TV-based iterative tomographic reconstructions can be overcome.

}, keywords = {Adaptive weighted Total Variation, CBCT, higher order derivatives, low-dose}, author = {Debatin, Maurice and Dzimitry, Stsepankou and Hesser, J{\"u}rgen} } @article { Zygmanski2013, title = {Dependence of Monte Carlo microdosimetric computations on the simulation geometry of gold nanoparticles.}, journal = {Physics in medicine and biology}, volume = {58}, number = {22}, year = {2013}, month = {nov}, pages = {7961{\textendash}77}, issn = {1361-6560}, doi = {10.1088/0031-9155/58/22/7961}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24169737}, author = {Zygmanski , Piotr and Liu , Bo and Tsiamas , Panagiotis and Cifter , Fulya and Petersheim , Markus and Hesser , Juergen and Sajo , Erno} } @article { Seker2013, title = {Dose-response relationship of locally applied nimodipine in an ex vivo model of cerebral vasospasm.}, journal = {Neuroradiology}, volume = {55}, number = {1}, year = {2013}, month = {jan}, pages = {71{\textendash}6}, abstract = {INTRODUCTION: Cerebral vasospasm is a severe complication of subarachnoid hemorrhage (SAH). The calcium channel inhibitor nimodipine has been used for treatment of cerebral vasospasm. No evidence-based recommendations for local nimodipine administration at the site of vasospasm exist. The purpose of this study was to quantify nimodipine{\textquoteright}s local vasodilatory effect in an ex vivo model of SAH-induced vasospasm. METHODS: SAH-induced vasospasm was modeled by contracting isolated segments of rat superior cerebellar arteries with a combination of serotonin and a synthetic analog of prostaglandin A(2). A pressure myograph system was used to determine vessel reactivity of spastic as well as non-spastic arteries. RESULTS: Compared to the initial vessel diameter, a combination of serotonin and prostaglandin induced considerable vasospasm. Locally applied nimodipine dilated the arteries in a concentration-dependent manner starting at concentrations as low as 1 nM. Concentrations higher than 100 nM did not relevantly increase the vasodilatory effect. Nimodipine{\textquoteright}s vasodilatory effect was smaller in spastic than in non-spastic vessels which we assume to be due to structural changes in the vessel wall. CONCLUSION: The described ex vivo model allows to investigate the dose-dependent efficacy of spasmolytic drugs prior to in vivo experiments. Low concentrations of locally applied nimodipine have a strong vasodilatory effect, which is of relevance when considering the local application of nimodipine in cerebral vasospasm.}, keywords = {Animals, Cerebral Arteries, Cerebral Arteries: drug effects, Cerebral Arteries: physiopathology, Dose-Response Relationship, Drug, Hesser, Intracranial, Intracranial: drug therapy, Intracranial: physiopathology, Male, Nimodipine, Nimodipine: administration \& dosage, Rats, Treatment Outcome, Vascular Resistance, Vascular Resistance: drug effects, Vasodilator Agents, Vasodilator Agents: administration \& dosage, Vasospasm, Wistar}, issn = {1432-1920}, doi = {10.1007/s00234-012-1079-8}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22864556}, author = {Seker , Fatih and Hesser , Juergen and Neumaier-Probst , Eva and Groden , Christoph and Brockmann , Marc A and Schubert , Rudolf and Brockmann , Carolin} } @article { harth_estimation_2013, title = {Estimation of intracranial failure risk following hippocampal-sparing whole brain radiotherapy}, journal = {Radiotherapy and Oncology}, volume = {109}, number = {1}, year = {2013}, month = {oct}, pages = {152{\textendash}158}, issn = {0167-8140}, doi = {10.1016/j.radonc.2013.09.009}, url = {http://www.sciencedirect.com/science/article/pii/S0167814013004672}, author = {Harth , Saskia and Abo-Madyan , Yasser and Lei Zheng and Siebenlist , Kerstin and Herskind , Carsten and Wenz , Frederik and Giordano , Frank A.} } @article { Marco-Rius2013, title = {A fast analytic dose calculation method for arc treatments for kilovoltage small animal irradiators.}, journal = {Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)}, volume = {29}, number = {5}, year = {2013}, month = {sep}, pages = {426{\textendash}35}, abstract = {Arc treatments require calculation of dose for collections of discrete gantry angles. The sampling of angles must balance between short computation time of small angle sets and the better calculation reliability of large sets. In this paper, an analytical formula is presented that allows calculation of dose delivered during continuous rotation of the gantry. The formula holds valid for continuous short arcs of up to about 30deg and is derived by integrating a dose formula over gantry angles within a small angle approximation. Doses for longer arcs may be obtained in terms of doses for shorter arcs. The formula is derived with an empirical beam model in water and extended to inhomogeneous media. It is validated with experimental data obtained by applying arc treatment using kV small animal irradiator to a phantom of solid water and lung-equivalent material. The results are a promising step towards efficient 3D dose calculation and inverse planning purposes. In principle, this method also applies to VMAT dose calculation and optimization but requires extensions.}, issn = {1724-191X}, doi = {10.1016/j.ejmp.2013.02.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23490038}, author = {Marco-Rius , I and Wack , L and Tsiamas , P and Tryggestad , E and Berbeco , R and Hesser , J and Zygmanski , P} } @conference { 0, title = {Fast noise variance estimation by principal component analysis}, booktitle = {IS\&T/SPIE Electronic Imaging 2013}, year = {2013}, month = {February}, publisher = {SPIE}, organization = {SPIE}, abstract = {Noise variance estimation is required in many image denoising, compression, and segmentation applications. In this work, we propose a fast noise variance estimation algorithm based on principal component analysis of image blocks. First, we rearrange image blocks into vectors and compute the covariance matrix of these vectors. Then, we use Bartlett{\textquoteright}s test in order to select the covariance matrix eigenvalues, which correspond only to noise. This allows estimating the noise variance as the average of these eigenvalues. Since the maximum possible number of eigenvalues corresponding to noise is utilized, it is enough to process only a small number of image blocks, which allows reduction of the execution time. The blocks to process are selected from image regions with the smallest variance. During our experiments involving seven state of the art methods, the proposed approach was significantly faster than the methods with similar or higher accuracy. Meanwhile, the relative error of our estimator was always less than 15\%. We also show that the proposed method can process images without homogeneous areas.}, keywords = {additive white Gaussian noise, image denoising, Noise variance estimation, Principal component analysis}, url = {http://dx.doi.org/10.1117/12.2000276}, author = {S. Pyatykh and Lei Zheng and Hesser , J{\"u}rgen} } @article { gass_haloperidol_2013, title = {Haloperidol modulates midbrain-prefrontal functional connectivity in the rat brain}, journal = {European Neuropsychopharmacology}, volume = {23}, number = {10}, year = {2013}, month = {oct}, pages = {1310{\textendash}1319}, issn = {0924-{977X}}, doi = {10.1016/j.euroneuro.2012.10.013}, url = {http://www.sciencedirect.com/science/article/pii/S0924977X12003045}, author = {Gass , Natalia and Schwarz , Adam James and Sartorius , Alexander and Cleppien , Dirk and Lei Zheng and Schenker , Esther and Risterucci , Celine and Meyer-Lindenberg , Andreas and Weber-Fahr , Wolfgang} } @article { 0, title = {Image Noise Level Estimation by Principal Component Analysis}, journal = {IEEE Transactions on Image Processing}, volume = {22}, number = {2}, year = {2013}, month = {Feb}, pages = {687-699}, publisher = {IEEE}, abstract = {

The problem of blind noise level estimation arises in many image processing applications, such as denoising, compression, and segmentation. In this article, we propose a new noise level estimation method based on principal component analysis of image blocks. We show that the noise variance can be estimated as the smallest eigenvalue of the image block covariance matrix. Compared with 13 existing methods, the proposed approach shows a good compromise between speed and accuracy. It is at least 15 times faster compared with the methods with similar accuracy; and it is at least 2 times more accurate than other methods. Our method does not assume the existence of homogeneous areas in the input image, hence it can successfully process images containing only textures.

}, keywords = {Additive white noise, Estimation, Image Processing, Principal component analysis}, url = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6316174}, author = {S. Pyatykh and Hesser , Juergen and Lei Zheng} } @article { schwarz_low-frequency_2013, title = {The low-frequency blood oxygenation level-dependent functional connectivity signature of the hippocampal{\textendash}prefrontal network in the rat brain}, journal = {Neuroscience}, volume = {228}, year = {2013}, month = {jan}, pages = {243{\textendash}258}, issn = {0306-4522}, doi = {10.1016/j.neuroscience.2012.10.032}, url = {http://www.sciencedirect.com/science/article/pii/S0306452212010470}, author = {Schwarz , A.J. and Gass , N. and Sartorius , A. and Lei Zheng and Spedding , M. and Schenker , E. and Risterucci , C. and Meyer-Lindenberg , A. and Weber-Fahr , W.} } @article {harth2013mapping, title = {Mapping of Brain Metastases to Evaluate the Risk of Hippocampus-Sparing Prophylactic and Therapeutic Cranial Irradiation}, journal = {International Journal of Radiation Oncology{\textbullet} Biology{\textbullet} Physics}, volume = {87}, year = {2013}, pages = {S103{\textendash}S104}, author = {Harth, S and Lei Zheng and Abo-Madyan, Y and Wenz, F and Giordano, FA} } @article { Burger2013, title = {Real-time GPU-based ultrasound simulation using deformable mesh models.}, journal = {IEEE transactions on medical imaging}, volume = {32}, number = {3}, year = {2013}, month = {mar}, pages = {609{\textendash}18}, abstract = {This paper presents a real-time capable graphics processing unit (GPU)-based ultrasound simulator suitable for medical education. The main focus of the simulator is to synthesize realistic looking ultrasound images in real-time including artifacts, which are essential for the interpretation of this data. The simulation is based on a convolution-enhanced ray-tracing approach and uses a deformable mesh model. Deformations of the mesh model are calculated using the PhysX engine. Our method advances the state of the art for real-time capable ultrasound simulators by following the path of the ultrasound pulse, which enables better simulation of ultrasound-specific artifacts. An evaluation of our proposed method in comparison with recent generative slicing-based strategies as well as real ultrasound images is performed. Hereby, a gelatin ultrasound phantom containing syringes filled with different media is scanned with a real transducer. The obtained images are then compared to images which are simulated using a slicing-based technique and our proposed method. The particular benefit of our method is the accurate simulation of ultrasound-specific artifacts, like range distortion, refraction and acoustic shadowing. Several test scenarios are evaluated regarding simulation time, to show the performance and the bottleneck of our method. While being computationally more intensive than slicing techniques, our simulator is able to produce high-quality images in real-time, tracing over 5000 rays through mesh models with more than 2 000 000 triangles of which up to 200 000 may be deformed each frame.}, keywords = {Computer Graphics, Computer Simulation, Computer-Assisted, Computer-Assisted: methods, Humans, Image Processing, Imaging, Kidney, Kidney: ultrasonography, Liver, Liver: ultrasonography, Models, Phantoms, Theoretical, Ultrasonography, Ultrasonography: instrumentation, Ultrasonography: methods}, issn = {1558-254X}, doi = {10.1109/TMI.2012.2234474}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23268382}, author = {B{\"u}rger , Benny and Bettinghausen , Sascha and R{\"a}dle , Matthias and Hesser , J{\"u}rgen} } @article {Schock-Kusch2013, title = {Reliability of transcutaneous measurement of renal function in various strains of conscious mice.}, journal = {PloS one}, volume = {8}, number = {8}, year = {2013}, month = {jan}, pages = {e71519}, publisher = {Public Library of Science}, abstract = {

Measuring renal function in laboratory animals using blood and/or urine sampling is not only labor-intensive but puts also a strain on the animal. Several approaches for fluorescence based transcutaneous measurement of the glomerular filtration rate (GFR) in laboratory animals have been developed. They allow the measurement of GFR based on the elimination kinetics of fluorescent exogenous markers. None of the studies dealt with the reproducibility of the measurements in the same animals. Therefore, the reproducibility of a transcutaneous GFR assessment method was investigated using the fluorescent renal marker FITC-Sinistrin in conscious mice in the present study. We performed two transcutaneous GFR measurements within three days in five groups of mice (Balb/c, C57BL/6, SV129, NMRI at 3-4 months of age, and a group of 24 months old C57BL/6). Data were evaluated regarding day-to-day reproducibility as well as intra- and inter-strain variability of GFR and the impact of age on these parameters. No significant differences between the two subsequent GFR measurements were detected. Fastest elimination for FITC-Sinistrin was detected in Balb/c with significant differences to C57BL/6 and SV129 mice. GFR decreased significantly with age in C57BL/6 mice. Evaluation of GFR in cohorts of young and old C57BL/6 mice from the same supplier showed high consistency of GFR values between groups. Our study shows that the investigated technique is a highly reproducible and reliable method for repeated GFR measurements in conscious mice. This gentle method is easily used even in old mice and can be used to monitor the age-related decline in GFR.

}, keywords = {Anatomy and physiology, Animal models, Biology, Biostatistics, Drug excretion, Drugs and devices, Engineering, Image Processing, Mathematics, Medicine, Model organisms, Mouse, Nephrology, Renal system, Research Article, Signal processing, Statistical methods, Statistics}, issn = {1932-6203}, doi = {10.1371/journal.pone.0071519}, url = {http://dx.plos.org/10.1371/journal.pone.0071519}, author = {Schock-Kusch , Daniel and Geraci , Stefania and Ermeling , Esther and Shulhevich , Yury and Sticht , Carsten and Hesser , Juergen and Dzimitry Stsepankou and Neudecker , Sabine and Pill , Johannes and Schmitt , Roland and Melk , Anette}, editor = {Remuzzi, Giuseppe} } @conference { ManuelBlessingAnnaArnsDzmitryStsepankouHansjoergWertzFrankLohrJurgenHesser2013, title = {Workflow automation for ultrafast Kilovoltage-Megavoltage Cone-Beam CT for Image Guided Radiotherapy}, booktitle = {2nd ESTRO Forum, Geneva, Switzerland}, year = {2013}, author = {Blessing , Manuel and Arns , Anna and Dzimitry Stsepankou and Wertz , Hansjoerg and Lohr , Frank and Hesser , J{\"u}rgen and Wenz , Frederik} } @conference { ManuelBlessingAnnaArnsDzmitryStsepankouHansjoergWertzFrankLohrJurgenHesser2013, title = {Workflow automation for ultrafast Kilovoltage-Megavoltage Cone-Beam CT for Image Guided Radiotherapy}, booktitle = {2nd ESTRO Forum, Geneva, Switzerland}, year = {2013}, author = {Frederik Wenz , Manuel Blessing} } @conference { brunner_3d-angiograms_2012, title = {3D-Angiograms from 4 MR-Projections: A Quantitative Analysis}, booktitle = {Proceedings 20th Scientific Meeting, International Society for Magnetic Resonance in Medicine}, year = {2012}, month = {may}, pages = {523}, author = {Brunner , Alexander and Lei Zheng and Zyl , Alexander and Maier , Florian and Semmler , Wolfhard and Hesser , J\ and Bock , Michael} } @proceedings {Debatin2012, title = {CT Reconstruction from Few-Views by Anisotropic Total Variation Minimization}, year = {2012}, publisher = {IEEE Nuclear Science Symposium and Medical Imaging Conference}, abstract = {

Dose reduction is an important factor in medical imaging. One of the key strategies to reduce the dose in CT reconstruction is undersampling. The recently proposed Compressed Sensing (CS) paradigm has shown that nearly exact CT reconstructions can be obtained from highly under-sampled projection sets using e.g. regularized iterative reconstruction algorithms. For the regularization, the standard Total Variation (TV) minimization method is commonly applied. The TV has a sparse setting and can therefore be utilized in the CS framework. It can smooth undesired discontinuities related to noise and preserve edges of the field-of-interest objects. It has developed a de facto standard method in CS based CT reconstructions. Nevertheless, the utilization of the Total Variation method has several drawbacks. One of these is oversmoothing of some fine objects, structures and textures and at the same time great spatial resolution loss. The purpose of this work is to develop a new Anisotropic Total Variation (ATV) method that can overcome these disadvantages and produce strong results in the sparse environment. In this work it will be shown that the usage of ATV regularization leads to edges, objects and fine structures which are sharper and clearer in contrast to the standard TV method. In addition to that the spatial resolution for the ATV method is much higher than for the TV method. The performance of both methods will be evaluated visually by means of digital simulated data, as well as real data scans obtained from an Elekta cone-beam synergy system.

}, keywords = {Anisotropic Total Variation Minimization, CBCT, Compressed Sensing, low-dose, spatial resolution}, author = {Debatin, Maurice and Zygmanski, Piotr and Dzimitry, Stsepankou and Hesser, J{\"u}rgen} } @article { 0, title = {Denoising by second order statistics}, journal = {Signal Processing}, volume = {92}, number = {12}, year = {2012}, pages = {2837-2847}, author = {Teuber , T. and Remmele , S. and Hesser , J. and Steidl , G.} } @conference { cleppien_differential_2012, title = {Differential Pattern of Striatal Cerebral Blood Volume After a Haloperidol Challenge in Rats}, booktitle = {Proceedings 20th Scientific Meeting, International Society for Magnetic Resonance in Medicine}, year = {2012}, month = {may}, pages = {799}, author = {Cleppien , Dirk Ernst and Sartorius , Alexander and Falf{\'a}n-Melgoza , Claudia and Gass , Natalia and Lei Zheng and Weber-Fahr , Wolfgang} } @article { , title = {Efficient method of pixel neighborhood traversal}, journal = {Journal of Visual Communication and Image Representation}, volume = {23}, year = {2012}, month = {July}, pages = {719-728}, publisher = {Elsevier}, abstract = {The processing of a pixel neighborhood is a common operation in image processing. Therefore, a flexible, computationally efficient and easy-to-use strategy for neighborhood traversal is required. In this paper, a new neighborhood traversal method and its implementation in C++ are presented. In the proposed method, the pixel neighbor access is organized without boundary checks and without image extension, which yields to significant improvements of computational efficiency. The method is based on a partition of the image domain, for which valid neighbor pixel offsets can be precomputed for each subset. The proposed C++ implementation is based on generic programming and can handle images of arbitrary dimensionality. It hides all implementation details from the user and can be extended in order to support additional boundary conditions. The evaluation demonstrates that the proposed method is considerably faster than neighborhood traversal implementations from other libraries.}, url = {http://www.sciencedirect.com/science/article/pii/S1047320312000582?v=s5}, author = {S. Pyatykh and Lei Zheng and Hesser , J{\"u}rgen} } @article {Stsepankou2012, title = {Evaluation of robustness of maximum likelihood cone-beam CT reconstruction with total variation regularization.}, journal = {Physics in medicine and biology}, volume = {57}, number = {19}, year = {2012}, month = {sep}, pages = {5955{\textendash}5970}, issn = {1361-6560}, doi = {10.1088/0031-9155/57/19/5955}, url = {http://stacks.iop.org/0031-9155/57/i=19/a=5955}, author = {Dzimitry Stsepankou and Arns , A. and Ng , S K and Zygmanski , P. and Hesser , J.} } @article { jahnke2012gmc, title = {GMC: a GPU implementation of a Monte Carlo dose calculation based on Geant4}, journal = {Physics in Medicine and Biology}, volume = {57}, year = {2012}, pages = {1217}, publisher = {IOP Publishing}, url = {http://iopscience.iop.org/0031-9155/57/5/1217}, author = {Jahnke , L. and Fleckenstein , J. and Wenz , F. and Hesser , J.} } @article { biedermann_vivo_2012, title = {In vivo voxel based morphometry: Detection of increased hippocampal volume and decreased glutamate levels in exercising mice}, journal = {NeuroImage}, volume = {61}, number = {4}, year = {2012}, month = {jul}, pages = {1206{\textendash}1212}, abstract = {Voluntary exercise has tremendous effects on adult hippocampal plasticity and metabolism and thus sculpts the hippocampal structure of mammals. High-field {1H} magnetic resonance {(MR)} investigations at {9.4\&\#xa0;T} of metabolic and structural changes can be performed non-invasively in the living rodent brain. Numerous molecular and cellular mechanisms mediating the effects of exercise on brain plasticity and behavior have been detected in vitro. However, in vivo attempts have been rare. In this work a method for voxel based morphometry {(VBM)} was developed with automatic tissue segmentation in mice using a {9.4\&\#xa0;T} animal scanner equipped with a {1H-cryogenic} coil. The thus increased signal to noise ratio enabled the acquisition of high resolution T2-weighted images of the mouse brain in vivo and the creation of group specific tissue class maps for the segmentation and normalization with {SPM.} The method was used together with hippocampal single voxel {1H} {MR} spectroscopy to assess the structural and metabolic differences in the mouse brain due to voluntary wheel running. A specific increase of hippocampal volume with a concomitant decrease of hippocampal glutamate levels in voluntary running mice was observed. An inverse correlation of hippocampal gray matter volume and glutamate concentration indicates a possible implication of the glutamatergic system for hippocampal volume.}, issn = {1053-8119}, doi = {10.1016/j.neuroimage.2012.04.010}, url = {http://www.sciencedirect.com/science/article/pii/S1053811912003916}, author = {Biedermann , Sarah and Fuss , Johannes and Lei Zheng and Sartorius , Alexander and Falf{\'a}n-Melgoza , Claudia and Demirakca , Traute and Gass , Peter and Ende , Gabriele and Weber-Fahr , Wolfgang} } @article { biedermann_increase_2011, title = {Increase of hippocampal glutamate after electroconvulsive treatment: A quantitative proton MR spectroscopy study at 9.4 T in an animal model of depression}, journal = {World Journal of Biological Psychiatry}, volume = {13}, year = {2012}, month = {jul}, pages = {447-57}, chapter = {447}, issn = {1562-2975}, doi = {10.3109/15622975.2011.580778}, url = {http://informahealthcare.com/doi/abs/10.3109/15622975.2011.580778}, author = {Biedermann , Sarah and Weber-Fahr , Wolfgang and Lei Zheng and Hoyer , Carolin and Vollmayr , Barbara and Gass , Peter and Ende , Gabriele and Sartorius , Alexander} } @booklet { , title = {Kilovoltage beam model for flat panel imaging system with bow-tie filter for scatter prediction and correction}, howpublished = {European Journal of Medical Physics}, year = {2012}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21570884}, author = {Blessing , M. and Bhagwat , M.S. and Lyatskaya , Y. and Bellon , J.R. and Hesser , J. and Zygmanski , P.} } @proceedings { , title = {Optimierung des Energiespektrums fuer die perkutane Strahlentherapie mit Goldnanopartikeln}, year = {2012}, publisher = {DEGRO}, abstract = {Die Goldnanopartikel-basierte Strahlentherapie zeigt sowohl experimentell, als auch aufgrund von Simulationen vielversprechende Aussichten f{\"u}r den klinischen Einsatz. Insbesondere wird eine perkutane Bestrahlung mit niederenergetischer R{\"o}ntgenstrahlung vorgeschlagen. Dabei sollen viele einzelne Einstrahlrichtungen mit Fokus im Nanopartikel-gef{\"u}llten Tumorvolumen zu einer verbesserten Dosisverteilung f{\"u}hren. Aufgrund der Tiefendosiseigenschaften ist dies jedoch auf nicht zu tief liegende Targets limitiert. Ziel der vorliegenden Studie war es, in Abh{\"a}ngigkeit von der Tumortiefe diejenige Photonenenergie zu finden, bei der das gesunde Gewebe unter Ber{\"u}cksichtigung der definierten Tumorkontrolle optimal geschont wird. Weiterhin sollte das Potential zur Erzeugung eines daran angepassten Spektrums untersucht werden.}, author = {Kretz , Dominik and Petersheim , Markus and Hesser , Juergen and Wenz , Frederik} } @conference { Muders2011, title = {Accuracy Evaluation and Exploration of Measurement Uncertainty for Exact Helical Cone Beam Reconstruction Using Katsevich Filtered Backprojection in Comparison to Circular Feldkamp Reconstruction with Respect to Industrial CT Metrology}, booktitle = {International Symposium on Digital Industrial Radiology and Computed Tomography}, year = {2011}, pages = {1{\textendash}8}, author = {Muders , Jens and Hesser , J{\"u}rgen and Lachner , Andreas and Reinhart , Christof} } @booklet {SRemele_SPIE2011_2, title = {Automated cell analysis tool for a genome-wide RNAi screen with support vector machine based supervised learning}, howpublished = {Proc. SPIE Medical Imaging}, volume = {7962}, year = {2011}, author = {Remmele , Steffen and Ritzerfeld , Julia and Nickel , Walter and Hesser , J{\"u}rgen} } @booklet { Ng2011, title = {Automation of clip localization in Digital Tomosynthesis for setup of breast cancer patients}, howpublished = {Physica medica : PM : an international journal devoted to the applications of physics to medicine and biology : official journal of the Italian Association of Biomedical Physics (AIFB)}, year = {2011}, month = {dec}, publisher = {Istituti Editoriali e Poligrafici Internazionali}, keywords = {Breast, CBCT, Digital Tomosynthesis, Patient setup}, isbn = {1120-1797}, url = {http://linkinghub.elsevier.com/retrieve/pii/S1120179711001578?showall=true}, author = {Ng , Sook Kien and Lyatskaya , Yulia and Dzimitry Stsepankou and Hesser , J{\"u}rgen and Bellon , Jennifer R and Wong , Julia S and Zygmanski , Piotr} } @article { Remmele2011, title = {A deconvolution approach for PET-based dose reconstruction in proton radiotherapy.}, journal = {Physics in medicine and biology}, volume = {56}, number = {23}, year = {2011}, month = {nov}, pages = {7601{\textendash}7619}, abstract = {Positron emitters are activated by proton beams in proton radiotherapy, and positron emission tomography (PET) images can thus be used for dose verification. Since a PET image is not directly proportional to the delivered radiation dose distribution, predicted PET images are compared to measured PET images and an agreement of both indicates a successful irradiation. Such predictions are given on the basis of Monte Carlo calculations or a filtering approach which uses a convolution of the planned dose with specific filter functions to estimate the PET activity. In this paper, we describe and evaluate a dose reconstruction method based on PET images which reverses the just mentioned convolution approach using appropriate deconvolution methods. Deconvolution is an ill-posed inverse problem, and suitable regularization techniques are required in order to guarantee a stable solution. The basic convolution approach is developed for homogeneous media and additional procedures are necessary to generalize the PET estimation to inhomogeneous media. This generalization formalism is used in our dose deconvolution approach as well. Various simulations demonstrate that the dose reconstruction method is able to reverse the PET estimation method both in homogeneous and inhomogeneous media. Measured PET images are however degraded by noise and artifacts and the dose reconstructions become more difficult and the results suffer from artifacts as well. Recently used in-room PET scanners allow a decreased delay time between irradiation and imaging, and thus the influence of short-lived positron emitters on the PET images increases considerably. We extended our dose reconstruction method to process PET images which contain several positron emitters and simulated results are shown.}, issn = {1361-6560}, doi = {10.1088/0031-9155/56/23/017}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22086216}, author = {Remmele , Steffen and Hesser , J{\"u}rgen and Paganetti , Harald and Bortfeld , Thomas} } @article { cleppien_high_2011, title = {High -resolution regional cerebral blood volume mapping by using pharmacological high-field magnetic resonance imaging}, journal = {European neuropsychopharmacology : the journal of the European College of Neuropsychopharmacology}, volume = {21}, year = {2011}, pages = {S307{\textendash}S308}, issn = {0924-977X}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0924977X11704862?showall=true}, author = {Cleppien , D. and Sartorius , A. and Gass , N. and Noori , H. and Lei Zheng and Weber-Fahr , W.} } @conference { weber-fahr_influence_2011, title = {The influence of physical activity on the structure and metabolism of the mouse hippocampus - combining 1H MRS and VBM at 9.4T}, booktitle = {Proceedings 19th Scientific Meeting, International Society for Magnetic Resonance in Medicine}, year = {2011}, month = {may}, author = {Weber-Fahr , W. and Biedermann , S. and Lei Zheng and Falfan-Melgoza , C. and Fuss , J. and Sartorius , A. and Gass , P. and Ende , G.} } @article { wertz2011novel, title = {A novel lateral disequilibrium inclusive (LDI) pencil-beam based dose calculation algorithm: Evaluation in inhomogeneous phantoms and comparison with Monte Carlo calculations}, journal = {Medical Physics}, volume = {38}, year = {2011}, pages = {1627}, author = {Wertz , H. and Jahnke , L. and Schneider , F. and Polednik , M. and Fleckenstein , J. and Lohr , F. and Wenz , F.} } @article { boggula2011patient, title = {Patient-Specific 3D Pretreatment and Potential 3D Online Dose Verification of Monte Carlo{\textendash}Calculated IMRT Prostate Treatment Plans}, journal = {International Journal of Radiation Oncology Biology Physics}, volume = {81}, number = {4}, year = {2011}, pages = {1168{\textendash}1175}, publisher = {Elsevier}, author = {Boggula , R. and Jahnke , L. and Wertz , H. and Lohr , F. and Wenz , F.} } @article { Ritzerfeld2011, title = {Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of Src kinases.}, journal = {Genome research}, volume = {21}, number = {11}, year = {2011}, month = {jul}, pages = {1955{\textendash}68}, abstract = {Src proteins are non-receptor tyrosine kinases that play key roles in regulating signal transduction by a diverse set of cell surface receptors. They contain N-terminal SH4 domains that are modified by fatty acylation and are functioning as membrane anchors. Acylated SH4 domains in turn are both necessary and sufficient to mediate specific targeting of Src kinases to the inner leaflet of plasma membranes. Acylation of most Src kinases proceeds in two steps with co-translational N-terminal myristoylation being followed by palmitoylation of cysteine residues, a process that occurs at the cytoplasmic leaflet of Golgi membranes. Intracellular transport of Src kinases from Golgi membranes to the inner leaflet of the plasma membrane depends on microdomains into which Src kinases partition upon palmitoylation. In the current study, we established a live cell imaging screening system to identify gene products involved in plasma membrane targeting of Src kinases. Based on siRNA arrays and a human model cell line expressing two kinds of SH4 reporter molecules, we conducted a genome-wide analysis of SH4-dependent protein targeting using an automated microscopy platform. We identified and validated 54 gene products whose down-regulation causes intracellular retention of SH4 reporter molecules. To detect and quantify this phenotype, we developed a software-based image analysis tool. Among the identified gene products we found factors involved in lipid metabolism, intracellular transport and cellular signalling processes. Furthermore, we identified proteins that are either associated with Src kinases or are related to various known functions of Src kinases such as other kinases and phosphatases potentially involved in Src-mediated signal transduction. Finally, we identified gene products whose function is less defined or entirely unknown. The complete list of validated gene products demonstrated to be involved in Src kinase targeting represents a major resource for future studies unravelling the molecular mechanisms that underlie proper targeting of Src kinases to the inner leaflet of plasma membranes.}, issn = {1549-5469}, doi = {10.1101/gr.116087.110}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3205579\&tool=pmcentrez\&rendertype=abstract}, author = {Ritzerfeld , Julia and Remmele , Steffen and Wang , Tao and Temmerman , Koen and Br{\"u}gger , Britta and Wegehingel , Sabine and Tournaviti , Stella and Strating , Jeroen Rpm and Wieland , Felix T and Neumann , Beate and Ellenberg , Jan and Lawerenz , Chris and Hesser , J{\"u}rgen and Erfle , Holger and Pepperkok , Rainer and Nickel , Walter} } @booklet {SRemele_SPIE2011 , title = {Reconstruction of high-resolution fluorescence microscopy images based on axial tomography}, howpublished = {Proc. SPIE Medical Imaging}, volume = {7962}, year = {2011}, author = {Remmele , Steffen and Oehm , Bianca and Staier , Florian and Eipel , Heinz and Cremer , Christoph and Hesser , J{\"u}rgen} } @article { Hoegele2011, title = {Stochastic formulation of patient positioning using linac-mounted cone beam imaging with prior knowledge.}, journal = {Medical physics}, volume = {38}, number = {2}, year = {2011}, month = {mar}, pages = {668{\textendash}81}, abstract = {In this work, a novel stochastic framework for patient positioning based on linac-mounted CB projections is introduced. Based on this formulation, the most probable shifts and rotations of the patient are estimated, incorporating interfractional deformations of patient anatomy and other uncertainties associated with patient setup.}, keywords = {Algorithms, Bayes Theorem, Computer-Assisted, Cone-Beam Computed Tomography, Cone-Beam Computed Tomography: methods, Humans, Image Processing, Imaging, Patient Positioning, Patient Positioning: methods, Phantoms, Stochastic Processes}, issn = {0094-2405}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21452704}, author = {Hoegele , W and Loeschel , R and Dobler , B and Hesser , J and Koelbl , O and Zygmanski , P} } @article { Schock-Kusch2011, title = {Transcutaneous assessment of renal function in conscious rats with a device for measuring FITC-sinistrin disappearance curves}, journal = {Kidney Int}, volume = {79}, number = {11}, year = {2011}, month = {jun}, pages = {1254{\textendash}1258}, issn = {0085-2538}, url = {http://dx.doi.org/10.1038/ki.2011.31}, author = {Schock-Kusch , Daniel and Xie , Qing and Shulhevich , Yury and Hesser , Juergen and Dzimitry Stsepankou and Sadick , Maliha and Koenig , Stefan and Hoecklin , Friederike and Pill , Johannes and Gretz , Norbert} } @conference { pyatykh_automatic_2010, title = {Automatic 3D tissue segmentation from MRI for hyperthermia treatment planning}, booktitle = {ESHO 2010}, year = {2010}, month = {may}, pages = {27{\textendash}28}, address = {Rotterdam, The Netherlands}, author = {S. Pyatykh and Lei Zheng and Wehner , Catharina and Ehmann , Michael and Fleckenstein , Katharina and Wenz , Frederik and Hesser , J{\"u}rgen} } @booklet { , title = {Breath-hold Target Localization with simultaneous Kilovoltage/Megavoltage Cone-Beam CT and fast Reconstruction}, howpublished = {Int. J. Radiation Oncology Biol. Phys}, year = {2010}, author = {Blessing , Manuel and Dzimitry Stsepankou and Wertz , Hansjoerg and Arns , Anna and Lohr , Frank and Hesser , J{\~A}{\textonequarter}rgen and Wenz , Frederik} } @article { Ueltzhoffer2010, title = {Clinical application of varian OBI CBCT system and dose reduction techniques in breast cancer patients setup.}, journal = {Medical physics}, volume = {37}, number = {6}, year = {2010}, month = {jun}, pages = {2985{\textendash}98}, abstract = {To characterize the standard modes of Varian on board imaging (OBI) v1.4 system and identify techniques to further optimize imaging parameters, in particular, for breast treatment setup.}, keywords = {Body Burden, Breast Neoplasms, Breast Neoplasms: radiography, Female, Humans, Mammography, Mammography: methods, Radiation Dosage, Radiation Protection, Radiation Protection: methods, Radiometry, Radiometry: methods, Tomography, X-Ray Computed, X-Ray Computed: instrumentation}, issn = {0094-2405}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20632611}, author = {Ueltzh{\"o}ffer , Stefan and Zygmanski , Piotr and Hesser , J{\"u}rgen and H{\"o}gele , Wolfgang and Wong , Julia and Bellon , Jennifer R and Lyatskaya , Yulia} } @proceedings { ESTROFleck2010, title = {Effects of interfractional motion on the dose distribution in volumetric modulated arc therapy (VMAT)}, year = {2010}, publisher = {ESTRO}, author = {Fleckenstein , J. and Boggula , R. and Stieler , F. and Jahnke , L. and Wenz , F. and Lohr , F.} } @article { Wertz2010, title = {Fast kilovoltage/megavoltage (kVMV) breathhold cone-beam CT for image-guided radiotherapy of lung cancer.}, journal = {Physics in medicine and biology}, volume = {55}, number = {15}, year = {2010}, month = {aug}, pages = {4203{\textendash}17}, abstract = {Long image acquisition times of 60-120 s for cone-beam CT (CBCT) limit the number of patients with lung cancer who can undergo volume image guidance under breathhold. We developed a low-dose dual-energy kilovoltage-megavoltage-cone-beam CT (kVMV-CBCT) based on a clinical treatment unit reducing imaging time to < or =15 s. Simultaneous kVMV-imaging was achieved by dedicated synchronization hardware controlling the output of the linear accelerator (linac) based on detector panel readout signals, preventing imaging artifacts from interference of the linac{\textquoteright}s MV-irradiation and panel readouts. Optimization was performed to minimize the imaging dose. Single MV-projections, reconstructed MV-CBCT images and images of simultaneous 90 degrees kV- and 90 degrees MV-CBCT (180 degrees kVMV-CBCT) were acquired with different parameters. Image quality and imaging dose were evaluated and compared to kV-imaging. Hardware-based kVMV synchronization resulted in artifact-free projections. A combined 180 degrees kVMV-CBCT scan with a total MV-dose of 5 monitor units was acquired in 15 s and with sufficient image quality. The resolution was 5-6 line pairs cm(-1) (Catphan phantom). The combined kVMV-scan dose was equivalent to a kV-radiation scan dose of approximately 33 mGy. kVMV-CBCT based on a standard linac is promising and can provide ultra-fast online volume image guidance with low imaging dose and sufficient image quality for fast and accurate patient positioning for patients with lung cancer under breathhold.}, keywords = {Cone-Beam Computed Tomography, Cone-Beam Computed Tomography: instrumentation, Cone-Beam Computed Tomography: methods, Humans, Imaging, Lung Neoplasms, Lung Neoplasms: physiopathology, Lung Neoplasms: radiography, Lung Neoplasms: radiotherapy, Phantoms, Radiation Dosage, Respiration, Rotation, Time Factors}, issn = {1361-6560}, doi = {10.1088/0031-9155/55/15/001}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20616405}, author = {Wertz , Hansjoerg and Dzimitry Stsepankou and Blessing , Manuel and Rossi , Michael and Knox , Chris and Brown , Kevin and Gros , Uwe and Boda-Heggemann , Judit and Walter , Cornelia and Hesser , Juergen and Lohr , Frank and Wenz , Frederik} } @proceedings { Degro2010proton, title = {On the feasibility of rotational proton treatments in compensator based proton radiotherapy in an energy stacking beam line}, year = {2010}, publisher = {DEGRO}, author = {Jahnke , L. and Fleckenstein , J. and Pack , D. and Anferov , V. and Fitzek , M.} } @article { Brockmann2010, title = {Graph-matching-based computed tomography angiography in peripheral arterial occlusive disease.}, journal = {Clinical imaging}, volume = {34}, number = {5}, year = {2010}, pages = {367{\textendash}74}, abstract = {The objective of this study is to compare a graph-matching-based software and a conventional tool for postprocessing of computed tomography angiography (CTA) in correlation with the gold standard digital subtraction angiography. Sensitivity, specificity, accuracy, and interobserver agreement increased from 80.3\% to 92.9\%, from 69.1\% to 92.4\%, from 73.5\% to 92.8\%, and from 0.45 to 0.96, respectively, using the graph-matching-based technique. Graph-matching-based CTA increases sensitivity, specificity, accuracy, and interobserver agreement in comparison to a conventional bone elimination tool in the assessment of peripheral arterial occlusive disease.}, keywords = {80 and over, Aged, Angiography, Angiography: methods, Computer-Assisted, Computer-Assisted: methods, Contrast Media, Contrast Media: diagnostic use, Digital Subtraction, Digital Subtraction: methods, Female, Humans, Image Processing, Imaging, Iohexol, Iohexol: analogs \& derivatives, Iohexol: diagnostic use, Male, Middle Aged, Observer Variation, Peripheral Arterial Disease, Peripheral Arterial Disease: radiography, Prospective Studies, Radiographic Image Enhancement, Radiographic Image Enhancement: methods, Reproducibility of Results, Sensitivity and Specificity, Software, Three-Dimensional, Three-Dimensional: methods, Tomography, X-Ray Computed, X-Ray Computed: methods}, issn = {1873-4499}, doi = {10.1016/j.clinimag.2009.10.034}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20813301}, author = {Brockmann , Carolin and Jochum , Susanne and Hesser , J{\"u}rgen and Maksimov , Dzmitry and Schnitzer , Andreas and Weiss , Christel and Diezler , Patricius and Schoenberg , Stefan O and Diehl , Steffen} } @proceedings { AAPM2010, title = {Implementation of a Geant4 Based GPU Monte Carlo Algorithm and Benchmarking of an IMRT Patient Plan}, year = {2010}, publisher = {AAPM}, url = {http://www.aapm.org/meetings/2010am/PRAbs.asp?mid=49\&aid=14005}, author = {Jahnke , L. and Fleckenstein , J. and Hesser , J. and Wenz , F.} } @conference { , title = {MRI artefact correction for (hyperthermia) treatment planning}, booktitle = {DEGRO 2010}, year = {2010}, month = {June}, publisher = {Deutschen Gesellschaft f{\"u}r Radioonkologie e.V. (DEGRO)}, organization = {Deutschen Gesellschaft f{\"u}r Radioonkologie e.V. (DEGRO)}, address = {Magdeburg, Germany}, author = {S. Pyatykh and Lei Zheng and Wehner , Catharina and Ehmann , Michael and Fleckenstein , Katharina and Wenz , Frederik and Hesser , J{\"u}rgen} } @conference { 4, title = {Breath-hold Target Localization with simultaneous Kilovoltage/Megavoltage Cone-Beam CT and fast Reconstruction}, booktitle = {World Congress 2009, medical physics and biomedical engineering, 11 international congress of IUPESM}, year = {2009}, abstract = {Hypofractionated high dose radiotherapy of small lung tumors is very effective and was based on stereotaxy until now. It has recently become possible to achieve a high patient positioning precision based on on-line imaging with cone-beam CT (CBCT) and breath-hold techniques. The CBCT acquisition time of roughly 60 seconds, however, is too long for one breath-hold, resulting in image degradation by respiratory motion artifacts. By using megavoltage (MV) an kilovoltage (kV) pho-ton source (mounted perpendicularly on the Linac gantry) for volume reconstruction, we could reduce the acquisition time to 15 seconds. An Elekta Synergy 6MV linear accelerator, iViewGT as an MV- and XVI as a kV-imaging device were used. In {\textquoteright}movie mode{\textquoteright} both systems were used for continuous image acquisi-tion passing the angle interval of 90{\textdegree} in 15 seconds. In total, the MV frames needed 8.25 Monitor Units. The kV dose was neg-ligible herein. In order to deduce the missing angle informa-tion, a marble with high absorption coefficient was put next to the thorax phantom. After preprocessing the data a GPU was used for the reconstruction of 100 projections generating a 512 x 512 x 512 volume in 6 seconds. The full acquisition and reconstruction workflow was au-tomated. Structures with high contrast interfaces can be rec-ognized easily in the reconstructed volume. These results show that fast on-board imaging based on combined kV-MV CBCT is promising for patient positioning. The scan duration of 15 seconds is short enough to perform single rotation breath-hold imaging for most patients.}, author = {Blessing , Manuel and Dzimitry Stsepankou and Wertz , Hansjoerg and Arns , Anna and Lohr , Frank and Hesser , J{\"u}rgen and Wenz , Frederik} } @article { b{\~A}�{\^A}{\textonequarter}rger2009, title = {Concurrent Particle Tracking using an iterative Kalman Filter approach}, journal = {Bildverarbeitung f{\~A}�{\^A}{\textonequarter}r die Medizin 2009}, year = {2009}, pages = {430{\textendash}433}, abstract = {Particle tracking is a widespread research question for quantitative biology. In contrast to other approaches, we developed a local greedy technique based on the Kalman filter. To overcome the problem of guessing the first state of a particle, the algorithm runs iteratively in forward and backward direction. The algorithm was successfully tested with simulated and real data.}, author = {Buerger , Benny and Hesser , Juergen} } @conference {SRemele_WCMP2009, title = {Constrained RLTV Deblurring for Confocal Microscopy}, booktitle = {World Congress on Medical Physics and Biomedical Engineering - 2009}, year = {2009}, publisher = {IUPESM}, organization = {IUPESM}, author = {Remmele , Steffen and Hesser , J{\"u}rgen} } @article { Buehler2009, title = {Evaluation of clip localization for different kilovoltage imaging modalities as applied to partial breast irradiation setup}, journal = {Medical Physics}, volume = {36}, number = {3}, year = {2009}, month = {mar}, pages = {821{\textendash}834}, abstract = {Surgical clip localization and image quality were evaluated for different types of kilovoltage cone beam imaging modalities as applied to partial breast irradiation (PBI) setup. These modalities included (i) clinically available radiographs and cone beam CT (CB-CT) and (ii) various alternative modalities based on partial/sparse/truncated CB-CT. An anthropomorphic torso-breast phantom with surgical clips was used for the imaging studies. The torso phantom had artificial lungs, and the attached breast phantom was a mammographic phantom with realistic shape and tissue inhomogeneities. Three types of clips of variable size were used in two orthogonal orientations to assess their in-/cross-plane characteristics for image-guided setup of the torso-breast phantom in supine position. All studies were performed with the Varian on-board imaging (OBI, Varian) system. CT reconstructions were calculated with the standard Feldkamp-Davis-Kress algorithm. First, the radiographs were studied for a wide range of viewing angles to characterize image quality for various types of body anatomy in the foreground/background of the clips. Next, image reconstruction quality was evaluated for partial/sparse/truncated CB-CT. Since these modalities led to reconstructions with strong artifacts due to insufficient input data, a knowledge-based CT reconstruction method was also tested. In this method, the input data to the reconstruction algorithm were modified by combining complementary data sets selected from the treatment and reference projections. Different partial/sparse/truncated CB-CT scan types were studied depending on the total are angle, angular increment between the consequent views (CT projections), orientation of the arc center with respect to the imaged breast and chest wall, and imaging field size. The central angles of the viewing arcs were either tangential or orthogonal to the chest wall. Several offset positions of the phantom with respect to the reference position were studied. The acquired and reconstructed image data sets were analyzed using home-built software focusing on the ability to localize clips in 3D. Streaking and leakage reconstruction artifacts and spatial distortions of breast surface were analyzed as well. Advantages and disadvantages of each kilovoltage CB imaging modality as applied to partial breast setup evaluation based on clips are presented. Because clips were found to be difficult to recognize in radiographs, 3D reconstructions were preferred. Even though it was possible to localize clips with about +/-1 mm accuracy based on reconstructions for short arcs of 40 degrees and incremental angle up to about 5 degrees, identification of clips in such reconstructions is difficult. Reconstructions obtained for arcs of as low as 80 degrees and incremental angle of as high as 3 degrees were suggested for easier clip identification. For more severely undersampled data, iterative CB-CT reconstruction is recommended to decrease the artifacts.}, keywords = {Algorithms, Biophysical Phenomena, Breast Neoplasm}, issn = {0094-2405}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19378743}, author = {Buehler , Andreas and Ng , Sook-Kien and Lyatskaya , Yulia and Dzimitry Stsepankou and Hesser , J{\"u}rgen and Zygmanski , Piotr} } @article { D.Maksimov2009, title = {Graph-matching based CTA}, journal = {IEEE Transactions on Medical Imaging}, volume = {28}, number = {12}, year = {2009}, pages = {1940-1954}, author = {Maksimov , D. and Hesser , J. and Dietz , T. and Schnitzer , A. and D{\"u}ber , C. and Sch{\"o}nberg , S. and Diehl , S.} } @conference { biedermann_hippocampal_2009, title = {Hippocampal alterations in congenital learned helpless rats after electroconvulsive seizures detected with in vivo 1H MR-Spectroscopy at 9.4T}, booktitle = {Proceedings 17th Scientific Meeting, International Society for Magnetic Resonance in Medicine}, year = {2009}, month = {apr}, pages = {3289}, abstract = {Psychiatric patients suffer from the time-delayed onset of antidepressive treatments. Electroconvulsive treatment (ECT) has a more rapid acting onset of the antidepressive effect. With the help of high field 1H magnetic resonance spectroscopy at 9.4 T we examined congenital learned helpless (cLH) rats\{\textquoteright} hippocampi after a six days course of ECS. We found a significant increase in choline, glutamate and GABA concentrations after ECS. The increase of glutamate correlated significantly with an increase of GABA. Glutamine was unaltered by ECS. These results support the hypothesis of ECS induced neurogenesis and increased synaptic plasticity.}, author = {Biedermann , Sarah and Sartorius , Alexander and Lei Zheng and Vollmayr , Barbara and Gass , Peter and Ende , Gabriele and Weber-Fahr , Wolfgang} } @conference { , title = {Klinische Implementation von GEANT4 zur Verifikation komplexer IMRT-Dosisverteilungen eines ELEKTA SYNERGY Linearbeschleunigers}, booktitle = {DEGRO2009}, year = {2009}, publisher = {Deutsche Gesellschaft f{\"u}r Radioonkologie}, organization = {Deutsche Gesellschaft f{\"u}r Radioonkologie}, author = {Fleckenstein , Jens and Jahnke , Lennard and Petersheim , Markus and Hesser , J{\"u}rgen and Wenz , Frederik} } @conference { 5, title = {kV beam model for flat panel imaging system with bow tie filter}, booktitle = {2009 Munich: World Congress 2009, medical physics and biomedical engineering, 11 international congress of IUPESM}, year = {2009}, abstract = {Purpose: Kilovoltage flat-panel imaging systems are used for cone-beam Computed Tomography (CBCT) and digital Tomosynthesis (DTS). Hereby, the presence of scatter and relatively large dose from imaging are challenging factors. In this project a phenomenological beam model was developed to characterize imager response to imaging beams with a bow tie filter (Varian OBI system). Materials and Method: The kilovoltage beam model is based on dose ratio formalism and thus is using standard concepts of megavoltage dose calculation such as scatter factors, tissue maximum ratio and off-axis ratio. Primary and scatter (head and phantom scatter) are modeled with three Gaussian kernels. Parameters were derived with slabs of solid water and various jaw settings. Results: The beam model was used to evaluate contribu-tions from primary, secondary and tertiary photons for different geometrical objects such as cylinders and steps of solid water. Predictions of radiographs using the model for known objects are consistent with the measurements. Conclusion: Secondary and tertiary contributions were interpreted as scatter and can be subtracted from CBCT projections. Therefore our model can provide a basis for improvement of image quality (less artifacts due to scatter, better contrast and resolution) in CBCT reconstruction.}, author = {Blessing , Manuel and Bhagwat , Mandar and Lyatskaya , Yulia and Bellon , Jennifer and Zygmanski , Piotr} } @article { Boggula2009, title = {A new strategy for online adaptive prostate radiotherapy based on cone-beam CT.}, journal = {Zeitschrift f{\"u}r medizinische Physik}, volume = {19}, number = {4}, year = {2009}, month = {jan}, pages = {264{\textendash}76}, abstract = {Interfractional organ motion and patient positioning errors during prostate radiotherapy can have deleterious clinical consequences. It has become clinical practice to re-position the patient with image-guided translational position correction before each treatment to compensate for those errors. However, tilt errors can only be corrected with table corrections in six degrees of freedom or "full" adaptive treatment planning strategies. Organ shape deformations can only be corrected by "full" plan adaptation. This study evaluates the potential of instant treatment plan adaptation (fast isodose line adaptation with real-time dose manipulating tools) based on cone-beam CT (CBCT) to further improve treatment quality.}, keywords = {Computer-Assisted, Computer-Assisted: methods, Humans, Imaging, Male, Online Systems, Patient Positioning, Phantoms, Prostate, Prostate: anatomy \& histology, Prostate: radiography, Prostatic Neoplasms, Prostatic Neoplasms: radiography, Prostatic Neoplasms: radiotherapy, Radiotherapy Dosage, Radiotherapy Planning, Rectum, Rectum: anatomy \& histology, Rectum: radiography, Tomography, X-Ray Computed, X-Ray Computed: methods}, issn = {0939-3889}, doi = {10.1016/j.zemedi.2009.05.007}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19962084}, author = {Boggula , Ramesh and Lorenz , Friedlieb and Abo-Madyan , Yasser and Lohr , Frank and Wolff , Dirk and Boda-Heggemann , Judit and Hesser , Juergen and Wenz , Frederik and Wertz , Hansjoerg} } @conference { , title = {Novel procedures for highly conformal percutaneous radiation with keV-photons for tumor treatment in skin proximity}, booktitle = {World Congress on Medical Physics and Biomedical Engineering - 2009}, year = {2009}, publisher = {IUPESM}, organization = {IUPESM}, abstract = {Photon beams in the energy range of keV are more cost effective and require less shielding efforts compared to MeV-photons or particle beams. The absent build-up effect for low-energetic X-rays however is challenging for percutaneous radiotherapy. In this work, we study a possible improvement of the TCP-NTCP ratio (tumor control vs. normal tissue complication) by geometrically superimposing different collimated beamlets. Furthermore, inducing gold (Au) particles into the cancerous tissue leads to a local dose enhancement by additional emission of low-energetic electrons. We analyze this setup with regards to its suitability for clinical use. The study is based on the example of the X-ray source Axxent S700 from Xoft Inc., which is sampled in a Monte Carlo calculation (Geant4). After developing a source model, irradiation with single beams from different directions and distances is simulated and the resulting dose kernels are stored. The weighting factors of the superposition are optimized using linear programming. These simulations are repeated for a tumor volume containing different dosages of gold. The results show that keV-photon irradiation alone does not seem to be suitable for external radiotherapy below the skin. In combination with dose enhancement, however, a two times higher dose to the tumor, compared to skin dose can be achieved. With narrow collimation, a dose ratio of five is generated, though only in a very small focal volume. Since primarily the analysis of the local dose enhancement is promising, we suggest to further explore this method including a combination with intracavitary electronic Brachytherapy.}, author = {Petersheim , Markus and Hesser , J{\~A}{\textonequarter}rgen and Wenz , Frederik} } @conference { , title = {Percutaneous conformal radiotherapy with keV-photons using a large number of incident beam directions and artificial dose enhancement}, booktitle = {DEGRO2009}, number = {P278}, year = {2009}, publisher = {Deutsche Gesellschaft f{\~A}{\textonequarter}r Radioonkologie}, organization = {Deutsche Gesellschaft f{\~A}{\textonequarter}r Radioonkologie}, abstract = {Percutaneous conformal radiotherapy with keV-photons using a large number of incident beam directions and artificial dose enhancement Purpose: This study investigates a dedicated strategy for percutaneous conformal radiotherapy with keV-photons. Despite the striking advantages of less equipment cost and less shielding overhead, low energetic X-rays suffer from the lack of the build-up effect demanding sophisticated methods to ensure suitable tumor conformity using dose enhancement and many focused beam directions. Method and Materials: A 50 kVp X-ray source (Axxent S700, Xoft Inc.) was modeled based on its AAPM task group 42 emission properties. The source was equipped with a cylindrical collimator to enable directional irradiation distal to the tube only. A phase-space of the emitted particles was calculated and validated using the Geant4 Monte Carlo toolkit. In the next step, irradiation of a water phantom with a defined tumor volume (depth of tumor center = (50mm), tumor volume = (50mm x 50 mm x 50mm)) was simulated and single beamlet dose distributions were acquired for an optimal arrangement of 13 different incident polar angles and 5 distances. Cylindrical symmetry was used to expand these dose distributions over 45 different incident azimuthal angles by rotating the voxel grid around the propagation axis, thus gaining a total number of 2950 dose kernels. A linear programming based optimization algorithm was implemented to achieve the optimal weightings of each beamlet. These weighting factors correspond to irradiation time in a real treatment. In the simulation, a superposition of the weighted dose kernels led to the resulting dose distribution and hence to the depth dose curve in the water phantom. For further amplification of tumor dose, the simulation was repeated modeling different dosages of uniformly distributed gold particles in the tumor volume. Comparison of the resulting depth dose characteristics should give information about the suitability of dose enhancement by secondary electrons from artificially induced high-Z materials. Results: It was found, that even with optimized combination of a large number of different beams from different angles, keV-photon irradiation alone is not suitable for external radiotherapy of structures below the skin. In combination with dose enhancement, however, a two times higher dose to the tumor, compared to skin could be achieved. With very narrow collimation, even a dose ratio of five could be generated, though only to a very small focal volume (8mm x 8mm x 16mm). Conclusion: Since primarily the analysis of the local dose enhancement was promising, further exploration of this method is suggested, especially transferring the simulation to real patient data and expanding the analysis to micro-dosimetric measures. In combination with intra-cavitary electronic brachytherapy, the artificial dose enhancement could also be very supportive for ensuring local dose conformality.}, author = {Petersheim , Markus and Hesser , J{\~A}{\textonequarter}rgen and Wenz , Frederik} } @booklet {Abkai2009, title = {Physiological Modeling and Real-Time Simulations Based on Dynamic Bayesian Networks}, howpublished = {MICCAI2009}, year = {2009}, abstract = {

This paper discusses a new strategy for describing physiological models by Dynamic Bayesian Networks (DBN). These networks allow to mod- el event based dynamic changes of physiological parameters in an independent way, e.g. for medications, interventions, and complications. Hierarchical struc- tures and the graph structures enable knowledge-based modeling and thus to mitigate model complexity. By its statistical nature, the strategy consequently allows handling uncertainty directly. Furthermore, learning routines yield pa- rameter estimation from real data. The applicability is shown for a real-time human patient simulator. Simulation time is dependent to the number of nodes and discrete values, which represent the range of system dynamics. Due to pa- rameter reduction a speed up in comparison to standard integrative approaches is possible. We simulate a circulatory system within 2.5 ms each simulation step on a standard PC.

}, author = {Abkai , Ciamak and Hesser , J{\"u}rgen} } @article { , title = {Psychomotor Profiling with Bayesian Neworks: Prediction of User Abilities based on Inputs of Motorized Wheelchair Parameters}, journal = {SMC2009}, year = {2009}, abstract = {A high level of psychomotor abilities often is essential for successfully operating many technical systems and especially medical and rehabilitation devices. This paper introduces an approach to enable a technical system to automatically assess its user{\textquoteright}s level of psychomotor abilities, so that it can adapt its level of automation and provide the user with more or less assistance depending on the individual user profile. For this purpose, a study has been conducted during which the motor abilities of the participants have been assessed and their wheelchair control behavior recorded. Bayesian Networks (BN) and Structural Equation Models (SEM) have been applied to model the relationships between the wheelchair control behavior and the motor abilities of the participants. The BN demonstrate usefulness and magnificent advantages compared to the SEM for modeling uncertainty in structure and parameter dependencies, which are shown by validation experiments. Although only a small amount of data samples (23 participants) was available for model generation, a target variable reflecting the user{\'s} precision ability was successfully classified based on real data input in more than 82\% of cases.}, author = {Jipp , Meike and Bartolein , Christian and Badreddin , Essam and Abkai , Ciamak and Hesser , Juergen} } @conference { zheng_rat_2009, title = {A rat brain template of class distribution maps based on diffeomorphic image registration}, booktitle = {Proceedings 17th Scientific Meeting, International Society for Magnetic Resonance in Medicine}, year = {2009}, month = {apr}, pages = {2897}, abstract = {Brain tissue segmentation is an important step to post-process MR images. From part of the data, the rat brain was extracted and segmented. The individual segmentation results were co-registered based on diffeomorphic image registration to generate a rat brain template of class distribution maps. With this template, later, the segmentation of rat brain can be achieved automatically.}, author = {Lei Zheng and Biedermann , Sarah and Hesser , J{\"u}rgen and Sartorius , Alexander and Weber-Fahr , Wolfgang} } @article { abkai2009_2, title = {Real-Time ECG Emulation: A Multiple Dipole Model for Electrocardiography Simulation}, journal = {Studies in Health Technology and Informatics}, volume = {142}, year = {2009}, pages = {7{\textendash}9}, abstract = {A new model for describing electrocardiography (ECG) is presented, which is based on multiple dipoles compared to standard single dipole approaches in vector electrocardiography. The multiple dipole parameters are derived from real data (e.g. four dipoles from 12-channel ECG) by solving the backward problem of ECG numerically. Results are transformed to a waveform description based on Gaussian mixture for every dimension of each dipole. These compact parameterized descriptors are used for a very realistic real-time simulation applying the forward solution of the proposed model.}, author = {Abkai , Ciamak and Hesser , J} } @article { , title = {Reasoning and Risk Assessment based on Real-Time Physiological Simulations and Dependable Vital Parameter Monitoring}, journal = {WC2009}, year = {2009}, abstract = {We present a novel approach for dependability analysis of medical devices. As focus, we considered vital pa- rameter monitoring. The basic strategy relies on using me- thods from system theory. For the first time not only the tech- nical device but also the patient is taken into consideration. Including the patient requires prediction of physiology which is achieved by a real-time physiological simulation in a conti- nuous time domain, whereby one of the main ingredients is a temporal reasoning element. The quality of the reasoning is expressed by a dependability analysis strategy. Thereby, ano- malies are expressed as differences between simulation and real world data. Deviations are detected for current and they are forecasted for future points in time. By this method, pa- tient specific differences in terms of physiological reactions are described, allowing early detection of critical states. The inter- play of the different elements and the consequences are ex- plained in a realistic model.}, author = {Abkai , Ciamak and Hesser , Juergen} } @conference { , title = {Robust and reliable stripe detection for CBCT}, booktitle = {DEGRO}, year = {2009}, abstract = {Purpose: Combined kV-MV cone-beam CT reduces scanning time by up to 75\% compared to the standard scanning procedure. Hence, this technology is enabling on-board imaging for IGRT of lung cancer within a breathhold. 60 kV and 40 MV projections are acquired. MV projections are mapped onto kV energy by histogram adaptation and then reconstructed by filtered back projection. Since readout and irradiation are not synchronized, brightness variations on the projection data manifest as stripes. Robust and problem independent stripe detection is thus a necessary processing task for solving this problem and is discussed in detail. Methods and Materials: Projection data was acquired from an Elekta Synergy 6MV Linac. In the processing workflow, the variance of gradient locations along the stripe direction was used to generate a profile which was then selected for locating stripes. Although these profiles showed articulated peaks in the presence of stripes, their amplitude and width were not uniform indicating that thresholding was neither sufficient, nor stable for extracting them from the background. Standard methods for automatic threshold detection thus failed. In our approach, the variance of high gradient locations coincided with peak maxima but other structures in the image led to maxima as well, although being smaller. Since the stripes had a certain width, threshold selection failed. Non-maximum-suppression overcame this problem leading to a large gap between peaks in the profile originating from stripes and those coming from other structures. Finding the largest gap separating these two classes was found to be a robust and reliable method for classifying stripes and other structures. Results: Using this automated processing, we determined stripes for four different projection data sets with each 150-160 images. The sensitivity of this method was 92.8\% while the specificity was 100\%. Running on a PC Pentium{\textregistered} 4 CPU 3GHz and non-optimized Matlab, processing time per 754x754 pixel image was 3.9 {\textpm} 0.9 [s]. In case of very bright background structures, not all stripes were detected, because the magnitude of the stripes only marginally differed from the magnitude of these other structures. Therefore, the variance profile was very unsteady regarding to peak maxima and thus the threshold was set too high. Conclusions: Using this automated stripe detection, the kV-MV-preprocessing and reconstruction software now automatically reconstructs acquired projections into volumes. High contrast structures like tumors in the lung can then be easily detected in the reconstructed volume and thus potential misalignment of patients can be found.}, author = {Arns , Anna and Blessing , Manuel and Dzimitry Stsepankou and Wertz , Hansj{\"o}rg and Lohr , Frank and Hesser , J{\"u}rgen and Wenz , Frederik} } @conference { SR4, title = {Robust Segmentation of Blurred CT Data Sets}, booktitle = {DEGRO09}, year = {2009}, address = {Bremen}, author = {Remmele , Steffen and Hesser , Juergen and Wenz , Frederik} } @conference { SR3, title = {Vector Extrapolation Based Acceleration of Regularized Richardson Lucy Image Deblurring}, booktitle = {BVM09}, year = {2009}, pages = {400{\textendash}404}, address = {Heidelberg}, author = {Remmele , Steffen and Hesser , J{\"u}rgen} } @conference { abkai2009_1, title = {Virtual Intensive Care Unit (ICU): Real-Time Simulation Environment Applying Hybrid Approach Using Dynamic Bayesian Networks and ODEs}, booktitle = {Studies in Health Technology and Informatics}, volume = {142}, year = {2009}, pages = {1{\textendash}6}, abstract = {Combining deterministic (e.g. differential equations) and probabilistic (Bayesian Networks) approaches to model physiological processes in a real-time software environment leads to a novel model for simulation of human patient physiology especially relevant for intensive care units (ICU). Using dedicated HW/SW interfaces simulated patient signals are measurable with standard monitoring systems. Therefore, this system, based on realistic simulations, is very well suited for teaching and education. Additionally, the environment is usable for inferring patient-specific model structures and parameters. We introduce a hierarchical modeling approach, which allows building complex models based on aggregation of simple sub models. The simulation is controlled to run in real-time with typical sampling times of 1?10 ms (depending on model complexity) on a standard PC (Pentium 2.66 GHz CPU).}, author = {Abkai , Ciamak and Hesser , J{\"u}rgen} } @article { Boda-Heggemann2008, title = {Accuracy of ultrasound-based (BAT) prostate-repositioning: a three-dimensional on-line fiducial-based assessment with cone-beam computed tomography.}, journal = {International journal of radiation oncology, biology, physics}, volume = {70}, number = {4}, year = {2008}, month = {mar}, pages = {1247{\textendash}55}, abstract = {To assess the accuracy of ultrasound-based repositioning (BAT) before prostate radiation with fiducial-based three-dimensional matching with cone-beam computed tomography (CBCT).}, keywords = {Algorithms, Calcinosis, Calcinosis: radiography, Calcinosis: ultrasonography, Calibration, Cone-Beam Computed Tomography, Cone-Beam Computed Tomography: methods, Humans, Imaging, Intensity-Modulated, Iodine Radioisotopes, Iodine Radioisotopes: diagnostic use, Male, Pelvic Bones, Pelvic Bones: radiography, Pelvic Bones: ultrasonography, Prostate, Prostate: radiography, Prostate: ultrasonography, Prostatic Diseases, Prostatic Diseases: radiography, Prostatic Diseases: ultrasonography, Prostatic Neoplasms, Prostatic Neoplasms: radiography, Prostatic Neoplasms: radiotherapy, Prostatic Neoplasms: ultrasonography, Radiotherapy, Three-Dimensional, Three-Dimensional: methods}, issn = {0360-3016}, doi = {10.1016/j.ijrobp.2007.12.003}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18313531}, author = {Boda-Heggemann , Judit and K{\"o}hler , Frederick Marc and K{\"u}pper , Beate and Wolff , Dirk and Wertz , Hansj{\"o}rg and Mai , Sabine and Hesser , J{\"u}rgen and Lohr , Frank and Wenz , Frederik} } @conference { SR2, title = {Automated Cell Analysis Tool for a genome-wide RNAi screen}, booktitle = {MIAAB08}, year = {2008}, address = {New York}, author = {Remmele , Steffen and Ritzerfeld , Julia and Nickel , Walter and Hesser , J{\"u}rgen} } @conference { 3, title = {Fast On-board Imaging Based On Combined Kilovoltage Megavoltage Cone-beam Reconstruction Manuel Blessing and Dzmitry Stsepankou and Frank Lohr and J{\~A}{\textonequarter}rgen Hesser and Frederik Wenz}, booktitle = {ASTRO2008}, year = {2008}, author = {Blessing , Manuel and Dzimitry Stsepankou and Lohr , Frank and Hesser , Juergen and Wenz , Frederik} } @conference { SR1, title = {Fluorescence Microscopy Deconvolution based on Bregman Iteration and Richardson-Lucy Algorithm with TV Regularization}, booktitle = {BVM08}, year = {2008}, pages = {72{\textendash}76}, address = {Berlin}, author = {Remmele , Steffen and Seeland , Madeleine and Hesser , J{\"u}rgen} } @proceedings { Astro 2008, title = {GPU-acceleration of GEANT4-based Monte Carlo Simulations for Radio Therapy}, year = {2008}, publisher = {ASTRO}, author = {Jahnke , L. and Fleckenstein , J. and Clausen , S. and Hesser , J. and Lohr , F. and Wenz , F.} } @article { abkai2008_2, title = {Individual Ability-based System Configuration - Cognitive Profiling with Bayesian Networks}, journal = {Studies in Health Technology and Informatics}, volume = {132}, year = {2008}, abstract = {In this paper, we present a new method to model individual cognitive abilities, which were originally described by structural equation models and which can be used to reduce the possibility of human error when interacting with complex technical system. Our proposed model is based on hierarchical Bayesian Networks and deals therefore with uncertain and noisy data. The validity of the method is demonstrated on the basis of simulations of real-life data. The inference from the Bayesian Network demonstrates that estimating the user{\^a}{\texteuro}{\texttrademark}s cognitive abilities is possible in a reliable manner in real-time. Structural and data dependency analyses further show that less evidence data are necessary to provide cognitive profile classification. This especially highlights the advantage of our new method in comparison to the {\^a}{\texteuro}{\textquotedblleft} in psychology {\^a}{\texteuro}{\textquotedblleft} traditionally used structural equation models. Such cognitive profiling will allow adapting a system{\^a}{\texteuro}{\texttrademark}s demand character to the cognitive ability level of an individual user, which will make operating that system less error-prone, as many human errors result out of systems requesting more cognitive abilities than the operator has available.}, author = {Jipp , Meike and Abkai , Ciamak and Badreddin , Essam and Hesser , J{\~A}{\textonequarter}rgen} } @conference {zheng2008removal, title = {Removal of bone information in dual energy CT}, booktitle = {Proceedings of the MICCAI-CVII Workshop}, year = {2008}, pages = {120{\textendash}127}, address = {New York, USA}, abstract = {

Computer tomography angiography (CTA) allows to assess the degree of stenosis in vascular systems, but requires the separation of vessels against bone and calcifications. In this paper, a new technique of converting dual energy data into a virtual native and contrast agent scan pair allows to use a graph based method of bone removal for CTA. For evaluation purposes, patients with a high degree of calcification, i.e. complicated cases, are considered. Our automatic bone-removal technique requires 28-30 minutes on a Intel Core 2 Quad 2.66 GHz with 4 GByte RAM for a 1.2 GByte data set and is applied in the clinic for evaluation purposes. For 10 evaluated patients, sensitivity, specificity, and accuracy are 90\%. A further improvement of the differentiation quality is limited by the noise of the CT images.

}, author = {Lei Zheng and Maksimov, Dmitry and Stutzmann, Tobias and Jochum, Susanne and Brockmann, Carolin and Diehl, Steffen and Hesser, J{\"u}rgen} } @conference { 2, title = {Schnelle Bildgebung auf Basis von kombinierter kV-MV Rekonstruktion}, booktitle = {DEGRO2008}, year = {2008}, author = {Blessing , Manuel and Dzimitry Stsepankou and Lohr , Frank and Wenz , Frederik and Hesser , Juergen} } @article { abkai2008_1, title = {Simulation of Dynamic Ultrasound Based on CT Models for Medical Education}, journal = {Studies in Health Technology and Informatics}, volume = {132}, year = {2008}, pages = {65-61}, abstract = {In our approach, we first specify a 3D model of the image structure by segmenting a CT dataset into the respective tissues followed by assigning the acoustic properties (velocity, impedance, scattering mean and standard deviation, damping factor and packing factor). Given that model, we simulate the ray propagation, beam forming, and finally the backscattering. Due to the inhomogenities of tissue, different physical models for ultrasound simulation are required: Rayleigh scattering is applied for homogenous regions and ray tracing techniques handle abrupt changes in acoustic impedance on tissue boundaries. The latter leads to different phenomena like refraction (Snell\\\\\\{\'s} law), reflection and transmission (Fresnel equation). The gradients needed for these methods are precomputed for each model using a central-difference method with multiple neighbours. Absorption is calculated by the Beer-Lambert law.}, url = {images/Publication/2008/2008_buerger_us.pdf}, author = {Buerger , Benny and Abkai , Ciamak and Hesser , Juergen} } @conference { NicoBecherer2007, title = {Interactive Physical Simulation of Catheter Motion for Mayor Vessel Structures and Cavities for ASD/VSD Treatment}, booktitle = {Proc. SPIE Medical Imaging}, volume = {6509}, year = {2007}, author = {Becherer , N. and Hesser , J. and Kornmesser , U. and Schranz , D.} } @article { abkai2007_1, title = {Real-Time Simulator for Intravascular Ultrasound (IVUS)}, journal = {Proc. SPIE Medical Imaging}, volume = {8}, year = {2007}, abstract = {Intravascular Ultrasound (IVUS) plays a significant role in diagnostics of atherosclerotic diseases. Simulation of imaging techniques promises a better understanding of the physical background and segmentation strategies. Most simulation approaches describe ultrasonic backscattering using wave-equation based simplifications. More complicated real-time simulation techniques are not available so far. In this paper, we present an empirical model derived from wave-equations given by the Rayleigh integration method. According to boundary conditions and weak scatterers, a hybrid approach including the Beer-Lambert law to model attenuation is introduced. Scatterers are described by a 4D vessel-system model based on elastic tubes. Sophisticated discretization and numerical simplifications in addition to a highly optimized implementation of the model yields a real-time and realistic IVUS simulation with 20 frames/s on a 3.2 GHz Pentium 4 PC.}, url = {images/Publication/2007/2007_abkai_ivus.pdf}, author = {Abkai , Ciamak and Becherer , Nico and Hesser , Juergen and Maenner , Reinhard} } @conference { S.Koenig2006, title = {3D Live-Wires on Mosaic Volumes}, booktitle = {Medicine Meets Virtual Reality 14}, volume = {119}, year = {2006}, pages = {264-266}, author = {K{\"o}nig , S. and Hesser , J. and M{\"a}nner , R.} } @article { ChristophBock2006, title = {Analysis and prediction of helix shift errors in homology modeling}, journal = {In Silico Biology}, volume = {6}, year = {2006}, pages = {131-145}, author = {Bock , C. and Hesser , J.} } @conference { 1, title = {Analysis of the Point Spread Function of Isocentric Digital Tomosynthesis (DTS)}, booktitle = {AAPM2006}, year = {2006}, abstract = {Purpose: This project presents an analysis of the point spread function (PSF) of isocentric digital tomosynthesis (DTS). DTS is a limited angle 3- dimensional reconstruction from cone beam projections, with high resolution for excellent imaging of both bony anatomy and soft tissue. Its major application is on-board imaging. The scans can be acquired during a single breath hold, thus eliminating respiratory motion artifacts without gating techniques. Method and Materials: The geometry of a linear accelerator (Clinac 21EX from Varian) equipped with a kV on-board imager and CBCT capability was used. We simulated projection data sets of a single point source (PS) for different total scan angles from 26{\textdegree} to 58{\textdegree}. The PS was located along the horizontal axis through the isocenter from the kV x-ray source to the detector (z-axis). DTS reconstructions were generated from the simulated projections, using a standard Feldkamp technique. The full width at half maximum (FWHM) of the resulting PSF was computed along the z-direction in stacks of DTS slices. Results: The PSF shows a bow-tie shape in the z-direction. The spread of the blurring function increases for larger scan angles. Furthermore, the FWHM decreases as both distance from the detector and the scan angle increase. FWHM values ranged from ~2.5mm to ~5mm near the kV source, and from ~5mm to ~11mm near the detector, as the scan angle was varied. For a typical 44~ scan, the FWHM varied from ~3mm when the PS was moved 20cm towards the source away from the isocenter, to ~6mm when was moved 24cm towards the detector. Conclusion: The blurring effect of isocentric DTS is dependent on the total scan angle and the point of interest. These characteristics will provide guidance to imaging techniques using DTS for clinical applications.This project is partially supported by Varian Medical System.}, author = {Blessing , Manuel and Godfrey , Devon and Lohr , Frank and Yin , Fang-Fang} } @conference { , title = {Clinical Evaluation of the Performance of a Fuzzy Logic Guided Parameter Optimization for Inverse Treatment Planning}, booktitle = {Medical Physics}, volume = {33}, number = {6}, year = {2006}, pages = {2077}, publisher = {AAPM}, organization = {AAPM}, abstract = {Purpose: To evaluate the effectiveness of a Fuzzy Logic guided parameter optimization method for inverse treatment planning, in comparison with the results achieved by routine trial-and-error method. Method and Materials: The optimization algorithm was developed and integrated into a commercial planning system (Varian Eclipse). 10 prostate IMRT cases previously planned and approved by experienced planners were re-optimized using this automated method with the same beam geometry. The original dose-volume histogram (DVH) constraints were used as the initial parameter setup of the automated method. For each organ, the output dose was evaluated based on the percentage of dose received by a specific percentage of volume. The average dose difference between the automated and manual plans was calculated over a set of specified percentage volumes (99\%, 80\%, 60\%, 40\%, 20\%, 10\%, 5\%, 1\%). In addition, an experienced clinical physicist evaluated the acceptability of the plans generated by the automated method in terms of isodose distributions and DVHs. Results: Adoption of the automated method achieved both a comparable coverage of the planning target volume (PTV) and a substantial dose sparing of organs at risk (OARs). The mean dose was reduced by 30\% for bladder, and 25\% for rectum. There were few hot spots observed on OARs due to the overemphasis of PTV dose coverage. Conclusion: Preliminary results show that the automated parameter optimization method results in a significant dose reduction of OARs while maintaining a comparable PTV dose coverage. The automated method is able to relieve the burden of routine trial-and-error procedures done by planners, and has the potential to improve the resulting plan. However, minor manual intervention is still necessary to incorporate certain case-specific information, which is beyond the capability of the automated method. This study is partially supported by a research grant from Varian Medical Systems.}, url = {http://dx.doi.org/10.1118/1.2241049}, author = {Petersheim , Markus and Yan , Hui and Wenz , Frederik and Yin , Fang-Fang} } @article { jahnke2006intensity, title = {Dynamic IMRT treatments of sinus region tumors: comparison of Monte Carlo calculations with treatment planning system calculations and ion chamber measurements.}, journal = {Technology in cancer research \& treatmentTechnol Cancer Res Treat.}, volume = {5}, number = {5}, year = {2006}, pages = {489{\textendash}495}, publisher = {Adenine Press}, author = {Jahnke , L. and Chin , D. and Song , Jun and Cormack , R. and Zygmanski , P. and Tishler , R.B. and Chin , L.} } @conference { V.Vengrinovich2006, title = {New hull-voxel approach to image reconstruction from limited projection and views}, booktitle = {ECNDT}, year = {2006}, pages = {11}, author = {Vengrinovich , V. and Zolotarev , S. and Hesse , B. and Schlegel , W. and Hesser , J.} } @conference { N.Becherer2007, title = {On Soft Clipping of Zernike Moments for Deblurring and Enhancement of Optical Point Spread Functions}, booktitle = {Image Processing: Algorithms and Systems, Neural Networks, and Machine Learning, Proceedings of the SPIE}, volume = {6065}, year = {2006}, pages = {73-83}, author = {Becherer , N. and J{\"o}dicke , H. and Schlosser , G. and Hesser , J. and Zeilfelder , F. and M{\"a}nner , R.} } @conference { S.Koenig2005, title = {3D Live-Wires on Pre-Segmented Volume Data}, booktitle = {SPIE Medical Imaging 2005}, year = {2005}, pages = {1674-1679}, author = {K{\"o}nig , S. and Hesser , J.} } @conference { P.Buehler2005, title = {Automated 3D reconstruction of coronary artery tree based on stachastic branch\&bound}, booktitle = {Proc. SPIE Medical Imaging}, volume = {5747}, year = {2005}, pages = {741-746}, author = {Buehler , P. and Rebholz , P. and Hesser , J.} } @conference { D.Stsepankou2005a, title = {Cone-Beam CT Reconstruction Using a Combination of FPGAs and GPUs}, booktitle = {HVC Workshop 2005}, year = {2005}, author = {Dzimitry Stsepankou and Hesser , J.} } @conference { A.Kryvanos2005a, title = {Fast Total Variation Image Restoration Methods}, booktitle = {In 8th Intern. Conf. On Pattern Recognition and Information Processing}, year = {2005}, pages = {140-143}, author = {Kryvanos , A. and Hesser , J.} } @conference { G.Schlosser2005, title = {Fast Visualization by Shear-Warp on Quadratic Super-Spline Models Using Wavelet Data Decomposition}, booktitle = {IEEE Visualization}, year = {2005}, pages = {351-358}, author = {Schlosser , G. and Hesser , J. and Zeilfelder , F. and R{\"o}ssl , C. and M{\"a}nner , R. and N{\"u}rnberger , G. and Seidel , H.-P.} } @conference { D.Stsepankou2005, title = {Iterative Cone-Beam tomographic reconstruction,using hardware accelerated forward and back projectors}, booktitle = {PRIP 2005}, year = {2005}, pages = {337-340}, author = {Dzimitry Stsepankou and Kornmesser , K. and Hesser , J. and M{\"a}nner , R.} } @inbook { J.Hesser2005, title = {New Technologies in Radiation Oncology}, year = {2005}, pages = {9-16}, publisher = {Springer}, organization = {Springer}, chapter = {3D Reconstruction}, author = {Hesser , J. and Dzimitry Stsepankou}, editor = {W. Schlegel, T. Bortfeld, A.-L. Grosu} } @conference { A.Kryvanos2005, title = {Nonlinear image restoration methods for marker extraction in 3D fluorescent microscopy}, booktitle = {IS\\\&T/SPIE 17th Annual Symposium EI05 - Electronic Imaging}, year = {2005}, pages = {432-443}, author = {Kryvanos , A. and Hesser , J. and Steidl , G.} } @conference { U.Mueller2005, title = {Parameter Choice for Fast Rigid Multimodal Registration}, booktitle = {Proc. SPIE Medical Imaging}, volume = {5747}, year = {2005}, pages = {163-169}, author = {M{\"u}ller , U. and Hesser , J. and M{\"a}nner , R.} } @conference { P.Rebholz2004, title = {Cathi - From Patient Data Generation to Cardiological Training Systems}, booktitle = {MMVR 12}, year = {2004}, pages = {313-315}, author = {Rebholz , P. and Kornmesser , U. and Hesser , J.} } @conference { P.Rebholz2004a, title = {CathI: Training system for PTCA - A Step Closer to Reality}, booktitle = {2nd Int. Symp. on Medical Simulation Emerging Science | Enabling Technologies}, volume = {LNCS 3078}, year = {2004}, pages = {249-255}, author = {Rebholz , P. and Bieneck , C. and Dzimitry Stsepankou and Heser , J.} } @conference { D.Maier2004, title = {Clustering and Link Propagation for Surface Reconstruction}, booktitle = {Siggraph 2004}, year = {2004}, author = {Maier , D. and Hesser , J. and M{\"a}nner , R.} } @conference { J.Coburger2004, title = {Evaluation of the Training System CathI for Minimal Invasive Vascular Interventions on the Example of PTCAs}, booktitle = {CARS 2004}, year = {2004}, pages = {1339}, author = {Coburger , J. and Voelker , W. and Holbach , B. and Nziki , J. and Hesser , J.} } @conference { UlrichMueller2004, title = {Fast Rigid 2D-2D Multimodal Registration}, booktitle = {MICCAI 2004}, volume = {LNCS 3216}, number = {1}, year = {2004}, pages = {887-894}, author = {M{\"u}ller , U. and Hesser , J. and M{\"a}nner , R.} } @conference { D.Stsepankou2004a, title = {FPGA-acceleration of cone-beam reconstruction for the X-ray CT}, booktitle = {FPT 04}, year = {2004}, pages = {327-330}, author = {Dzimitry Stsepankou and Kornmesser , K. and Hesser , J. and M{\"a}nner , R.} } @conference { D.Maksimov2004, title = {An Interactive Application for Removal of Bone Information in CT-Angiography}, booktitle = {IEEE CBMS}, year = {2004}, pages = {396}, author = {Maksimov , D. and Finkel , F. and Dietz , T. and Diehl , S. and D{\"u}ber , C. and Rebholz , P. and Hesser , J. and M{\"a}nner , R.} } @conference { S.Koenig2004, title = {Live-Wires Using Path-Graphs}, booktitle = {Methods of Information in Medicine}, volume = {5}, number = {43}, year = {2004}, pages = {371-375}, author = {K{\"o}nig , S. and Hesser , J.} } @conference { UlrichMueller2004a, title = {Rigid Multimodal Registration without Markers}, booktitle = {Curac 2004}, year = {2004}, author = {M{\"u}ller , U. and Hesser , J.} } @conference { G.Schlosser2004, title = {Volume Rendering on one RLE compressed data set by a new combination of Ray-Casting and Shear-Warp}, booktitle = {SIGGRAPH 2004}, year = {2004}, author = {Schlosser , G. and Hesser , J.} } @conference { O.Krivonos2003a, title = {Automated ultrasound based classification of myocardial regions}, booktitle = {PRIP: Proceedings of 7th International Conference}, volume = {1}, year = {2003}, pages = {1231-1236}, author = {Krivonos , O. and Hesser , J. and M{\"a}nner , R. and P{\"o}rner , T. and G{\"o}ble , B. and Kralev , S. and Haase , K.K.} } @conference { U.Kornmesser2003, title = {CathI - A new training concept in interventional cardiology}, booktitle = {SESAM 2003}, year = {2003}, author = {Kornmesser , U. and Coburger , J. and Sch{\"u}tz , M. and M{\"o}nk , S. and Hesser , J. and Voelker , W.} } @conference { UlrichMueller2003, title = {Correction of C-arm Projection Matrices by 3D-2D Rigid Registration of CT-Images Using Mutual Information}, booktitle = {WIBR 03}, volume = {LNCS 2717}, year = {2003}, pages = {161-170}, author = {M{\"u}ller , U. and Bruck , S. and Hesser , J. and M{\"a}nner , R.} } @conference { D.Maier2003b, title = {Dense Disparity Maps Respecting Occlusions and Object Separation Using Partial Differential Equations}, booktitle = {Digital Image Computing: Techniques and Applications, DICTA2003}, volume = {2}, year = {2003}, pages = {613-622}, author = {Maier , D. and R{\"o}{\ss}le , A. and Hesser , J. and M{\"a}nner , R.} } @conference { D.Maier2003a, title = {Fast and Accurate Closest Point Search on Triangulated Surfaces and its Application to Head Motion Estimation}, booktitle = {3rd WSEAS International Conference on Signal, Speech and Image Processing (ICOSSIP2003)}, volume = {2}, year = {2003}, pages = {874-878}, author = {Maier , D. and Hesser , J. and M{\"a}nner , R.} } @conference { D.Stsepankou2003, title = {FPGA-Accelerated Volume Reconstruction from X-Ray}, booktitle = {World Conference on Medical Physics and Biomedical Engineering}, year = {2003}, author = {Dzimitry Stsepankou and M{\"u}ller , U. and Kornmesser , K. and Hesser , J. and M{\"a}nner , R.} } @article { H.Chen2003, title = {A Hardware Architecture for Efficient and Flexible Volume Rendering}, journal = {Computer \& Graphics}, volume = {5}, year = {2003}, pages = {715-724}, author = {Chen , H. and Deutscher , M. and Vettermann , B. and Hesser , J. and M{\"a}nner , R.} } @conference { S.Koenig2003, title = {Live-Wires on Edges of Pre-Segmented Data}, booktitle = {BVM 2003}, year = {2003}, pages = {156-160}, author = {K{\"o}nig , S. and Hesser , J. and M{\"a}nner , R.} } @article { EckartBindewald2003, title = {MANIFOLD: protein fold recognition based on secondary structure, sequence similarity and enzyme classification}, journal = {Protein Engineering}, volume = {16}, number = {11}, year = {2003}, pages = {785-789}, author = {Bindewald , E. and Cestaro , A. and Hesser , J. and Heiler , M. and Tosatto , S.} } @conference { N.Strobel2003, title = {Multiresolution Data Handling for Visualization of Very Large Volume Data Sets}, booktitle = {BVM 2003}, year = {2003}, author = {Strobel , N. and Gosch , C. and Hesser , J. and Poliwoda , C.} } @conference { O.Krivonos2003, title = {Precise Computer Aided Correction of Bone Deformities}, booktitle = {WC2003}, year = {2003}, author = {Krivonos , O. and Hesser , J. and M{\"a}nner , R. and Keppler , P. and Gebhard , F. and Kinzl , L. and Sakalouski , A.A. and Sakalouski , A.M.} } @article { H.Chen2003, title = {Ray-Casting Free-Form Deformed Volume Objects}, journal = {J. Vis. and Comp. Anim.}, volume = {14}, year = {2003}, pages = {61-72}, author = {Chen , H. and Hesser , J. and M{\"a}nner , R.} } @conference { D.Maier2003, title = {Robust Head Tracking for fMRI and MEG}, booktitle = {7th World Multiconference on Systemics, Cybernetics and Informatics, Voll IV}, year = {2003}, pages = {159-163}, author = {Maier , D. and Hesser , J. and M{\"a}nner , R.} } @article { KarstenMuehlmann2002, title = {Calculating Dense Disparity Maps from Color Stereo Images, an Efficient Implementation}, journal = {Int. J. of Comp. Vision}, volume = {47}, number = {1-3}, year = {2002}, pages = {79-88}, author = {M{\"u}hlmann , K. and Maier , D. and Hesser , J. and M{\"a}nner , R.} } @conference { U.Hoefer2002, title = {CathI - Catheter Instruction System}, booktitle = {CARS 2002}, year = {2002}, pages = {101-106}, author = {Hl{\"o}fer , U. and Langen , T. and Nziki , J. and Schmid , O. and Zeitler , F. and Hesser , J. and Voelker , W. and M{\"a}nner , R.} } @conference { Kornmesser2002, title = {CathI - ein virtuelles Trainingssystem fuer PTCA}, booktitle = {26. Herbsttagung der Deutschen Gesellschaft fuer Kardiologie- Herz- und Kreislaufforschung}, year = {2002}, author = {Kornmesser , U. and Voelker , W. and Hesser , J. and M{\"a}nner , R.} } @conference { U.Kornmesser2002, title = {CATHI Training on virtual patients for catheter interventions}, booktitle = {BMT 2002}, volume = {1}, number = {1}, year = {2002}, pages = {121-123}, author = {Kornmesser , U. and Hesser , J. and Voelker , W. and M{\"a}nner , R.} } @conference { O.Krivonos2002, title = {Computer Analysis of Doppler Myocardial Images}, booktitle = {Int. Congr. On Biol. \& Med. Engineering (ICBME)}, year = {2002}, author = {Krivonos , O. and Poerner , T. and Goebel , B. and Haase , K.K. and Borggrefe , M. and Hesser , J. and M{\"a}nner , R.} } @article { S.Tosatto2002, title = {A Divide and Conquer Approach to Fast Loop Modeling}, journal = {Prot. Eng.}, volume = {15}, number = {4}, year = {2002}, pages = {279-286}, author = {Tosatto , S. and Bindewald , E. and Hesser , J. and M{\"a}nner , R.} } @conference { K.Kornmesser2002, title = {Fast Feldkamp-Reconstruction for Real-Time Reconstruction using C-Arm-Systems}, booktitle = {CARS 2002}, year = {2002}, pages = {430-434}, author = {Kornmesser , K. and Sch{\"a}dler , B. and Ebert , M. and Hesser , J. and Schlegel , W. and M{\"a}nner , R.} } @conference { J.Hesser2002, title = {Operation Planning of Correction Osteotomies in 3D}, booktitle = {BMT 2002}, year = {2002}, pages = {90-92}, author = {Hesser , J. and Krivonos , O. and M{\"a}nner , R. and Keppler , P. and Gebhard , F. and Kinzl , L.} } @conference { D.Maier2002, title = {Real-Time-functional MRI Explorer}, booktitle = {Int. Congr. On Biol. and Med. Engineering (ICBME)}, year = {2002}, author = {Maier , D. and Storck , S. and K{\"o}nig , S. and Hesser , J. and M{\"a}nner , R. and Amann , M. and Baudendistel , K. and Schad , L.R. and Kleinb{\"o}hl , D. and H{\"o}lzl , R.} } @conference { H.Chen2001, title = {An Adaptive Distance-coding Based Volume Rendering Accelerator}, booktitle = {Proc. 1st Int. Game Technology Conference}, year = {2001}, address = {Honkong}, author = {Chen , H. and Hesser , J. and Vettermann , B. and M{\"a}nner , R.} } @conference { K.Muehlmann2001, title = {Calculating Dense Disparity Maps from Color Stereo Images, an Efficient Implementation}, booktitle = {IEEE Workshop on Stereo and Multi-Baseline Vision}, year = {2001}, pages = {30-36}, address = {{Kaua{\'\i} Hawai{\'\i}}, author = {M{\"u}hlmann , K. and Maier , D. and Hesser , J. and M{\"a}nner , R.} } @conference { O.Krivonos2001, title = {Computer Assisted Treatment Of Pelvis Fractures}, booktitle = {Medicine Meets Virtual Reality 2001}, year = {2001}, pages = {242-246}, author = {Krivonos , O. and Gebhard , F. and Keppler , P. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @conference { O.Krivonos2001a, title = {Computer Simulation Of Osteotomy Correction}, booktitle = {Medicine Meets Virtual Reality 2001}, year = {2001}, pages = {247-249}, author = {Krivonos , O. and Moskalenko , D. and Keppler , P. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @conference { O.Krivonos2001c, title = {Computer-Aided Osteotomy Correction: Planning And Operation Support}, booktitle = {6th Intern. Conf. On Pattern Recognition and Information Processing}, year = {2001}, pages = {101-105}, author = {Krivonos , O. and Keppler , P. and Hesser , J.} } @conference { GebhardF2001, title = {Computer-assisted surgery: developments and prospects in 2001}, booktitle = {Results of a workshop at Schloss Reisenburg}, series = {8}, volume = {4}, year = {2001}, pages = {782-788}, edition = {Unfallchirurg 2001}, author = {Gebhard , F. and Arand , M. and Fleiter , T. and Hebecker , A. and Heeckt , P. and Hesser , J. and Messmer , P. and Hufner , T. and Visarius , H. and Regazzoni , P. and Kinzl , L.} } @conference { O.Krivonos2001b, title = {From Planning of Complex Bone Deformities Correction to Computer Aided Operation}, booktitle = {14th IEEE Symposium on Computer-Based Medical Systems}, year = {2001}, pages = {210-215}, author = {Krivonos , O. and Keppler , P. and Gebhard , F. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @conference { H.Chen2001a, title = {Inverse Ray Deformation Based Fast Volume Free-Form-Deformation}, booktitle = {Conference on Visualization, Imaging and Image Processing, VIIP2001}, year = {2001}, address = {Marbella}, author = {Chen , H. and Hesser , J. and M{\"a}nner , R.} } @article { U.C.Liener, title = {Ultrasound - A New Tool For Surface Matching In Computer Navigated Surgery}, journal = {J. Milit. Medicine}, year = {2001}, pages = {151-154}, author = {Liener , U.C. and Krivonos , O. and M{\"a}nner , R. and Hesser , J. and Kinzl , L. and Gebhard , F.} } @conference { P.Keppler2001, title = {Virtual planning and simulation of complex posttraumatic deformities}, booktitle = {1th Annual Meeting Computer Assisted Orthopaedic Surgery}, year = {2001}, author = {Keppler , P. and Krivonos , O. and Moskalenko , D. and Gebhard , F. and Kinzil , L. and Hesser , J. and M{\"a}nner , R.} } @conference { S.Tosatto2000, title = {Ab Initio Loop Modeling with Precalculated Synthetic Loops and Sidechain Placement}, booktitle = {CASP4}, year = {2000}, pages = {A-119}, author = {Tosatto , S. and Bindewald , E. and Maydt , J. and Trabold , A. and Hesser , J. and M{\"a}nner , R.} } @conference { H.X.Chen2000, title = {Adaptive Sampling Distance Acceleration in Volume Rendering}, booktitle = {Late Breaking Hot Topics, Visualization}, year = {2000}, author = {Chen , H.X. and Hesser , J. and M{\"a}nner , R.} } @conference { O.Brosch2000, title = {ATLANTIS A Hybrid FPGA/RISC Based Re configurable System; Proc. 7th Reconfigurable Architectures}, booktitle = {Int. Parallel \& Distrib. Proc. Symp}, year = {2000}, pages = {890-897}, author = {Brosch , O. and Hesser , J. and Hinkelbein , C. and Kornmesser , K. and Kuberka , T. and Kugel , A. and M{\"a}nner , R. and Singpiel , H. and Vettermann , B.} } @conference { F.Gebhard2000, title = {Bone extraction from ultrasound images and surface matching with CT}, booktitle = {CAOS: Computer Assisted Orthopaedic Surgery}, year = {2000}, author = {Gebhard , F. and Krivonos , O. and Liener , U.C. and Keppler , P. and Kinzl , L. and Hesser , J.} } @conference { O.Krivonos2000b, title = {Computer Aided Correction Of Osteotomies}, booktitle = {10 ICBME, Biomedical Engineering in the New Millennium: Integration and Breakthroughs}, year = {2000}, pages = {565}, author = {Krivonos , O. and Moskalenko , D. and Keppler , P. and Gebhard , F. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @conference { GebhardF2000, title = {Computer assisted surgery, 2001 development and prospects}, booktitle = {Results of a congress at Reisensburg Castle}, year = {2000}, author = {Gebhard , F. and Arand , M. and Fleiter , T. and Hebecker , A. and Heeckt , P. and Hesser , J. and Messmer , P. and Hufner , T. and Visarius , H. and Regazzoni , P. and Kinzl , L.} } @conference { P.Keppler2000, title = {Computer-aided correction of bone deformities}, booktitle = {CAOS: Computer Assisted Orthopaedic Surgery}, year = {2000}, author = {Keppler , P. and Gebhard , F. and Moskalenko , D. and Hesser , J. and M{\"a}nner , R. and Kinzl , L.} } @article { KepplerP2000, title = {Computerunterstuetzte Planung von Korrekturosteotomien}, journal = {Hefte z.d. Unfallchirurg.}, volume = {282}, year = {2000}, pages = {300-301}, author = {Keppler , P.. and Moskalenko , D. and Gebhard , F. and Hesser , J. and Kinzl , L. and M{\"a}nner , R.} } @article {Meyer2000, title = {A constraint-based framework for diagrammatic reasoning}, journal = {Applied Artificial Intelligence}, volume = {14}, year = {2000}, pages = {327{\textendash}344}, author = {TEST} } @conference { M.deBoer2000, title = {Distributed Web-Based Image Processing Tool}, booktitle = {Int. Conf. Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS)}, year = {2000}, pages = {657-663}, author = {Boer , M. and Hesser , J. and M{\"a}nner , R.} } @conference { O.Krivonos2000a, title = {Implementation of Ultrasound for Treatment Of Pelvis Fractures}, booktitle = {10 ICBME, Biomedical Engineering in the New Millennium: Integration and Breakthroughs}, year = {2000}, pages = {479-480}, author = {Krivonos , O. and Gebhard , F. and Keppler , P. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @conference { F.Gebhard2000a, title = {Knochenextraktion aus Ultraschallbildern zum Surface Matching mit CT- Daten}, booktitle = {Jahrestagung der DGU}, year = {2000}, author = {Gebhard , F. and Krivonos , O. and Liener , U. and Keppler , P. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @article { GebhardF2000a, title = {Knochenextraktion aus Ultraschallbildern zum Surface Matching mit CT Daten}, journal = {Hefte z.d. Unfallchirurg.}, volume = {282}, year = {2000}, pages = {301-302}, author = {Gebhard , F. and Krivonos , O. and Liener , U. and Keppler , P. and Kinzl , L. and Hesser , J. and M{\"a}nner , R.} } @conference { O.Krivonos2000, title = {Minimal Invasive Surgery of the Pelvis using Ultrasound}, booktitle = {Proc. 4th CAOSUSA: Computer Assisted Orthopaedic Surgery}, year = {2000}, pages = {203-205}, author = {Krivonos , O. and Hesser , J. and M{\"a}nner , R. and Gebhard , F. and Liener , U. and Keppler , P. and Kinzl , L.} } @conference { E.Bindewald2000, title = {Protein Structure Prediction Using Combinatorial Optimization}, booktitle = {Int. Conf. Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS)}, year = {2000}, pages = {233-238}, author = {Bindewald , E. and Hesser , J. and M{\"a}nner , R.} } @conference { E.Bindewald200, title = {Secondary Structure and Function Based Protein Fold Recognition}, booktitle = {CASP4}, year = {2000}, pages = {A-9}, author = {Bindewald , E. and Tosato , S. and Maydt , J. and Trabold , A. and Hesser , J. and M{\"a}nner , R.} } @conference { EckartBindewald1999, title = {Ab initio protein structure prediction with MOLEGO}, booktitle = {International Conference on Intelligent Systems for Molecular Biology (ISMB 99)}, year = {1999}, pages = {9}, author = {Bindewald , E. and Heiler , M. and H{\"o}fer , U. and Sch{\"u}le , T. and Beiersd{\"o}rfer , S. and Tosatto , S. and Hesser , J. and M{\"a}nner , R.} } @inbook { J.Hesser1998a, title = {Computer Vision Handbook}, volume = {2 (Signal Processing and Pattern Recognition)}, year = {1999}, pages = {875-905}, publisher = {Academic Press}, organization = {Academic Press}, chapter = {Volume Visualization}, author = {Hesser , J. and Poliwoda , C.}, editor = {B. Jaehne, H. Haussecker, P. Geissler} } @conference { SilvioTosatto1999, title = {A Divide \& Conquer Approach for the Ring Closure Problem}, booktitle = {Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB 99),}, year = {1999}, author = {Tosatto , S. and Beiersd{\"o}rfer , S. and Pr{\"u}mmer , M. and Bindewald , E. and Hesser , J. and M{\"a}nner , R.} } @conference { B.Vettermann1999a, title = {Implementation of Algorithmically Optimized Volume Rendering on FPGA-Hardware}, booktitle = {Late Breaking Hot Topics, Visualization 99}, year = {1999}, author = {Vettermann , B, and Hesser , J. and M{\"a}nner , R. and Kugel , A.} } @article { J.Hesser1999a, title = {Realistische Reisen durch den menschlichen Koerper}, journal = {Sp. d. Wissenschaft, Dossier}, volume = {1/99}, year = {1999}, pages = {34-35}, author = {Hesser , J. and Maenner , R.} } @article { J.Hesser1999b, title = {Realistische Reisen durch den menschlichen K{\"o}rper}, journal = {Sp. d. Wissenschaft, Digest}, volume = {2/99}, year = {1999}, pages = {104-106}, author = {Hesser , J. and M{\"a}nner , R.} } @conference { M.Deyssenroth1999, title = {A Shading and Compositing Processor based on Crossbar Switches and SRAM Memory}, booktitle = {Volume Graphics Workshop 99}, year = {1999}, pages = {161-170}, author = {Deyssenroth , M. and de Boer , M. and Gr{\"o}pl , A. and Hesser , J. and M{\"a}nner , R.} } @conference { B.Vettermann1999, title = {Solving the Hazard Problem for Algorithmically Optimized Real-Time Volume Rendering}, booktitle = {Volume Graphics Workshop}, year = {1999}, pages = {171-184}, author = {Vettermann , B. and Hesser , J. and M{\"a}nner , R.} } @conference { J.Hesser1999, title = {Volume Rendering FPGA Hardware}, booktitle = {11th Symp. Comp. Arch. and High Perf. Comp., SBAC 99}, year = {1999}, author = {Hesser , J. and Kugel , A. and Singpiel , H. and Vettermann , B. and M{\"a}nner , R.} } @conference { J.Hesser1998, title = {ATLANTIS A Hybrid Approach Combining the Power of FPGA and RISC Processors based on CompactPCI}, booktitle = {FCCM 98, IEEE Symposium on Field-Programmable Custom Computing Machines}, year = {1998}, author = {Hesser , J. and Hinkelbein , C. and Kornmesser , K. and Kuberka , T. and Kugel , A. and M{\"a}nner , R. and Singpiel , H. and Vettermann , B.} } @conference { E.Bindewald1998, title = {Implementing genetic algorithms with sterical constraints for protein structure prediction}, booktitle = {Parallel Problem Solving in Nature (PPSN VII)}, year = {1998}, pages = {959-967}, author = {Bindewald , E. and Hesser , J. and M{\"a}nner , R.} } @inbook { S.Beiersdoerfer1998, title = {Industrielle Anwendungen Evolutionaerer Algorithmen}, year = {1998}, pages = {25-35}, publisher = {Oldenburg Verlag}, organization = {Oldenburg Verlag}, chapter = {Optimierung von fluoreszierenden Farbstoffen mittels Evolutionaerer Algorithmen}, author = {Beiersdoerfer , S. and Hesser , J. and M{\"a}nner , R. and Schulz , A. and Wolfrum , J.}, editor = {S. Hafner} } @conference { E.Bindewald1998a, title = {Protein structure prediction with combinatorial optimization}, booktitle = {Third Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, CASP3}, year = {1998}, pages = {77}, author = {Bindewald , E. and H{\"o}fer , U. and Heiler , M. and Hesser , J. and M{\"a}nner , R.} } @article { M.deBoer1997c, title = {Evaluation of a Real-Time Direct Volume Rendering System}, journal = {Computer \& Graphics}, volume = {21}, number = {2}, year = {1997}, pages = {189-198}, author = {Boer , M. and Hesser , J. and Gr{\"o}pl , A. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and M{\"a}nner , R.} } @conference { G.Kuehne1997, title = {Interactive Segmentation and Visualization of Volume Data Sets}, booktitle = {Late Breaking Hot Topics, Visualization 97}, year = {1997}, pages = {9-12}, author = {Kuehne , G. and Poliwoda , C. and Hesser , J. and M{\"a}nner , R.} } @article { M.deBoer1997a, title = {Latency-Free and Hazard-Free Volume Memory Architecture for Direct Volume Rendering}, journal = {Computers \& Graphics}, volume = {21}, number = {2}, year = {1997}, pages = {179-187}, author = {Boer , M. and Gr{\"o}pl , A. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and Hesser , J. and M{\"a}nner , R.} } @article { M.Makhaniok1997, title = {Limit Cycles of a Planar Vector Field}, journal = {Acta Appl. Math.}, volume = {48}, year = {1997}, pages = {13-32}, author = {Makhaniok , M. and Hesser , J. and M{\"a}nner , R. and Noethe , S.} } @conference { S.Beiersdoerfer1997a, title = {Optimierung von Fluoreszenzmarkern mittels evolutionaerer Algorithmen}, booktitle = {Anwendungstechnische Praxis}, volume = {10/97}, year = {1997}, author = {Beiersdoerfer , S. and Hesser , J. and M{\"a}nner , R. and Schulz , A. and Wolfrum , J.} } @conference { Hesser1997, title = {Real-Time Direct Volume Rendering and Interactive Segmentation of Medical Volume Data Sets}, booktitle = {Herbsttagung 97: 3D Bildanalyse und Synthese}, year = {1997}, pages = {89-96}, author = {Hesser , J.} } @article { J.Hesser1997, title = {Real-Time direct volume rendering in functional magnetic resonance imaging}, journal = {Magma}, volume = {5}, year = {1997}, pages = {87-91}, author = {Hesser , J. and M{\"a}nner , R. and Braus , D.F. and Ende , G. and Henn , F.A.} } @conference { M.deBoer1997, title = {Reducing Artifacts in Volume Rendering by Higher Order Integration}, booktitle = {Late Breaking Hot Topics, Visualization 97}, year = {1997}, pages = {1-4}, author = {de Boer , M. and Gr{\"o}pl , A. and Hesser , J. and M{\"a}nner , R.} } @conference { S.Beiersdoerfer1997, title = {Search for Native Conformations of Organic Molecules by Genetic Algorithms}, booktitle = {Euromicro 97, Euromicro Worksh. on Computational Intelligence}, year = {1997}, pages = {624-630}, author = {Beiersdoerfer , S. and Hesser , J. and Schmitt , J. and Schulz , A. and M{\"a}nner , R. and Wolfrum , J.} } @conference { M.Schill1997, title = {Simulation of Brain Tissue and Realtime Volume Visualization}, booktitle = {Computer Aided Radiology CAR97}, year = {1997}, pages = {283-288}, author = {Schill , M. and Reinhart , C. and G{\"u}nther , T. and Poliwoda , C. and Hesser , J. and Schinkmann , M. and Bender , H.-J. and M{\"a}nner , R.} } @conference { J.Ludvig1997, title = {Tackling the Representation Problem by Stochastic Averaging}, booktitle = {Int. Conf. on GA ICGA 97}, year = {1997}, pages = {196-203}, author = {Ludvig , J. and Hesser , J. and M{\"a}nner , R.} } @conference { T.Guenther1997, title = {Vergleich zweier Ansaetze zur interaktiven Volumenvisualisierung}, booktitle = {BMBF-Statustagung}, year = {1997}, pages = {225-244}, author = {Guenther , T. and Poliwoda , C. and Hesser , J. and M{\"a}nner , R. and Mayer , A. and Meinzer , H.-P.} } @conference { M.deBoer1997b, title = {Evaluation of a Real-Time Direct Volume Rendering System}, booktitle = {Eurographics Workshop}, year = {1996}, pages = {121-131}, author = {M. de de Boer , M. and Hesser , J. and Gr{\"o}pl , A. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and M{\"a}nner , R.} } @conference { S.Beiersdoerfer1996, title = {Finding the Conformation of Organic Molecules with Genetic Algorithms}, booktitle = {Int. Conf. on Evolutionary Computation PPSN IV}, year = {1996}, pages = {972-981}, author = {Beiersdoerfer , S. and Schmitt , J. and Sauer , M. and Schulz , A. and Siebert , S. and Hesser , J. and M{\"a}nner , R. and Wolfrum , J..} } @conference { A.Groepl1996, title = {Interactive Operation Planning and Control with VIRIM}, booktitle = {Medicine Meets Virtual Reality 4}, year = {1996}, pages = {121-133}, author = {Gr{\"o}pl , A. and G{\"u}nther , T. and Hesser , J. and Kr{\"o}ll , J. and M{\"a}nner , R. and Poliwoda , C. and Reinhart , C. and Hassfeld , S. and J{\"a}ger , W. and Quien , N. and Simon , J. and Wirth , J.} } @conference { M.deBoer1996, title = {Latency-Free and Hazard-Free Volume Memory Architecture for Direct Volume Rendering}, booktitle = {Eurographics Workshop}, year = {1996}, pages = {109-119}, author = {M. de de Boer , M. and Hesser , J. and Gr{\"o}pl , A. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and M{\"a}nner , R.} } @conference { J.Hesser1996a, title = {Parallel Workstation for 3D Data Processing}, booktitle = {Supercomputer 96; FOKUSPraxis, Information und Kommunikation}, volume = {14}, year = {1996}, pages = {138-149}, author = {Hesser , J. and M{\"a}nner , R.} } @conference { A.Groepl1996a, title = {Planning and Controlling Minimal Invasive Operations by Real-Time Direct Volume Rendering}, booktitle = {Computer Assisted Radiology CAR}, year = {1996}, pages = {237-242}, author = {Groepl , A. and G{\"u}nther , T. and Hesser , J. and M{\"a}nner , R. and Poliwoda , C. and Reinhart , C. and J{\"a}ger , W. and Wirth , J. and Hassfeld , S.} } @conference { J.Hesser1996b, title = {Real-Time Direct Volume Rendering in Functional Imaging}, booktitle = {13th Ann. Sci. Meeting - ESMRMB 96}, year = {1996}, pages = {290}, author = {Hesser , J. and Groepl , A. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and M{\"a}nner , R. and Braus , D.F.} } @conference { J.Hesser1996, title = {Real-Time Optimization by Hardware Supported Genetic Algorithms}, booktitle = {2nd Int. Mendel Conf. on GA}, year = {1996}, pages = {52-59}, author = {Ludvig , J. and Hesser , J. and M{\"a}nner , R.} } @conference { S.Beiersdoerfer1996a, title = {Search for Conformation of Organic Molecules by Genetic Algorithms}, booktitle = {Comp. Sci. and Biol., Proc. Germ. Conf. Bioinformatics GCB96}, year = {1996}, pages = {165-167}, author = {Beiersd{\"o}rfer , S. and Hesser , J. and Schmitt , J. and Schulz , A. and M{\"a}nner , R. and Wolfrum , J.} } @conference { O.Bohnenberger1995, title = {Automatic Design of Truss Structures using Evolutionary Algorithms}, booktitle = {IEEE Int. Conf. on Evolutionary Comp.}, year = {1995}, pages = {143-147}, author = {Bohnenberger , O. and Hesser , J. and M{\"a}nner , R.} } @conference { R.Maenner1995a, title = {Echtzeitvisualisierung in der Medizin mittels volumenorientiertem Raytracing}, booktitle = {Proc. Statustagung BMBF HPSC 95}, year = {1995}, pages = {213-215}, author = {M{\"a}nner , R. and Hessser , J. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and Meinzer , H.-P. and Baur , U. and Deminis , T. and Engelmann , U. and Kochner , B. and Makabee , M. and Mayer , A. and Niebsch , R. and Schroeter , A.} } @conference { R.Maenner1995, title = {Real-Time Direct Volume Rendering}, booktitle = {Proc. Statustagung BMBF HPSC 95}, year = {1995}, pages = {219-224}, author = {M{\"a}nner , R. and Hesser , J. and G{\"u}nther , T. and Poliwoda , C. and Reinhart , C.} } @conference { J.Hesser1995, title = {Three Architectures for Volume Rendering}, booktitle = {Eurographics 95}, volume = {14}, number = {3}, year = {1995}, pages = {111-122}, author = {Hesser , J. and M{\"a}nner , R. and Knittel , G. and Stra{\ss}er , W. and Pfister , H. and Kaufman , A.} } @conference { T.Guenther1995, title = {VIRIM: A Massively Parallel Processor for Real-Time Volume Visualization in Medicine}, booktitle = {Proc. Eurographics Workshop}, volume = {19}, number = {5}, year = {1995}, pages = {103-108}, author = {G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and Hesser , J. and M{\"a}nner , R. and Meinzer , H.-P. and Baur , H.-J.} } @article { T.Guenther1995a, title = {VIRIM: A Massively Parallel Processor for Real-Time Volume Visualization in Medicine}, journal = {Computer\&Graphics}, volume = {19}, number = {5}, year = {1995}, pages = {705-710}, author = {G{\"u}nther , T. and Poliwoda , C. and Reinhart , C. and Hesser , J. and M{\"a}nner , R. and Meinzer , H.-P. and Baur , H.-J.} } @conference { A.Groepl, title = {A Volume Rendering System for Medicine}, booktitle = {Proc. Informationssysteme im Unternehmen Krankenhaus}, year = {1995}, pages = {1-3}, author = {Groepl , A. and G{\"u}nther , T. and Hesser , J. and Kr{\"o}ll , J. and M{\"a}nner , R. and Poliwoda , C. and Reinhart , C.} } @conference { J.Hesser1994, title = {Real-Time Volume Visualization of CT and NMR Images.}, booktitle = {Minimal Invasive Therapy}, volume = {3}, number = {1}, year = {1994}, pages = {9}, author = {Hesser , J. and Poliwoda , C. and G{\"u}nther , T. and Reinhart , C. and M{\"a}nner , R. and Meinzer , H.-P. and Mayer , A.} } @conference { J.Hesser1994a, title = {VIRIM: The Real-Time 3D-Visualization System}, booktitle = {VDE/VDI-Workshop Integrative 3D Visualisierung}, year = {1994}, author = {Hesser , J. and M{\"a}nner , R.} } @conference { M.Makhaniok1992, title = {Attractors of Two-Dimensional Dynamical Systems}, booktitle = {WOPPLOT 92}, year = {1992}, author = {Makhaniok , M. and Hesser , J. and Noethe , S. and Maenner , R.} } @conference { J.Hesser1992, title = {Investigation of the M-Heuristic for Optimal Mutation Probabilities}, booktitle = {Parallel Problem Solving from Nature 2}, year = {1992}, pages = {115-124}, author = {Hesser , J. and M{\"a}nner , R.} } @conference { J.Hesser1991a, title = {An Alternative Genetic Algorithm}, booktitle = {Parallel Problem Solving from Nature; Lecture Notes in Comp. Sci.}, volume = {496}, year = {1991}, pages = {33-37}, author = {Hesser , J. and M{\"a}nner , R.} } @conference { J.Hesser1991, title = {On Steiner Trees and Genetic Algorithms}, booktitle = {Parallelism, Learning, Evolution, Lect. Notes in Comp. Sci.}, volume = {565}, year = {1991}, pages = {509-525}, author = {Hesser , J. and Stucky , O. and M{\"a}nner , R.} } @conference { J.Hesser1991b, title = {Towards an Optimal Mutation Probability for Genetic Algorithms}, booktitle = {Parallel Problem Solving from Nature, Lecture Notes in Comp. Sci.}, volume = {496}, year = {1991}, pages = {23-32}, author = {Hesser , J. and M{\"a}nner , R.} } @conference { J.Hesser1989, title = {Optimization of Steiner Trees using Genetic Algorithms}, booktitle = {Proc. 3rd Int. Conf. on Genetic Algorithms}, year = {1989}, pages = {231-236}, author = {Hesser , J. and Stucky , O. and Maenner , R.} }