TY - JOUR A1 - Stebani, Jannik A1 - Blaimer, Martin A1 - Zabler, Simon A1 - Neun, Tilmann A1 - Pelt, Daniël M. A1 - Rak, Kristen T1 - Towards fully automated inner ear analysis with deep-learning-based joint segmentation and landmark detection framework JF - Scientific Reports N2 - Automated analysis of the inner ear anatomy in radiological data instead of time-consuming manual assessment is a worthwhile goal that could facilitate preoperative planning and clinical research. We propose a framework encompassing joint semantic segmentation of the inner ear and anatomical landmark detection of helicotrema, oval and round window. A fully automated pipeline with a single, dual-headed volumetric 3D U-Net was implemented, trained and evaluated using manually labeled in-house datasets from cadaveric specimen (N = 43) and clinical practice (N = 9). The model robustness was further evaluated on three independent open-source datasets (N = 23 + 7 + 17 scans) consisting of cadaveric specimen scans. For the in-house datasets, Dice scores of 0.97 and 0.94, intersection-over-union scores of 0.94 and 0.89 and average Hausdorf distances of 0.065 and 0.14 voxel units were achieved. The landmark localization task was performed automatically with an average localization error of 3.3 and 5.2 voxel units. A robust, albeit reduced performance could be attained for the catalogue of three open-source datasets. Results of the ablation studies with 43 mono-parametric variations of the basal architecture and training protocol provided task-optimal parameters for both categories. Ablation studies against single-task variants of the basal architecture showed a clear performance beneft of coupling landmark localization with segmentation and a dataset-dependent performance impact on segmentation ability. KW - anatomy KW - bone imaging KW - diagnosis KW - medical imaging KW - software KW - three-dimensional imaging KW - tomography Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-357411 VL - 13 ER - TY - JOUR A1 - Ullherr, Maximilian A1 - Diez, Matthias A1 - Zabler, Simon T1 - Robust image reconstruction strategy for multiscalar holotomography JF - Journal of Imaging N2 - Holotomography is an extension of computed tomography where samples with low X-ray absorption can be investigated with higher contrast. In order to achieve this, the imaging system must yield an optical resolution of a few micrometers or less, which reduces the measurement area (field of view = FOV) to a few mm at most. If the sample size, however, exceeds the field of view (called local tomography or region of interest = ROI CT), filter problems arise during the CT reconstruction and phase retrieval in holotomography. In this paper, we will first investigate the practical impact of these filter problems and discuss approximate solutions. Secondly, we will investigate the effectiveness of a technique we call “multiscalar holotomography”, where, in addition to the ROI CT, a lower resolution non-ROI CT measurement is recorded. This is used to avoid the filter problems while simultaneously reconstructing a larger part of the sample, albeit with a lower resolution in the additional area. KW - reconstruction KW - region of interest KW - ROI KW - multiscalar holotomography KW - holotomography KW - computed tomography KW - CT KW - X-ray Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-262112 SN - 2313-433X VL - 8 IS - 2 ER - TY - JOUR A1 - Noyalet, Laurent A1 - Ilgen, Lukas A1 - Bürklein, Miriam A1 - Shehata-Dieler, Wafaa A1 - Taeger, Johannes A1 - Hagen, Rudolf A1 - Neun, Tilmann A1 - Zabler, Simon A1 - Althoff, Daniel A1 - Rak, Kristen T1 - Vestibular aqueduct morphology and Meniere’s disease - development of the vestibular aqueduct score by 3D analysis JF - Frontiers in Surgery N2 - Improved radiological examinations with newly developed 3D models may increase understanding of Meniere's disease (MD). The morphology and course of the vestibular aqueduct (VA) in the temporal bone might be related to the severity of MD. The presented study explored, if the VA of MD and non-MD patients can be grouped relative to its angle to the semicircular canals (SCC) and length using a 3D model. Scans of temporal bone specimens (TBS) were performed using micro-CT and micro flat panel volume computed tomography (mfpVCT). Furthermore, scans were carried out in patients and TBS by computed tomography (CT). The angle between the VA and the three SCC, as well as the length of the VA were measured. From these data, a 3D model was constructed to develop the vestibular aqueduct score (VAS). Using different imaging modalities it was demonstrated that angle measurements of the VA are reliable and can be effectively used for detailed diagnostic investigation. To test the clinical relevance, the VAS was applied on MD and on non-MD patients. Length and angle values from MD patients differed from non-MD patients. In MD patients, significantly higher numbers of VAs could be assigned to a distinct group of the VAS. In addition, it was tested, whether the outcome of a treatment option for MD can be correlated to the VAS. KW - vestibular aqueduct (VA) KW - 3D analysis KW - temporal bone KW - saccotomy KW - computed tomography KW - Meniere’s disease Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-312893 SN - 2296-875X VL - 9 ER - TY - JOUR A1 - Vogel, Patrick A1 - Markert, Jonathan A1 - Rückert, Martin A. A1 - Herz, Stefan A1 - Keßler, Benedikt A1 - Dremel, Kilian A1 - Althoff, Daniel A1 - Weber, Matthias A1 - Buzug, Thorsten M. A1 - Bley, Thorsten A. A1 - Kullmann, Walter H. A1 - Hanke, Randolf A1 - Zabler, Simon A1 - Behr, Volker C. T1 - Magnetic Particle Imaging meets computed tomography: first simultaneous imaging JF - Scientific Reports N2 - Magnetic Particle Imaging (MPI) is a promising new tomographic modality for fast as well as three-dimensional visualization of magnetic material. For anatomical or structural information an additional imaging modality such as computed tomography (CT) is required. In this paper, the first hybrid MPI-CT scanner for multimodal imaging providing simultaneous data acquisition is presented. KW - Applied physics KW - Biomedical engineering KW - Imaging techniques Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-202501 VL - 9 ER - TY - JOUR A1 - Dittmann, Jonas A1 - Balles, Andreas A1 - Zabler, Simon T1 - Optimization based evaluation of grating interferometric phase stepping series and analysis of mechanical setup instabilities JF - Journal of Imaging N2 - The diffraction contrast modalities accessible by X-ray grating interferometers are not imaged directly but have to be inferred from sine-like signal variations occurring in a series of images acquired at varying relative positions of the interferometer’s gratings. The absolute spatial translations involved in the acquisition of these phase stepping series usually lie in the range of only a few hundred nanometers, wherefore positioning errors as small as 10 nm will already translate into signal uncertainties of 1–10% in the final images if not accounted for. Classically, the relative grating positions in the phase stepping series are considered input parameters to the analysis and are, for the Fast Fourier Transform that is typically employed, required to be equidistantly distributed over multiples of the gratings’ period. In the following, a fast converging optimization scheme is presented simultaneously determining the phase stepping curves’ parameters as well as the actually performed motions of the stepped grating, including also erroneous rotational motions which are commonly neglected. While the correction of solely the translational errors along the stepping direction is found to be sufficient with regard to the reduction of image artifacts, the possibility to also detect minute rotations about all axes proves to be a valuable tool for system calibration and monitoring. The simplicity of the provided algorithm, in particular when only considering translational errors, makes it well suitable as a standard evaluation procedure also for large image series. KW - X-ray imaging KW - Talbot–Lau interferometer KW - grating interferometer KW - phase contrast imaging KW - darkfield imaging KW - phase stepping KW - optimization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-197723 SN - 2313-433X VL - 4 IS - 6 ER -