05 Fakultät Informatik, Elektrotechnik und Informationstechnik
Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/6
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Item Open Access Fourier spotting : a novel setup for single-color reflectometry(2022) Siegel, Johannes; Berner, Marcel; Werner, Jürgen H.; Proll, Günther; Fechner, Peter; Schubert, MarkusSingle-color reflectrometry is a sensitive and robust detection method in optical biosensor applications, for example for bioanalysis. It is based on the interference of reflected monochromatic radiation and is label free. We present a novel setup for single-color reflectometry based on the patented technology of Berner et al. from 2016. Tilting areas of micro-mirrors allow us to encode the optical reflection signal of an analyte and reference channel into a particular carrier frequency with the amplitude being proportional to the local reflection. Therefore, a single photodiode is sufficient to collect the signals from both channels simultaneously. A 180∘ phase shift in the tilt frequency of two calibrated micro-mirror areas leads to a superposition of the analyte and reference signal which enables an efficient reduction of the baseline offset and potential baseline offset drift. A performance test reveals that we are able to detect changes of the refractive index n down to Δn < 0.01 of saline solutions as regents. A further test validates the detection of heterogeneous binding interaction. This test compromises immobilized testosterone-bovine serum albumin on a three-dimensional layer of biopolymer as ligand and monoclonal anti-testosterone antibodies as analyte. Antibody/antigen binding induces a local growth of the biolayer and change in the refractive index, which is measured via the local change of the reflection. Reproducible measurements enable for the analysis of the binding kinetics by determining the affinity constant KA = 1.59 × 10- 7 M- 1. In summary, this work shows that the concept of differential Fourier spotting as novel setup for single-color reflectometry is suitable for reliable bioanalysis.Graphical AbstractItem Open Access Automated imaging-based abdominal organ segmentation and quality control in 20,000 participants of the UK Biobank and German National Cohort Studies(2022) Kart, Turkay; Fischer, Marc; Winzeck, Stefan; Glocker, Ben; Bai, Wenjia; Bülow, Robin; Emmel, Carina; Friedrich, Lena; Kauczor, Hans-Ulrich; Keil, Thomas; Kröncke, Thomas; Mayer, Philipp; Niendorf, Thoralf; Peters, Annette; Pischon, Tobias; Schaarschmidt, Benedikt M.; Schmidt, Börge; Schulze, Matthias B.; Umutle, Lale; Völzke, Henry; Küstner, Thomas; Bamberg, Fabian; Schölkopf, Bernhard; Rückert, Daniel; Gatidis, SergiosLarge epidemiological studies such as the UK Biobank (UKBB) or German National Cohort (NAKO) provide unprecedented health-related data of the general population aiming to better understand determinants of health and disease. As part of these studies, Magnetic Resonance Imaging (MRI) is performed in a subset of participants allowing for phenotypical and functional characterization of different organ systems. Due to the large amount of imaging data, automated image analysis is required, which can be performed using deep learning methods, e. g. for automated organ segmentation. In this paper we describe a computational pipeline for automated segmentation of abdominal organs on MRI data from 20,000 participants of UKBB and NAKO and provide results of the quality control process. We found that approx. 90% of data sets showed no relevant segmentation errors while relevant errors occurred in a varying proportion of data sets depending on the organ of interest. Image-derived features based on automated organ segmentations showed relevant deviations of varying degree in the presence of segmentation errors. These results show that large-scale, deep learning-based abdominal organ segmentation on MRI data is feasible with overall high accuracy, but visual quality control remains an important step ensuring the validity of down-stream analyses in large epidemiological imaging studies.Item Open Access Identification of radiomic biomarkers in a set of four skeletal muscle groups on Dixon MRI of the NAKO MR study(2023) Fischer, Marc; Küstner, Thomas; Pappa, Sofia; Niendorf, Thoralf; Pischon, Tobias; Kröncke, Thomas; Bette, Stefanie; Schramm, Sara; Schmidt, Börge; Haubold, Johannes; Nensa, Felix; Nonnenmacher, Tobias; Palm, Viktoria; Bamberg, Fabian; Kiefer, Lena; Schick, Fritz; Yang, BinIn this work, we propose a processing pipeline for the extraction and identification of meaningful radiomics biomarkers in skeletal muscle tissue as displayed using Dixon-weighted MRI. Diverse and robust radiomics features can be identified that may be of aid in the accurate quantification e.g. varying degrees of sarcopenia in respective muscles of large cohorts. As such, the approach comprises the texture feature extraction from raw data based on well established approaches, such as a nnU-Net neural network and the Pyradiomics toolbox, a subsequent selection according to adequate conditions for the muscle tissue of the general population, and an importance-based ranking to further narrow the amount of meaningful features with respect to auxiliary targets. The performance was investigated with respect to the included auxiliary targets, namely age, body mass index (BMI), and fat fraction (FF). Four skeletal muscles with different fiber architecture were included: the mm. glutaei, m. psoas, as well as the extensors and adductors of the thigh. The selection allowed for a reduction from 1015 available texture features to 65 for age, 53 for BMI, and 36 for FF from the available fat/water contrast images considering all muscles jointly. Further, the dependence of the importance rankings calculated for the auxiliary targets on validation sets (in a cross-validation scheme) was investigated by boxplots. In addition, significant differences between subgroups of respective auxiliary targets as well as between both sexes were shown to be present within the ten lowest ranked features by means of Kruskal-Wallis H-tests and Mann-Whitney U-tests. The prediction performance for the selected features and the ranking scheme were verified on validation sets by a random forest based multi-class classification, with strong area under the curve (AUC) values of the receiver operator characteristic (ROC) of 73.03 ± 0.70 % and 73.63 ± 0.70 % for the water and fat images in age, 80.68 ± 0.30 % and 88.03 ± 0.89 % in BMI, as well as 98.36 ± 0.03 % and 98.52 ± 0.09 % in FF.