TY - JOUR A1 - Michallek, Florian A1 - Genske, Ulrich A1 - Niehues, Stefan Markus A1 - Hamm, Bernd A1 - Jahnke, Paul T1 - Deep learning reconstruction improves radiomics feature stability and discriminative power in abdominal CT imaging BT - a phantom study JF - European Radiology N2 - Objectives To compare image quality of deep learning reconstruction (AiCE) for radiomics feature extraction with filtered back projection (FBP), hybrid iterative reconstruction (AIDR 3D), and model-based iterative reconstruction (FIRST). Methods Effects of image reconstruction on radiomics features were investigated using a phantom that realistically mimicked a 65-year-old patient's abdomen with hepatic metastases. The phantom was scanned at 18 doses from 0.2 to 4 mGy, with 20 repeated scans per dose. Images were reconstructed with FBP, AIDR 3D, FIRST, and AiCE. Ninety-three radiomics features were extracted from 24 regions of interest, which were evenly distributed across three tissue classes: normal liver, metastatic core, and metastatic rim. Features were analyzed in terms of their consistent characterization of tissues within the same image (intraclass correlation coefficient >= 0.75), discriminative power (Kruskal-Wallis test p value < 0.05), and repeatability (overall concordance correlation coefficient >= 0.75). Results The median fraction of consistent features across all doses was 6%, 8%, 6%, and 22% with FBP, AIDR 3D, FIRST, and AiCE, respectively. Adequate discriminative power was achieved by 48%, 82%, 84%, and 92% of features, and 52%, 20%, 17%, and 39% of features were repeatable, respectively. Only 5% of features combined consistency, discriminative power, and repeatability with FBP, AIDR 3D, and FIRST versus 13% with AiCE at doses above 1 mGy and 17% at doses >= 3 mGy. AiCE was the only reconstruction technique that enabled extraction of higher-order features. Conclusions AiCE more than doubled the yield of radiomics features at doses typically used clinically. Inconsistent tissue characterization within CT images contributes significantly to the poor stability of radiomics features. KW - Tomography KW - X-ray computed KW - Phantoms KW - imaging KW - Liver neoplasms KW - Algorithms KW - Reproducibility of results Y1 - 2022 U6 - https://doi.org/10.1007/s00330-022-08592-y SN - 1432-1084 VL - 32 IS - 7 SP - 4587 EP - 4595 PB - Springer CY - New York ER - TY - JOUR A1 - Genske, Ulrich A1 - Jahnke, Paul T1 - Human observer net BT - a platform tool for human observer studies of image data JF - Radiology N2 - Background: Current software applications for human observer studies of images lack flexibility in study design, platform independence, multicenter use, and assessment methods and are not open source, limiting accessibility and expandability. Purpose: To develop a user-friendly software platform that enables efficient human observer studies in medical imaging with flexibility of study design. Materials and Methods: Software for human observer imaging studies was designed as an open-source web application to facilitate access, platform-independent usability, and multicenter studies. Different interfaces for study creation, participation, and management of results were implemented. The software was evaluated in human observer experiments between May 2019 and March 2021, in which duration of observer responses was tracked. Fourteen radiologists evaluated and graded software usability using the 100-point system usability scale. The application was tested in Chrome, Firefox, Safari, and Edge browsers. Results: Software function was designed to allow visual grading analysis (VGA), multiple-alternative forced-choice (m-AFC), receiver operating characteristic (ROC), localization ROC, free-response ROC, and customized designs. The mean duration of reader responses per image or per image set was 6.2 seconds 6 4.8 (standard deviation), 5.8 seconds 6 4.7, 8.7 seconds 6 5.7, and 6.0 seconds 6 4.5 in four-AFC with 160 image quartets per reader, four-AFC with 640 image quartets per reader, localization ROC, and experimental studies, respectively. The mean system usability scale score was 83 6 11 (out of 100). The documented code and a demonstration of the application are available online (https://github.com/genskeu/HON, https://hondemo.pythonanywhere.com/). Conclusion: A user-friendly and efficient open-source application was developed for human reader experiments that enables study design versatility, as well as platform-independent and multicenter usability. Y1 - 2022 U6 - https://doi.org/10.1148/radiol.211832 SN - 0033-8419 SN - 1527-1315 VL - 303 IS - 3 SP - 524 EP - 530 PB - Radiological Society of North America CY - Oak Brook, Ill. ER - TY - JOUR A1 - Wittig, Alice A1 - Miranda, Fabio Malcher A1 - Hölzer, Martin A1 - Altenburg, Tom A1 - Bartoszewicz, Jakub Maciej A1 - Beyvers, Sebastian A1 - Dieckmann, Marius Alfred A1 - Genske, Ulrich A1 - Giese, Sven Hans-Joachim A1 - Nowicka, Melania A1 - Richard, Hugues A1 - Schiebenhoefer, Henning A1 - Schmachtenberg, Anna-Juliane A1 - Sieben, Paul A1 - Tang, Ming A1 - Tembrockhaus, Julius A1 - Renard, Bernhard Y. A1 - Fuchs, Stephan T1 - CovRadar BT - continuously tracking and filtering SARS-CoV-2 mutations for genomic surveillance JF - Bioinformatics N2 - The ongoing pandemic caused by SARS-CoV-2 emphasizes the importance of genomic surveillance to understand the evolution of the virus, to monitor the viral population, and plan epidemiological responses. Detailed analysis, easy visualization and intuitive filtering of the latest viral sequences are powerful for this purpose. We present CovRadar, a tool for genomic surveillance of the SARS-CoV-2 Spike protein. CovRadar consists of an analytical pipeline and a web application that enable the analysis and visualization of hundreds of thousand sequences. First, CovRadar extracts the regions of interest using local alignment, then builds a multiple sequence alignment, infers variants and consensus and finally presents the results in an interactive app, making accessing and reporting simple, flexible and fast. Y1 - 2022 U6 - https://doi.org/10.1093/bioinformatics/btac411 SN - 1367-4803 SN - 1367-4811 VL - 38 IS - 17 SP - 4223 EP - 4225 PB - Oxford Univ. Press CY - Oxford ER -