TY - JOUR A1 - Souza Jr., Luis Antonio de A1 - Pacheco, André G.C. A1 - Passos, Leandro A. A1 - Santana, Marcos Cleison S. A1 - Mendel, Robert A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Palm, Christoph A1 - Papa, João Paulo T1 - DeepCraftFuse: visual and deeply-learnable features work better together for esophageal cancer detection in patients with Barrett’s esophagus JF - Neural Computing and Applications N2 - Limitations in computer-assisted diagnosis include lack of labeled data and inability to model the relation between what experts see and what computers learn. Even though artificial intelligence and machine learning have demonstrated remarkable performances in medical image computing, their accountability and transparency level must be improved to transfer this success into clinical practice. The reliability of machine learning decisions must be explained and interpreted, especially for supporting the medical diagnosis. While deep learning techniques are broad so that unseen information might help learn patterns of interest, human insights to describe objects of interest help in decision-making. This paper proposes a novel approach, DeepCraftFuse, to address the challenge of combining information provided by deep networks with visual-based features to significantly enhance the correct identification of cancerous tissues in patients affected with Barrett’s esophagus (BE). We demonstrate that DeepCraftFuse outperforms state-of-the-art techniques on private and public datasets, reaching results of around 95% when distinguishing patients affected by BE that is either positive or negative to esophageal cancer. KW - Deep Learning KW - Speiseröhrenkrebs KW - Adenocarcinom KW - Endobrachyösophagus KW - Diagnose KW - Maschinelles Lernen KW - Machine learning KW - Adenocarcinoma KW - Object detector KW - Barrett’s esophagus KW - Deep Learning Y1 - 2024 U6 - https://doi.org/10.1007/s00521-024-09615-z VL - 36 SP - 10445 EP - 10459 PB - Springer CY - London ER - TY - JOUR A1 - Souza, Luis A. A1 - Pacheco, André G.C. A1 - de Souza, Alberto F. A1 - Oliveira-Santos, Thiago A1 - Badue, Claudine A1 - Palm, Christoph A1 - Papa, João Paulo T1 - TransConv: a lightweight architecture based on transformers and convolutional neural networks for adenocarcinoma and Barrett’s esophagus identification JF - Neural Computing and Applications N2 - Barrett’s esophagus, also known as BE, is commonly associated with repeated exposure to stomach acid. If not treated properly, it may evolve into esophageal adenocarcinoma, aka esophageal cancer. This paper proposes TransConv, a hybrid architecture that benefits from features learned by pre-trained vision transformers (ViTs) and convolutional neural networks (CNNs), followed by a shallow neural network composed of three normalizations, ReLU activations, and fully connected layers, and a SoftMax head to distinguish between BE and esophageal cancer. TransConv is designed to be training-lightweight, and for the ViT and CNN backbone models, weights are kept frozen during training, i.e., the primary goal of TransConv is to learn the weights of the fully connected layer from both backbones only, avoiding the burden of updating their weights but still learning their final descriptions for the lightweight convolutional model. We report promising results with low computational training costs in two datasets, one public and another private. From our achievements, TransConv was able to deliver balanced accuracy results around 85% and 86% for each evaluated dataset, respectively, in a design that required only 50 epochs of model training, a very reduced number compared to state-of-the-art conducted studies in the same domain. Y1 - 2025 U6 - https://doi.org/10.1007/s00521-025-11299-y IS - 37 SP - 15535 EP - 15546 PB - Springer ER - TY - INPR A1 - Rückert, Tobias A1 - Rückert, Daniel A1 - Palm, Christoph T1 - Methods and datasets for segmentation of minimally invasive surgical instruments in endoscopic images and videos: A review of the state of the art N2 - In the field of computer- and robot-assisted minimally invasive surgery, enormous progress has been made in recent years based on the recognition of surgical instruments in endoscopic images. Especially the determination of the position and type of the instruments is of great interest here. Current work involves both spatial and temporal information with the idea, that the prediction of movement of surgical tools over time may improve the quality of final segmentations. The provision of publicly available datasets has recently encouraged the development of new methods, mainly based on deep learning. In this review, we identify datasets used for method development and evaluation, as well as quantify their frequency of use in the literature. We further present an overview of the current state of research regarding the segmentation and tracking of minimally invasive surgical instruments in endoscopic images. The paper focuses on methods that work purely visually without attached markers of any kind on the instruments, taking into account both single-frame segmentation approaches as well as those involving temporal information. A discussion of the reviewed literature is provided, highlighting existing shortcomings and emphasizing available potential for future developments. The publications considered were identified through the platforms Google Scholar, Web of Science, and PubMed. The search terms used were "instrument segmentation", "instrument tracking", "surgical tool segmentation", and "surgical tool tracking" and result in 408 articles published between 2015 and 2022 from which 109 were included using systematic selection criteria. Y1 - 2023 U6 - https://doi.org/10.48550/arXiv.2304.13014 ER - TY - CHAP A1 - Gutbrod, Max A1 - Rauber, David A1 - Weber Nunes, Danilo A1 - Palm, Christoph T1 - OpenMIBOOD: Open Medical Imaging Benchmarks for Out-Of-Distribution Detection T2 - 2025 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 10.-17. June 2025, Nashville N2 - The growing reliance on Artificial Intelligence (AI) in critical domains such as healthcare demands robust mechanisms to ensure the trustworthiness of these systems, especially when faced with unexpected or anomalous inputs. This paper introduces the Open Medical Imaging Benchmarks for Out-Of-Distribution Detection (OpenMIBOOD), a comprehensive framework for evaluating out-of-distribution (OOD) detection methods specifically in medical imaging contexts. OpenMIBOOD includes three benchmarks from diverse medical domains, encompassing 14 datasets divided into covariate-shifted in-distribution, nearOOD, and far-OOD categories. We evaluate 24 post-hoc methods across these benchmarks, providing a standardized reference to advance the development and fair comparison of OODdetection methods. Results reveal that findings from broad-scale OOD benchmarks in natural image domains do not translate to medical applications, underscoring the critical need for such benchmarks in the medical field. By mitigating the risk of exposing AI models to inputs outside their training distribution, OpenMIBOOD aims to support the advancement of reliable and trustworthy AI systems in healthcare. The repository is available at https://github.com/remic-othr/OpenMIBOOD. KW - Benchmark testing KW - Reliability KW - Trustworthiness KW - out-of-distribution Y1 - 2025 UR - https://openaccess.thecvf.com/content/CVPR2025/html/Gutbrod_OpenMIBOOD_Open_Medical_Imaging_Benchmarks_for_Out-Of-Distribution_Detection_CVPR_2025_paper.html SN - 979-8-3315-4364-8 U6 - https://doi.org/10.1109/CVPR52734.2025.02410 N1 - Die Preprint-Version ist ebenfalls in diesem Repositorium verzeichnet unter: https://opus4.kobv.de/opus4-oth-regensburg/8059 SP - 25874 EP - 25886 PB - IEEE ER - TY - INPR A1 - Rückert, Tobias A1 - Rauber, David A1 - Maerkl, Raphaela A1 - Klausmann, Leonard A1 - Yildiran, Suemeyye R. A1 - Gutbrod, Max A1 - Nunes, Danilo Weber A1 - Moreno, Alvaro Fernandez A1 - Luengo, Imanol A1 - Stoyanov, Danail A1 - Toussaint, Nicolas A1 - Cho, Enki A1 - Kim, Hyeon Bae A1 - Choo, Oh Sung A1 - Kim, Ka Young A1 - Kim, Seong Tae A1 - Arantes, Gonçalo A1 - Song, Kehan A1 - Zhu, Jianjun A1 - Xiong, Junchen A1 - Lin, Tingyi A1 - Kikuchi, Shunsuke A1 - Matsuzaki, Hiroki A1 - Kouno, Atsushi A1 - Manesco, João Renato Ribeiro A1 - Papa, João Paulo A1 - Choi, Tae-Min A1 - Jeong, Tae Kyeong A1 - Park, Juyoun A1 - Alabi, Oluwatosin A1 - Wei, Meng A1 - Vercauteren, Tom A1 - Wu, Runzhi A1 - Xu, Mengya A1 - an Wang, A1 - Bai, Long A1 - Ren, Hongliang A1 - Yamlahi, Amine A1 - Hennighausen, Jakob A1 - Maier-Hein, Lena A1 - Kondo, Satoshi A1 - Kasai, Satoshi A1 - Hirasawa, Kousuke A1 - Yang, Shu A1 - Wang, Yihui A1 - Chen, Hao A1 - Rodríguez, Santiago A1 - Aparicio, Nicolás A1 - Manrique, Leonardo A1 - Lyons, Juan Camilo A1 - Hosie, Olivia A1 - Ayobi, Nicolás A1 - Arbeláez, Pablo A1 - Li, Yiping A1 - Khalil, Yasmina Al A1 - Nasirihaghighi, Sahar A1 - Speidel, Stefanie A1 - Rückert, Daniel A1 - Feussner, Hubertus A1 - Wilhelm, Dirk A1 - Palm, Christoph T1 - Comparative validation of surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation in endoscopy: Results of the PhaKIR 2024 challenge N2 - Reliable recognition and localization of surgical instruments in endoscopic video recordings are foundational for a wide range of applications in computer- and robot-assisted minimally invasive surgery (RAMIS), including surgical training, skill assessment, and autonomous assistance. However, robust performance under real-world conditions remains a significant challenge. Incorporating surgical context - such as the current procedural phase - has emerged as a promising strategy to improve robustness and interpretability. To address these challenges, we organized the Surgical Procedure Phase, Keypoint, and Instrument Recognition (PhaKIR) sub-challenge as part of the Endoscopic Vision (EndoVis) challenge at MICCAI 2024. We introduced a novel, multi-center dataset comprising thirteen full-length laparoscopic cholecystectomy videos collected from three distinct medical institutions, with unified annotations for three interrelated tasks: surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation. Unlike existing datasets, ours enables joint investigation of instrument localization and procedural context within the same data while supporting the integration of temporal information across entire procedures. We report results and findings in accordance with the BIAS guidelines for biomedical image analysis challenges. The PhaKIR sub-challenge advances the field by providing a unique benchmark for developing temporally aware, context-driven methods in RAMIS and offers a high-quality resource to support future research in surgical scene understanding. Y1 - 2025 N1 - Der Aufsatz wurde peer-reviewed veröffentlicht und ist ebenfalls in diesem Repositorium verzeichnet unter: https://opus4.kobv.de/opus4-oth-regensburg/frontdoor/index/index/start/0/rows/10/sortfield/score/sortorder/desc/searchtype/simple/query/10.1016%2Fj.media.2026.103945/docId/8846 ER - TY - GEN A1 - Rückert, Tobias A1 - Rückert, Daniel A1 - Palm, Christoph T1 - Corrigendum to “Methods and datasets for segmentation of minimally invasive surgical instruments in endoscopic images and videos: A review of the state of the art” [Comput. Biol. Med. 169 (2024) 107929] T2 - Computers in Biology and Medicine N2 - The authors regret that the SAR-RARP50 dataset is missing from the description of publicly available datasets presented in Chapter 4. Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:898-opus4-70337 N1 - Aufsatz unter: https://opus4.kobv.de/opus4-oth-regensburg/frontdoor/index/index/docId/6983 PB - Elsevier ER - TY - JOUR A1 - Hammer, Simone A1 - Nunes, Danilo Weber A1 - Hammer, Michael A1 - Zeman, Florian A1 - Akers, Michael A1 - Götz, Andrea A1 - Balla, Annika A1 - Doppler, Michael Christian A1 - Fellner, Claudia A1 - Da Platz Batista Silva, Natascha A1 - Thurn, Sylvia A1 - Verloh, Niklas A1 - Stroszczynski, Christian A1 - Wohlgemuth, Walter Alexander A1 - Palm, Christoph A1 - Uller, Wibke T1 - Deep learning-based differentiation of peripheral high-flow and low-flow vascular malformations in T2-weighted short tau inversion recovery MRI JF - Clinical hemorheology and microcirculation N2 - BACKGROUND Differentiation of high-flow from low-flow vascular malformations (VMs) is crucial for therapeutic management of this orphan disease. OBJECTIVE A convolutional neural network (CNN) was evaluated for differentiation of peripheral vascular malformations (VMs) on T2-weighted short tau inversion recovery (STIR) MRI. METHODS 527 MRIs (386 low-flow and 141 high-flow VMs) were randomly divided into training, validation and test set for this single-center study. 1) Results of the CNN's diagnostic performance were compared with that of two expert and four junior radiologists. 2) The influence of CNN's prediction on the radiologists' performance and diagnostic certainty was evaluated. 3) Junior radiologists' performance after self-training was compared with that of the CNN. RESULTS Compared with the expert radiologists the CNN achieved similar accuracy (92% vs. 97%, p = 0.11), sensitivity (80% vs. 93%, p = 0.16) and specificity (97% vs. 100%, p = 0.50). In comparison to the junior radiologists, the CNN had a higher specificity and accuracy (97% vs. 80%, p <  0.001; 92% vs. 77%, p <  0.001). CNN assistance had no significant influence on their diagnostic performance and certainty. After self-training, the junior radiologists' specificity and accuracy improved and were comparable to that of the CNN. CONCLUSIONS Diagnostic performance of the CNN for differentiating high-flow from low-flow VM was comparable to that of expert radiologists. CNN did not significantly improve the simulated daily practice of junior radiologists, self-training was more effective. KW - magnetic resonance imaging KW - deep learning KW - Vascular malformation Y1 - 2024 U6 - https://doi.org/10.3233/CH-232071 SP - 1 EP - 15 PB - IOP Press ET - Pre-press ER - TY - GEN A1 - Scheppach, Markus W. A1 - Mendel, Robert A1 - Probst, Andreas A1 - Nagl, Sandra A1 - Meinikheim, Michael A1 - Yip, Hon Chi A1 - Lau, Louis Ho Shing A1 - Chiu, Philip Wai Yan A1 - Palm, Christoph A1 - Messmann, Helmut A1 - Ebigbo, Alanna T1 - Effekt eines Künstliche Intelligenz (KI) – Algorithmus auf die Gefäßdetektion bei third space Endoskopien T2 - Zeitschrift für Gastroenterologie N2 - Einleitung  Third space Endoskopieprozeduren wie die endoskopische Submukosadissektion (ESD) und die perorale endoskopische Myotomie (POEM) sind technisch anspruchsvoll und gehen mit untersucherabhängigen Komplikationen wie Blutungen und Perforationen einher. Grund hierfür ist die unabsichtliche Durchschneidung von submukosalen Blutgefäßen ohne präemptive Koagulation. Ziele Die Forschungsfrage, ob ein KI-Algorithmus die intraprozedurale Gefäßerkennung bei ESD und POEM unterstützen und damit Komplikationen wie Blutungen verhindern könnte, erscheint in Anbetracht des erfolgreichen Einsatzes von KI bei der Erkennung von Kolonpolypen interessant. Methoden  Auf 5470 Einzelbildern von 59 third space Endoscopievideos wurden submukosale Blutgefäße annotiert. Zusammen mit weiteren 179.681 nicht-annotierten Bildern wurde ein DeepLabv3+neuronales Netzwerk mit dem ECMT-Verfahren für semi-supervised learning trainiert, um Blutgefäße in Echtzeit erkennen zu können. Für die Evaluation wurde ein Videotest mit 101 Videoclips aus 15 vom Trainingsdatensatz separaten Prozeduren mit 200 vordefinierten Gefäßen erstellt. Die Gefäßdetektionsrate, -zeit und -dauer, definiert als der Prozentsatz an Einzelbildern eines Videos bezogen auf den Goldstandard, auf denen ein definiertes Gefäß erkannt wurde, wurden erhoben. Acht erfahrene Endoskopiker wurden mithilfe dieses Videotests im Hinblick auf Gefäßdetektion getestet, wobei eine Hälfte der Videos nativ, die andere Hälfte nach Markierung durch den KI-Algorithmus angesehen wurde. Ergebnisse  Der mittlere Dice Score des Algorithmus für Blutgefäße war 68%. Die mittlere Gefäßdetektionsrate im Videotest lag bei 94% (96% für ESD; 74% für POEM). Die mediane Gefäßdetektionszeit des Algorithmus lag bei 0,32 Sekunden (0,3 Sekunden für ESD; 0,62 Sekunden für POEM). Die mittlere Gefäßdetektionsdauer lag bei 59,1% (60,6% für ESD; 44,8% für POEM) des Goldstandards. Alle Endoskopiker hatten mit KI-Unterstützung eine höhere Gefäßdetektionsrate als ohne KI. Die mittlere Gefäßdetektionsrate ohne KI lag bei 56,4%, mit KI bei 71,2% (p<0.001). Schlussfolgerung  KI-Unterstützung war mit einer statistisch signifikant höheren Gefäßdetektionsrate vergesellschaftet. Die mediane Gefäßdetektionszeit von deutlich unter einer Sekunde sowie eine Gefäßdetektionsdauer von größer 50% des Goldstandards wurden für den klinischen Einsatz als ausreichend erachtet. In prospektiven Anwendungsstudien sollte der KI-Algorithmus auf klinische Relevanz getestet werden. KW - Künstliche Intelligenz Y1 - 2023 U6 - https://doi.org/10.1055/s-0043-1771980 VL - 61 IS - 08 PB - Thieme CY - Stuttgart ER - TY - GEN A1 - Roser, David A1 - Meinikheim, Michael A1 - Mendel, Robert A1 - Palm, Christoph A1 - Muzalyova, Anna A1 - Rauber, David A1 - Rückert, Tobias A1 - Parsa, Nasim A1 - Byrne, Michael F. A1 - Messmann, Helmut A1 - Ebigbo, Alanna T1 - Mensch-Maschine-Interaktion: Einfluss künstlicher Intelligenz auf das diagnostische Vertrauen von Endoskopikern bei der Beurteilung des Barrett-Ösophagus T2 - Zeitschrift für Gastroenterologie N2 - Ziele:  Das Ziel der Studie war es, den Einfluss von KI auf die diagnostische Sicherheit (Konfidenzniveau) von Endoskopikern anhand von BÖ-Videos zu untersuchen und mögliche Korrelationen mit der Untersuchungsqualität zu erforschen. Methodik:  22 Endoskopiker aus zwölf Zentren mit unterschiedlicher Barrett-Erfahrung untersuchten 96 standardisierte Endoskopievideos. Die Untersucher wurden in Experten und Nicht-Experten eingeteilt und nach dem Zufallsprinzip für die Bewertung der Videos mit oder ohne KI eingeteilt. Die Teilnehmer wurden in zwei Gruppen aufgeteilt: Arm A bewertete zunächst Videos ohne KI und dann mit KI, während Arm B die umgekehrte Reihenfolge einhielt. Die Untersucher hatten die Aufgabe, BÖ-assoziierte Neoplasien zu erkennen und ihr Konfidenzniveau sowohl mit als auch ohne KI auf einer Skala von 0 bis 9 anzugeben. Ergebnis:  In Arm A erhöhte der Einsatz von KI das Konfidenzniveau bei beiden signifikant (p<0.001). Bemerkenswert ist, dass jedoch nur Nicht-Experten durch die KI eine signifikante Verbesserung der Sensitivität und Spezifität (p<0.001 bzw. p<0.05) erfuhren. Während Experten ohne KI im Vergleich zu Nicht-Experten mit KI ein höheres Konfidenzniveau aufwiesen, gab es keinen signifikanten Unterschied in der Genauigkeit. In Arm B zeigten beide Gruppen eine signifikante Abnahme des Konfidenzniveaus (p<0.001) bei gleichbleibender Genauigkeit. Darüber hinaus wurden in 9% der Entscheidungen trotz korrekter KI eine falsche Wahl getroffen. Schlussfolgerung:  Der Einsatz künstlicher Intelligenz steigerte das Konfidenzniveau sowohl bei Experten als auch bei Nicht-Experten signifikant – ein Effekt, der im Studienmodell reversibel war. Darüber hinaus wiesen Experten mit oder ohne KI durchweg höhere Konfidenzniveaus auf als Nicht-Experten mit KI, trotz vergleichbarer Ergebnisse. Zudem konnte beobachtet werden, dass die Untersucher in 9% der Fälle die KI zuungunsten des Patienten ignorierten. Y1 - 2024 U6 - https://doi.org/10.1055/s-0044-1789656 VL - 62 IS - 09 SP - e575 EP - e576 PB - Georg Thieme Verlag KG ER - TY - JOUR A1 - Rueckert, Tobias A1 - Rauber, David A1 - Maerkl, Raphaela A1 - Klausmann, Leonard A1 - Yildiran, Suemeyye R. A1 - Gutbrod, Max A1 - Nunes, Danilo Weber A1 - Moreno, Alvaro Fernandez A1 - Luengo, Imanol A1 - Stoyanov, Danail A1 - Toussaint, Nicolas A1 - Cho, Enki A1 - Kim, Hyeon Bae A1 - Choo, Oh Sung A1 - Kim, Ka Young A1 - Kim, Seong Tae A1 - Arantes, Gonçalo A1 - Song, Kehan A1 - Zhu, Jianjun A1 - Xiong, Junchen A1 - Lin, Tingyi A1 - Kikuchi, Shunsuke A1 - Matsuzaki, Hiroki A1 - Kouno, Atsushi A1 - Manesco, João Renato Ribeiro A1 - Papa, João Paulo A1 - Choi, Tae-Min A1 - Jeong, Tae Kyeong A1 - Park, Juyoun A1 - Alabi, Oluwatosin A1 - Wei, Meng A1 - Vercauteren, Tom A1 - Wu, Runzhi A1 - Xu, Mengya A1 - Wang, An A1 - Bai, Long A1 - Ren, Hongliang A1 - Yamlahi, Amine A1 - Hennighausen, Jakob A1 - Maier-Hein, Lena A1 - Kondo, Satoshi A1 - Kasai, Satoshi A1 - Hirasawa, Kousuke A1 - Yang, Shu A1 - Wang, Yihui A1 - Chen, Hao A1 - Rodríguez, Santiago A1 - Aparicio, Nicolás A1 - Manrique, Leonardo A1 - Palm, Christoph A1 - Wilhelm, Dirk A1 - Feussner, Hubertus A1 - Rueckert, Daniel A1 - Speidel, Stefanie A1 - Nasirihaghighi, Sahar A1 - Al Khalil, Yasmina A1 - Li, Yiping A1 - Arbeláez, Pablo A1 - Ayobi, Nicolás A1 - Hosie, Olivia A1 - Lyons, Juan Camilo T1 - Comparative validation of surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation in endoscopy: Results of the PhaKIR 2024 challenge JF - Medical Image Analysis N2 - Reliable recognition and localization of surgical instruments in endoscopic video recordings are foundational for a wide range of applications in computer- and robot-assisted minimally invasive surgery (RAMIS), including surgical training, skill assessment, and autonomous assistance. However, robust performance under real-world conditions remains a significant challenge. Incorporating surgical context – such as the current procedural phase – has emerged as a promising strategy to improve robustness and interpretability. To address these challenges, we organized the Surgical Procedure Phase, Keypoint, and Instrument Recognition (PhaKIR) sub-challenge as part of the Endoscopic Vision (EndoVis) challenge at MICCAI 2024. We introduced a novel, multi-center dataset comprising thirteen full-length laparoscopic cholecystectomy videos collected from three distinct medical institutions, with unified annotations for three interrelated tasks: surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation. Unlike existing datasets, ours enables joint investigation of instrument localization and procedural context within the same data while supporting the integration of temporal information across entire procedures. We report results and findings in accordance with the BIAS guidelines for biomedical image analysis challenges. The PhaKIR sub-challenge advances the field by providing a unique benchmark for developing temporally aware, context-driven methods in RAMIS and offers a high-quality resource to support future research in surgical scene understanding. KW - Surgical phase recognition KW - Instrument keypoint estimation KW - Instrument instance segmentation KW - Robot-assisted surgery Y1 - 2026 U6 - https://doi.org/10.1016/j.media.2026.103945 SN - 1361-8415 N1 - Corresponding author der OTH Regensburg: Tobias Rueckert Die Preprint-Version ist ebenfalls in diesem Repositorium verzeichnet unter: https://opus4.kobv.de/opus4-oth-regensburg/solrsearch/index/search/start/0/rows/10/sortfield/score/sortorder/desc/searchtype/simple/query/2507.16559 VL - 109 PB - Elsevier ER -