TY - CHAP A1 - Mendel, Robert A1 - Rauber, David A1 - Palm, Christoph T1 - Exploring the Effects of Contrastive Learning on Homogeneous Medical Image Data T2 - Bildverarbeitung für die Medizin 2023: Proceedings, German Workshop on Medical Image Computing, July 2– 4, 2023, Braunschweig N2 - We investigate contrastive learning in a multi-task learning setting classifying and segmenting early Barrett’s cancer. How can contrastive learning be applied in a domain with few classes and low inter-class and inter-sample variance, potentially enabling image retrieval or image attribution? We introduce a data sampling strategy that mines per-lesion data for positive samples and keeps a queue of the recent projections as negative samples. We propose a masking strategy for the NT-Xent loss that keeps the negative set pure and removes samples from the same lesion. We show cohesion and uniqueness improvements of the proposed method in feature space. The introduction of the auxiliary objective does not affect the performance but adds the ability to indicate similarity between lesions. Therefore, the approach could enable downstream auto-documentation tasks on homogeneous medical image data. Y1 - 2023 U6 - https://doi.org/10.1007/978-3-658-41657-7 SP - 128 EP - 13 PB - Springer Vieweg CY - Wiesbaden ER - TY - GEN A1 - Mendel, Robert A1 - Souza Jr., Luis Antonio de A1 - Rauber, David A1 - Papa, João Paulo A1 - Palm, Christoph T1 - Abstract: Semi-supervised Segmentation Based on Error-correcting Supervision T2 - Bildverarbeitung für die Medizin 2021. Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7-9, 2021 N2 - Pixel-level classification is an essential part of computer vision. For learning from labeled data, many powerful deep learning models have been developed recently. In this work, we augment such supervised segmentation models by allowing them to learn from unlabeled data. Our semi-supervised approach, termed Error-Correcting Supervision, leverages a collaborative strategy. Apart from the supervised training on the labeled data, the segmentation network is judged by an additional network. KW - Deep Learning Y1 - 2021 SN - 978-3-658-33197-9 U6 - https://doi.org/10.1007/978-3-658-33198-6_43 SP - 178 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Ebigbo, Alanna A1 - Palm, Christoph A1 - Messmann, Helmut T1 - Barrett esophagus: What to expect from Artificial Intelligence? JF - Best Practice & Research Clinical Gastroenterology N2 - The evaluation and assessment of Barrett’s esophagus is challenging for both expert and nonexpert endoscopists. However, the early diagnosis of cancer in Barrett’s esophagus is crucial for its prognosis, and could save costs. Pre-clinical and clinical studies on the application of Artificial Intelligence (AI) in Barrett’s esophagus have shown promising results. In this review, we focus on the current challenges and future perspectives of implementing AI systems in the management of patients with Barrett’s esophagus. KW - Deep Learning KW - Künstliche Intelligenz KW - Computerunterstützte Medizin KW - Barrett KW - Adenocarcinoma KW - Artificial intelligence KW - Deep learning KW - Convolutional neural networks Y1 - 2021 U6 - https://doi.org/10.1016/j.bpg.2021.101726 SN - 1521-6918 VL - 52-53 IS - June-August PB - Elsevier ER - TY - JOUR A1 - Maier, Andreas A1 - Deserno, Thomas M. A1 - Handels, Heinz A1 - Maier-Hein, Klaus H. A1 - Palm, Christoph A1 - Tolxdorff, Thomas T1 - Guest editorial of the IJCARS - BVM 2018 special issue JF - International Journal of Computer Assisted Radiology and Surgery KW - Medical Image Computing Y1 - 2019 U6 - https://doi.org/10.1007/s11548-018-01902-0 VL - 14 SP - 1 EP - 2 PB - Springer ER - TY - JOUR A1 - Passos, Leandro A. A1 - Souza Jr., Luis Antonio de A1 - Mendel, Robert A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Palm, Christoph A1 - Papa, João Paulo T1 - Barrett's esophagus analysis using infinity Restricted Boltzmann Machines JF - Journal of Visual Communication and Image Representation N2 - The number of patients with Barret’s esophagus (BE) has increased in the last decades. Considering the dangerousness of the disease and its evolution to adenocarcinoma, an early diagnosis of BE may provide a high probability of cancer remission. However, limitations regarding traditional methods of detection and management of BE demand alternative solutions. As such, computer-aided tools have been recently used to assist in this problem, but the challenge still persists. To manage the problem, we introduce the infinity Restricted Boltzmann Machines (iRBMs) to the task of automatic identification of Barrett’s esophagus from endoscopic images of the lower esophagus. Moreover, since iRBM requires a proper selection of its meta-parameters, we also present a discriminative iRBM fine-tuning using six meta-heuristic optimization techniques. We showed that iRBMs are suitable for the context since it provides competitive results, as well as the meta-heuristic techniques showed to be appropriate for such task. KW - Speiseröhrenkrankheit KW - Diagnose KW - Boltzmann-Maschine KW - Barrett’s esophagus KW - Infinity Restricted Boltzmann Machines KW - Meta-heuristics KW - Deep learning KW - Metaheuristik KW - Maschinelles Lernen Y1 - 2019 U6 - https://doi.org/10.1016/j.jvcir.2019.01.043 VL - 59 SP - 475 EP - 485 PB - Elsevier ER - TY - CHAP A1 - Souza Jr., Luis Antonio de A1 - Afonso, Luis Claudio Sugi A1 - Palm, Christoph A1 - Papa, João Paulo T1 - Barrett's Esophagus Identification Using Optimum-Path Forest T2 - Proceedings of the 30th Conference on Graphics, Patterns and Images Tutorials (SIBGRAPI-T 2017), Niterói, Rio de Janeiro, Brazil, 2017, 17-20 October N2 - Computer-assisted analysis of endoscopic images can be helpful to the automatic diagnosis and classification of neoplastic lesions. Barrett's esophagus (BE) is a common type of reflux that is not straight forward to be detected by endoscopic surveillance, thus being way susceptible to erroneous diagnosis, which can cause cancer when not treated properly. In this work, we introduce the Optimum-Path Forest (OPF) classifier to the task of automatic identification of Barrett'sesophagus, with promising results and outperforming the well known Support Vector Machines (SVM) in the aforementioned context. We consider describing endoscopic images by means of feature extractors based on key point information, such as the Speeded up Robust Features (SURF) and Scale-Invariant Feature Transform (SIFT), for further designing a bag-of-visual-wordsthat is used to feed both OPF and SVM classifiers. The best results were obtained by means of the OPF classifier for both feature extractors, with values lying on 0.732 (SURF) - 0.735(SIFT) for sensitivity, 0.782 (SURF) - 0.806 (SIFT) for specificity, and 0.738 (SURF) - 0.732 (SIFT) for the accuracy. KW - Speiseröhrenkrankheit KW - Diagnose KW - Maschinelles Lernen KW - Bilderkennung KW - Automatische Klassifikation Y1 - 2017 U6 - https://doi.org/10.1109/SIBGRAPI.2017.47 SP - 308 EP - 314 ER - TY - CHAP A1 - Zehner, Alexander A1 - Szalo, Alexander Eduard A1 - Palm, Christoph T1 - GraphMIC: Easy Prototyping of Medical Image Computing Applications T2 - Interactive Medical Image Computing (IMIC), Workshop at the Medical Image Computing and Computer Assisted Interventions (MICCAI 2015), 2015, Munich N2 - GraphMIC is a cross-platform image processing application utilizing the libraries ITK and OpenCV. The abstract structure of image processing pipelines is visually represented by user interface components based on modern QtQuick technology and allows users to focus on arrangement and parameterization of operations rather than implementing the equivalent functionality natively in C++. The application's central goal is to improve and simplify the typical workflow by providing various high level features and functions like multi threading, image sequence processing and advanced error handling. A built-in python interpreter allows the creation of custom nodes, where user defined algorithms can be integrated to extend basic functionality. An embedded 2d/3d visual-izer gives feedback of the resulting image of an operation or the whole pipeline. User inputs like seed points, contours or regions are forwarded to the processing pipeline as parameters to offer semi-automatic image computing. We report the main concept of the application and introduce several features and their implementation. Finally, the current state of development as well as future perspectives of GraphMIC are discussed KW - Bildverarbeitung KW - Medizin Y1 - 2015 U6 - https://doi.org/10.13140/RG.2.1.3718.4725 N1 - Open-Access-Publikation SP - 395 EP - 400 ER - TY - CHAP A1 - Weber, Joachim A1 - Doenitz, Christian A1 - Brawanski, Alexander A1 - Palm, Christoph T1 - Data-Parallel MRI Brain Segmentation in Clinicial Use BT - Porting FSL-Fastv4 to GPGPUs T2 - Bildverarbeitung für die Medizin 2015; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 15. bis 17. März 2015 in Lübeck N2 - Structural MRI brain analysis and segmentation is a crucial part in the daily routine in neurosurgery for intervention planning. Exemplarily, the free software FSL-FAST (FMRIB’s Segmentation Library – FMRIB’s Automated Segmentation Tool) in version 4 is used for segmentation of brain tissue types. To speed up the segmentation procedure by parallel execution, we transferred FSL-FAST to a General Purpose Graphics Processing Unit (GPGPU) using Open Computing Language (OpenCL) [1]. The necessary steps for parallelization resulted in substantially different and less useful results. Therefore, the underlying methods were revised and adapted yielding computational overhead. Nevertheless, we achieved a speed-up factor of 3.59 from CPU to GPGPU execution, as well providing similar useful or even better results. KW - Brain Segmentation KW - Magnetic Resonance Imaging KW - Parallel Execution KW - Voxel Spacing KW - General Purpose Graphic Processing Unit KW - Kernspintomografie KW - Gehirn KW - Bildsegmentierung KW - Parallelverarbeitung Y1 - 2015 U6 - https://doi.org/10.1007/978-3-662-46224-9_67 SP - 389 EP - 394 PB - Springer CY - Berlin ER - TY - GEN A1 - Maier, Johannes A1 - Weiherer, Maximilian A1 - Huber, Michaela A1 - Palm, Christoph ED - Handels, Heinz ED - Deserno, Thomas M. ED - Maier, Andreas ED - Maier-Hein, Klaus H. ED - Palm, Christoph ED - Tolxdorff, Thomas T1 - Abstract: Imitating Human Soft Tissue with Dual-Material 3D Printing T2 - Bildverarbeitung für die Medizin 2019, Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 17. bis 19. März 2019 in Lübeck N2 - Currently, it is common practice to use three-dimensional (3D) printers not only for rapid prototyping in the industry, but also in the medical area to create medical applications for training inexperienced surgeons. In a clinical training simulator for minimally invasive bone drilling to fix hand fractures with Kirschner-wires (K-wires), a 3D printed hand phantom must not only be geometrically but also haptically correct. Due to a limited view during an operation, surgeons need to perfectly localize underlying risk structures only by feeling of specific bony protrusions of the human hand. KW - Handchirurgie KW - 3D-Druck KW - Lernprogramm KW - HaptiVisT Y1 - 2019 SN - 978-3-658-25325-7 U6 - https://doi.org/10.1007/978-3-658-25326-4_48 SP - 218 PB - Springer Vieweg CY - Wiesbaden ER - TY - GEN A1 - Rückert, Tobias A1 - Rieder, Maximilian A1 - Rauber, David A1 - Xiao, Michel A1 - Humolli, Eg A1 - Feussner, Hubertus A1 - Wilhelm, Dirk A1 - Palm, Christoph T1 - Augmenting instrument segmentation in video sequences of minimally invasive surgery by synthetic smoky frames T2 - International Journal of Computer Assisted Radiology and Surgery KW - Surgical instrument segmentation KW - smoke simulation KW - unpaired image-to-image translation KW - robot-assisted surgery Y1 - 2023 U6 - https://doi.org/10.1007/s11548-023-02878-2 VL - 18 IS - Suppl 1 SP - S54 EP - S56 PB - Springer Nature ER -