TY - CHAP A1 - Palm, Christoph A1 - Scholl, Ingrid A1 - Lehmann, Thomas M. A1 - Spitzer, Klaus ED - Greiser, E. ED - Wischnewsky, M. T1 - Nutzung eines Farbkonstanz-Algorithmus zur Entfernung von Glanzlichtern in laryngoskopischen Bildern T2 - Methoden der Medizinischen Informatik, Biometrie und Epidemiologie in der modernen Informationsgesellschaft N2 - 1 Einführung Funktionelle und organische Störungen im Larynx beeinträchtigen die Ausdrucksfähigkeit des Menschen. Zur Diagnostik und Verlaufkontrolle werden die Stimmlippen im Larynx mit Hilfe der Video-Laryngoskopie aufgenommen. Zur optimalen Farbmessung wird dazu an das Lupenendoskop eine 3-Chip-CCD-Kamera angeschlossen, die eine unabhängige Aufnahme der drei Farbkanäle erlaubt. Die bisherige subjektive Befundung ist von der Erfahrung des Untersuchers abhängig und läßt nur eine grobe Klassifikation der Krankheitsbilder zu. Zur Objektivierung werden daher quantitative Parameter für Farbe, Textur und Schwingung entwickelt. Neben dem Einfluß der wechselnden Lichtquellenfarbe auf den Farbeindruck ist die Sekretauflage auf den Stimmlippen ein Problem bei der Farb-und Texturanalyse. Sie kann zu ausgedehnten Glanzlichtern führen und so weite Bereiche der Stimmlippen für die Farb-und Texturanalyse unbrauchbar machen. Dieser Beitrag stellt einen Farbkonstanz-Algorithmus vor, der unabhängig von der Lichtquelle quantitative Farbwerte des Gewebes liefert und die Glanzlichtdetektion und -elimination ermöglicht. 2 Methodik Ziel des Farbkonstanz-Algorithmus ist die Trennung von Lichtquellen-und Gewebefarbe. Unter Verwendung des dichromatischen Reflexionsmodells [1] kann die Oberflächenreflexion mit der Farbe der Lichtquelle und die Körperreflexion mit der Gewebefarbe identifiziert werden. Der Farbeindruck entsteht aus der Linearkombination beider Farbkomponenten. Ihre Gewichtung ist von der Aufnahmegeometrie abhängig, insbesondere vom Winkel zwischen Oberflächennormalen und dem Positionsvektor der Lichtquelle. In einem zweistufigen Verfahren wird zunächst die Lichtquellenfarbe geschätzt, dann die Gewebefarbe ermittelt. Hieraus können beide Farbanteile durch die Berechnung der Gewichtsfaktoren pixelweise getrennt werden. KW - Farbkonstanz KW - Glanzlichtelimination KW - medizinische Bildverarbeitung KW - dichromatisches Reflexionsmodell Y1 - 1998 SN - 9783820813357 SP - 300 EP - 303 PB - MMV Medien und Medizin CY - München ER - TY - JOUR A1 - Palm, Christoph T1 - Color Texture Classification by Integrative Co-Occurrence Matrices JF - Pattern Recognition N2 - Integrative Co-occurrence matrices are introduced as novel features for color texture classification. The extended Co-occurrence notation allows the comparison between integrative and parallel color texture concepts. The information profit of the new matrices is shown quantitatively using the Kolmogorov distance and by extensive classification experiments on two datasets. Applying them to the RGB and the LUV color space the combined color and intensity textures are studied and the existence of intensity independent pure color patterns is demonstrated. The results are compared with two baselines: gray-scale texture analysis and color histogram analysis. The novel features improve the classification results up to 20% and 32% for the first and second baseline, respectively. KW - Color texture KW - Co-occurrence matrix KW - Integrative features KW - KolmogKorov distance KW - Image classification Y1 - 2004 U6 - https://doi.org/10.1016/j.patcog.2003.09.010 VL - 37 IS - 5 SP - 965 EP - 976 ER - TY - GEN A1 - Gräßel, David A1 - Axer, Markus A1 - Palm, Christoph A1 - Dammers, Jürgen A1 - Amunts, Katrin A1 - Pietrzyk, Uwe A1 - Zilles, Karl T1 - Visualization of Fiber Tracts in the Postmortem Human Brain by Means of Polarized Light T2 - NeuroImage KW - Gehirn KW - Bildgebendes Verfahren KW - Polarisiertes Licht KW - Pathologische Anatomie Y1 - 2009 U6 - https://doi.org/10.1016/S1053-8119(09)71415-6 VL - 47 IS - Suppl. 1 SP - 142 ER - TY - JOUR A1 - Palm, Christoph A1 - Axer, Markus A1 - Gräßel, David A1 - Dammers, Jürgen A1 - Lindemeyer, Johannes A1 - Zilles, Karl A1 - Pietrzyk, Uwe A1 - Amunts, Katrin T1 - Towards ultra-high resolution fibre tract mapping of the human brain BT - registration of polarised light images and reorientation of fibre vectors JF - Frontiers in Human Neuroscience N2 - Polarised light imaging (PLI) utilises the birefringence of the myelin sheaths in order to visualise the orientation of nerve fibres in microtome sections of adult human post-mortem brains at ultra-high spatial resolution. The preparation of post-mortem brains for PLI involves fixation, freezing and cutting into 100-μm-thick sections. Hence, geometrical distortions of histological sections are inevitable and have to be removed for 3D reconstruction and subsequent fibre tracking. We here present a processing pipeline for 3D reconstruction of these sections using PLI derived multimodal images of post-mortem brains. Blockface images of the brains were obtained during cutting; they serve as reference data for alignment and elimination of distortion artefacts. In addition to the spatial image transformation, fibre orientation vectors were reoriented using the transformation fields, which consider both affine and subsequent non-linear registration. The application of this registration and reorientation approach results in a smooth fibre vector field, which reflects brain morphology. PLI combined with 3D reconstruction and fibre tracking is a powerful tool for human brain mapping. It can also serve as an independent method for evaluating in vivo fibre tractography. KW - Bildgebendes Verfahren KW - Dreidimensionale Bildverarbeitung KW - Polarisiertes Licht KW - Gehirnkarte Y1 - 2010 U6 - https://doi.org/10.3389/neuro.09.009.2010 VL - 4 ER - TY - JOUR A1 - Becker, Johanna Sabine A1 - Matusch, Andreas A1 - Palm, Christoph A1 - Salber, Dagmar A1 - Morton, Kathryn A. A1 - Becker, Julia Susanne T1 - Bioimaging of metals in brain tissue by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and metallomics JF - Metallomics N2 - Laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) has been developed and established as an emerging technique in the generation of quantitative images of metal distributions in thin tissue sections of brain samples (such as human, rat and mouse brain), with applications in research related to neurodegenerative disorders. A new analytical protocol is described which includes sample preparation by cryo-cutting of thin tissue sections and matrix-matched laboratory standards, mass spectrometric measurements, data acquisition, and quantitative analysis. Specific examples of the bioimaging of metal distributions in normal rodent brains are provided. Differences to the normal were assessed in a Parkinson’s disease and a stroke brain model. Furthermore, changes during normal aging were studied. Powerful analytical techniques are also required for the determination and characterization of metal-containing proteins within a large pool of proteins, e.g., after denaturing or non-denaturing electrophoretic separation of proteins in one-dimensional and two-dimensional gels. LA-ICP-MS can be employed to detect metalloproteins in protein bands or spots separated after gel electrophoresis. MALDI-MS can then be used to identify specific metal-containing proteins in these bands or spots. The combination of these techniques is described in the second section. KW - ICP-Massenspektrometrie KW - Metalle KW - Metallproteide KW - Elektrophorese KW - Gehirn Y1 - 2010 U6 - https://doi.org/10.1039/b916722f IS - 2 SP - 104 EP - 111 PB - Oxford Academic Press ER - TY - JOUR A1 - Dammers, Jürgen A1 - Axer, Markus A1 - Gräßel, David A1 - Palm, Christoph A1 - Zilles, Karl A1 - Amunts, Katrin A1 - Pietrzyk, Uwe T1 - Signal enhancement in polarized light imaging by means of independent component analysis JF - NeuroImage N2 - Polarized light imaging (PLI) enables the evaluation of fiber orientations in histological sections of human postmortem brains, with ultra-high spatial resolution. PLI is based on the birefringent properties of the myelin sheath of nerve fibers. As a result, the polarization state of light propagating through a rotating polarimeter is changed in such a way that the detected signal at each measurement unit of a charged-coupled device (CCD) camera describes a sinusoidal signal. Vectors of the fiber orientation defined by inclination and direction angles can then directly be derived from the optical signals employing PLI analysis. However, noise, light scatter and filter inhomogeneities interfere with the original sinusoidal PLI signals. We here introduce a novel method using independent component analysis (ICA) to decompose the PLI images into statistically independent component maps. After decomposition, gray and white matter structures can clearly be distinguished from noise and other artifacts. The signal enhancement after artifact rejection is quantitatively evaluated in 134 histological whole brain sections. Thus, the primary sinusoidal signals from polarized light imaging can be effectively restored after noise and artifact rejection utilizing ICA. Our method therefore contributes to the analysis of nerve fiber orientation in the human brain within a micrometer scale. KW - Bildgebendes Verfahren KW - Polarisiertes Licht KW - Signalverarbeitung KW - Signaltrennung KW - Komponentenanalyse KW - Gehirn Y1 - 2010 U6 - https://doi.org/10.1016/j.neuroimage.2009.08.059 VL - 49 IS - 2 SP - 1241 EP - 1248 PB - Elsevier ER - TY - JOUR A1 - Axer, Markus A1 - Amunts, Katrin A1 - Gräßel, David A1 - Palm, Christoph A1 - Dammers, Jürgen A1 - Axer, Hubertus A1 - Pietrzyk, Uwe A1 - Zilles, Karl T1 - Novel Approach to the Human Connectome BT - Ultra-High Resolution Mapping of Fiber Tracts in the Brain JF - NeuroImage N2 - Signal transmission between different brain regions requires connecting fiber tracts, the structural basis of the human connectome. In contrast to animal brains, where a multitude of tract tracing methods can be used, magnetic resonance (MR)-based diffusion imaging is presently the only promising approach to study fiber tracts between specific human brain regions. However, this procedure has various inherent restrictions caused by its relatively low spatial resolution. Here, we introduce 3D-polarized light imaging (3D-PLI) to map the three-dimensional course of fiber tracts in the human brain with a resolution at a submillimeter scale based on a voxel size of 100 μm isotropic or less. 3D-PLI demonstrates nerve fibers by utilizing their intrinsic birefringence of myelin sheaths surrounding axons. This optical method enables the demonstration of 3D fiber orientations in serial microtome sections of entire human brains. Examples for the feasibility of this novel approach are given here. 3D-PLI enables the study of brain regions of intense fiber crossing in unprecedented detail, and provides an independent evaluation of fiber tracts derived from diffusion imaging data. KW - Connectome KW - Human brain KW - Method KW - Polarized light imaging KW - Tractography KW - Systems biology KW - Bildgebendes Verfahren KW - Dreidimensionale Bildverarbeitung KW - Polarisiertes Licht KW - Gehirnkarte Y1 - 2011 U6 - https://doi.org/10.1016/j.neuroimage.2010.08.075 VL - 54 IS - 2 SP - 1091 EP - 1101 ER - TY - JOUR A1 - Osterholt, Tobias A1 - Salber, Dagmar A1 - Matusch, Andreas A1 - Becker, Johanna Sabine A1 - Palm, Christoph T1 - IMAGENA: Image Generation and Analysis BT - An Interactive Software Tool handling LA-ICP-MS Data JF - International Journal of Mass Spectrometry N2 - Metals are involved in many processes of life. They are needed for enzymatic reactions, are involved in healthy processes but also yield diseases if the metal homeostasis is disordered. Therefore, the interest to assess the spatial distribution of metals is rising in biomedical science. Imaging metal (and non-metal) isotopes by laser ablation mass spectrometry with inductively coupled plasma (LA-ICP-MS) requires a special software solution to process raw data obtained by scanning a sample line-by-line. As no software ready to use was available we developed an interactive software tool for Image Generation and Analysis (IMAGENA). Unless optimised for LA-ICP-MS, IMAGENA can handle other raw data as well. The general purpose was to reconstruct images from a continuous list of raw data points, to visualise these images, and to convert them into a commonly readable image file format that can be further analysed by standard image analysis software. The generation of the image starts with loading a text file that holds a data column of every measured isotope. Specifying general spatial domain settings like the data offset and the image dimensions is done by the user getting a direct feedback by means of a preview image. IMAGENA provides tools for calibration and to correct for a signal drift in the y-direction. Images are visualised in greyscale as well a pseudo-colours with possibilities for contrast enhancement. Image analysis is performed in terms of smoothed line plots in row and column direction. KW - LA-ICP-MS KW - ICP-Massenspektrometrie KW - Bilderzeugung KW - Graphische Benutzeroberfläche KW - Image generation KW - Image analysis KW - Graphical user interface Y1 - 2011 U6 - https://doi.org/10.1016/j.ijms.2011.03.010 VL - 307 IS - 1-3 SP - 232 EP - 239 ER - TY - JOUR A1 - Becker, Johanna Sabine A1 - Matusch, Andreas A1 - Becker, Julia Susanne A1 - Wu, Bei A1 - Palm, Christoph A1 - Becker, Albert Johann A1 - Salber, Dagmar T1 - Mass spectrometric imaging (MSI) of metals using advanced BrainMet techniques for biomedical research JF - International Journal of Mass Spectrometry N2 - Mass spectrometric imaging (MSI) is a young innovative analytical technique and combines different fields of advanced mass spectrometry and biomedical research with the aim to provide maps of elements and molecules, complexes or fragments. Especially essential metals such as zinc, copper, iron and manganese play a functional role in signaling, metabolism and homeostasis of the cell. Due to the high degree of spatial organization of metals in biological systems their distribution analysis is of key interest in life sciences. We have developed analytical techniques termed BrainMet using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) imaging to measure the distribution of trace metals in biological tissues for biomedical research and feasibility studies—including bioaccumulation and bioavailability studies, ecological risk assessment and toxicity studies in humans and other organisms. The analytical BrainMet techniques provide quantitative images of metal distributions in brain tissue slices which can be combined with other imaging modalities such as photomicrography of native or processed tissue (histochemistry, immunostaining) and autoradiography or with in vivo techniques such as positron emission tomography or magnetic resonance tomography. Prospective and instrumental developments will be discussed concerning the development of the metalloprotein microscopy using a laser microdissection (LMD) apparatus for specific sample introduction into an inductively coupled plasma mass spectrometer (LMD-ICP-MS) or an application of the near field effect in LA-ICP-MS (NF-LA-ICP-MS). These nano-scale mass spectrometric techniques provide improved spatial resolution down to the single cell level. KW - Bioimaging KW - Brain tissue KW - Laser ablation inductively coupled plasma mass spectrometry KW - Laser microdissection inductively coupled plasma mass spectrometry KW - Metals KW - Metallomics KW - Nano-LA-ICP-MS KW - Tumour KW - Massenspektrometrie KW - Bildgebendes Verfahren KW - Metalle KW - Metallproteide KW - Gehirn Y1 - 2011 U6 - https://doi.org/10.1016/j.ijms.2011.01.015 VL - 307 IS - 1-3 SP - 3 EP - 15 PB - eLSEVIER CY - Elsevier ER - TY - JOUR A1 - Kolev, Kalin A1 - Kirchgeßner, Norbert A1 - Houben, Sebastian A1 - Csiszár, Agnes A1 - Rubner, Wolfgang A1 - Palm, Christoph A1 - Eiben, Björn A1 - Merkel, Rudolf A1 - Cremers, Daniel T1 - A variational approach to vesicle membrane reconstruction from fluorescence imaging JF - Pattern Recognition N2 - Biological applications like vesicle membrane analysis involve the precise segmentation of 3D structures in noisy volumetric data, obtained by techniques like magnetic resonance imaging (MRI) or laser scanning microscopy (LSM). Dealing with such data is a challenging task and requires robust and accurate segmentation methods. In this article, we propose a novel energy model for 3D segmentation fusing various cues like regional intensity subdivision, edge alignment and orientation information. The uniqueness of the approach consists in the definition of a new anisotropic regularizer, which accounts for the unbalanced slicing of the measured volume data, and the generalization of an efficient numerical scheme for solving the arising minimization problem, based on linearization and fixed-point iteration. We show how the proposed energy model can be optimized globally by making use of recent continuous convex relaxation techniques. The accuracy and robustness of the presented approach are demonstrated by evaluating it on multiple real data sets and comparing it to alternative segmentation methods based on level sets. Although the proposed model is designed with focus on the particular application at hand, it is general enough to be applied to a variety of different segmentation tasks. KW - 3D segmentation KW - Convex optimization KW - Vesicle membrane analysis KW - Fluorescence imaging KW - Dreidimensionale Bildverarbeitung KW - Bildsegmentierung KW - Konvexe Optimierung Y1 - 2011 U6 - https://doi.org/10.1016/j.patcog.2011.04.019 VL - 44 IS - 12 SP - 2944 EP - 2958 PB - Elsevier ER - TY - JOUR A1 - Deserno, Thomas M. A1 - Handels, Heinz A1 - Maier-Hein, Klaus H. A1 - Mersmann, Sven A1 - Palm, Christoph A1 - Tolxdorff, Thomas A1 - Wagenknecht, Gudrun A1 - Wittenberg, Thomas T1 - Viewpoints on Medical Image Processing BT - From Science to Application JF - Current Medical Imaging Reviews N2 - Medical image processing provides core innovation for medical imaging. This paper is focused on recent developments from science to applications analyzing the past fifteen years of history of the proceedings of the German annual meeting on medical image processing (BVM). Furthermore, some members of the program committee present their personal points of views: (i) multi-modality for imaging and diagnosis, (ii) analysis of diffusion-weighted imaging, (iii) model-based image analysis, (iv) registration of section images, (v) from images to information in digital endoscopy, and (vi) virtual reality and robotics. Medical imaging and medical image computing is seen as field of rapid development with clear trends to integrated applications in diagnostics, treatment planning and treatment. KW - Medical imaging KW - Image processing KW - Image analysis KW - Vizualization KW - Multi-modal imaging KW - Diffusion-weighted imaging KW - Model-based imaging KW - Digital endoscopy KW - Bildgebendes Verfahren KW - Bildverarbeitung KW - Medizin Y1 - 2013 U6 - https://doi.org/10.2174/1573405611309020002 VL - 9 IS - 2 SP - 79 EP - 88 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 - CHAP A1 - Szalo, Alexander Eduard A1 - Zehner, Alexander A1 - Palm, Christoph T1 - GraphMIC: Medizinische Bildverarbeitung in der Lehre T2 - Bildverarbeitung für die Medizin 2015; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 15. bis 17. März 2015 in Lübeck N2 - Die Lehre der medizinischen Bildverarbeitung vermittelt Kenntnisse mit einem breiten Methodenspektrum. Neben den Grundlagen der Verfahren soll ein Gefühl für eine geeignete Ausführungsreihenfolge und ihrer Wirkung auf medizinische Bilddaten entwickelt werden. Die Komplexität der Methoden erfordert vertiefte Programmierkenntnisse, sodass bereits einfache Operationen mit großem Programmieraufwand verbunden sind. Die Software GraphMIC stellt Bildverarbeitungsoperationen in Form interaktiver Knoten zur Verfügung und erlaubt das Arrangieren, Parametrisieren und Ausführen komplexer Verarbeitungssequenzen in einem Graphen. Durch den Fokus auf das Design einer Pipeline, weg von sprach- und frameworkspezifischen Implementierungsdetails, lassen sich grundlegende Prinzipien der Bildverarbeitung anschaulich erlernen. In diesem Beitrag stellen wir die visuelle Programmierung mit GraphMIC der nativen Implementierung äquivalenter Funktionen gegenüber. Die in C++ entwickelte Applikation basiert auf Qt, ITK, OpenCV, VTK und MITK. KW - Bildverarbeitung KW - Medizin KW - Hochschuldidaktik Y1 - 2015 U6 - https://doi.org/10.1007/978-3-662-46224-9_68 SP - 395 EP - 400 PB - Springer CY - Berlin ER - TY - CHAP A1 - Wöhl, Rebecca A1 - Huber, Michaela A1 - Loibl, Markus A1 - Riebschläger, Birgit A1 - Nerlich, Michael A1 - Palm, Christoph T1 - The Impact of Semi-Automated Segmentation and 3D Analysis on Testing New Osteosynthesis Material T2 - Bildverarbeitung für die Medizin 2017; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 12. bis 14. März 2017 in Heidelberg N2 - A new protocol for testing osteosynthesis material postoperatively combining semi-automated segmentation and 3D analysis of surface meshes is proposed. By various steps of transformation and measuring, objective data can be collected. In this study the specifications of a locking plate used for mediocarpal arthrodesis of the wrist were examined. The results show, that union of the lunate, triquetrum, hamate and capitate was achieved and that the plate is comparable to coexisting arthrodesis systems. Additionally, it was shown, that the complications detected correlate to the clinical outcome. In synopsis, this protocol is considered beneficial and should be taken into account in further studies. KW - Osteosynthese KW - Implantatwerkstoff KW - Materialprüfung KW - Bildsegmentierung KW - Dreidimensionale Bildverarbeitung Y1 - 2017 U6 - https://doi.org/10.1007/978-3-662-54345-0_30 SP - 122 EP - 127 PB - Springer CY - Berlin ER - TY - CHAP A1 - Mendel, Robert A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Palm, Christoph T1 - Barrett’s Esophagus Analysis Using Convolutional Neural Networks T2 - Bildverarbeitung für die Medizin 2017; Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 12. bis 14. März 2017 in Heidelberg N2 - We propose an automatic approach for early detection of adenocarcinoma in the esophagus. High-definition endoscopic images (50 cancer, 50 Barrett) are partitioned into a dataset containing approximately equal amounts of patches showing cancerous and non-cancerous regions. A deep convolutional neural network is adapted to the data using a transfer learning approach. The final classification of an image is determined by at least one patch, for which the probability being a cancer patch exceeds a given threshold. The model was evaluated with leave one patient out cross-validation. With sensitivity and specificity of 0.94 and 0.88, respectively, our findings improve recently published results on the same image data base considerably. Furthermore, the visualization of the class probabilities of each individual patch indicates, that our approach might be extensible to the segmentation domain. KW - Speiseröhrenkrebs KW - Diagnose KW - Maschinelles Lernen KW - Bilderkennung KW - Automatische Klassifikation Y1 - 2017 U6 - https://doi.org/10.1007/978-3-662-54345-0_23 SP - 80 EP - 85 PB - Springer CY - Berlin ER - TY - CHAP A1 - Souza Jr., Luis Antonio de A1 - Hook, Christian A1 - Papa, João Paulo A1 - Palm, Christoph T1 - Barrett's Esophagus Analysis Using SURF Features T2 - Bildverarbeitung für die Medizin 2017; Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 12. bis 14. März 2017 in Heidelberg N2 - The development of adenocarcinoma in Barrett’s esophagus is difficult to detect by endoscopic surveillance of patients with signs of dysplasia. Computer assisted diagnosis of endoscopic images (CAD) could therefore be most helpful in the demarcation and classification of neoplastic lesions. In this study we tested the feasibility of a CAD method based on Speeded up Robust Feature Detection (SURF). A given database containing 100 images from 39 patients served as benchmark for feature based classification models. Half of the images had previously been diagnosed by five clinical experts as being ”cancerous”, the other half as ”non-cancerous”. Cancerous image regions had been visibly delineated (masked) by the clinicians. SURF features acquired from full images as well as from masked areas were utilized for the supervised training and testing of an SVM classifier. The predictive accuracy of the developed CAD system is illustrated by sensitivity and specificity values. The results based on full image matching where 0.78 (sensitivity) and 0.82 (specificity) were achieved, while the masked region approach generated results of 0.90 and 0.95, respectively. KW - Speiseröhrenkrankheit KW - Diagnose KW - Maschinelles Sehen KW - Automatische Klassifikation Y1 - 2017 U6 - https://doi.org/10.1007/978-3-662-54345-0_34 SP - 141 EP - 146 PB - Springer CY - Berlin ER - TY - CHAP A1 - Franz, Daniela A1 - Dreher, Maria A1 - Prinzen, Martin A1 - Teßmann, Matthias A1 - Palm, Christoph A1 - Katzky, Uwe A1 - Perret, Jerome A1 - Hofer, Mathias A1 - Wittenberg, Thomas T1 - CT-basiertes virtuelles Fräsen am Felsenbein BT - Bild- und haptischen Wiederholfrequenzen bei unterschiedlichen Rendering Methoden T2 - Bildverarbeitung für die Medizin 2018; Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 11. bis 13. März 2018 in Erlangen N2 - Im Rahmen der Entwicklung eines haptisch-visuellen Trainingssystems für das Fräsen am Felsenbein werden ein Haptikarm und ein autostereoskopischer 3D-Monitor genutzt, um Chirurgen die virtuelle Manipulation von knöchernen Strukturen im Kontext eines sog. Serious Game zu ermöglichen. Unter anderem sollen Assistenzärzte im Rahmen ihrer Ausbildung das Fräsen am Felsenbein für das chirurgische Einsetzen eines Cochlea-Implantats üben können. Die Visualisierung des virtuellen Fräsens muss dafür in Echtzeit und möglichst realistisch modelliert, implementiert und evaluiert werden. Wir verwenden verschiedene Raycasting Methoden mit linearer und Nearest Neighbor Interpolation und vergleichen die visuelle Qualität und die Bildwiederholfrequenzen der Methoden. Alle verglichenen Verfahren sind sind echtzeitfähig, unterscheiden sich aber in ihrer visuellen Qualität. KW - Felsenbein KW - Fräsen KW - Virtualisierung KW - Computertomographie KW - Computerassistierte Chirurgie Y1 - 2018 SN - 978-3-662-56537-7 U6 - https://doi.org/10.1007/978-3-662-56537-7_51 SP - 176 EP - 181 PB - Springer CY - Berlin ER - TY - JOUR A1 - Wöhl, Rebecca A1 - Maier, Johannes A1 - Gehmert, Sebastian A1 - Palm, Christoph A1 - Riebschläger, Birgit A1 - Nerlich, Michael A1 - Huber, Michaela T1 - 3D Analysis of Osteosyntheses Material using semi-automated CT Segmentation BT - a case series of a 4 corner fusion plate JF - BMC Musculoskeletal Disorders N2 - Backround Scaphoidectomy and midcarpal fusion can be performed using traditional fixation methods like K-wires, staples, screws or different dorsal (non)locking arthrodesis systems. The aim of this study is to test the Aptus four corner locking plate and to compare the clinical findings to the data revealed by CT scans and semi-automated segmentation. Methods: This is a retrospective review of eleven patients suffering from scapholunate advanced collapse (SLAC) or scaphoid non-union advanced collapse (SNAC) wrist, who received a four corner fusion between August 2011 and July 2014. The clinical evaluation consisted of measuring the range of motion (ROM), strength and pain on a visual analogue scale (VAS). Additionally, the Disabilities of the Arm, Shoulder and Hand (QuickDASH) and the Mayo Wrist Score were assessed. A computerized tomography (CT) of the wrist was obtained six weeks postoperatively. After semi-automated segmentation of the CT scans, the models were post processed and surveyed. Results During the six-month follow-up mean range of motion (ROM) of the operated wrist was 60°, consisting of 30° extension and 30° flexion. While pain levels decreased significantly, 54% of grip strength and 89% of pinch strength were preserved compared to the contralateral healthy wrist. Union could be detected in all CT scans of the wrist. While X-ray pictures obtained postoperatively revealed no pathology, two user related technical complications were found through the 3D analysis, which correlated to the clinical outcome. Conclusion Due to semi-automated segmentation and 3D analysis it has been proved that the plate design can keep up to the manufacturers’ promises. Over all, this case series confirmed that the plate can compete with the coexisting techniques concerning clinical outcome, union and complication rate. KW - Handchirurgie KW - Osteosynthese KW - Arthrodese KW - 4FC KW - SLAC wrist KW - SNAC wrist KW - Semi-automated segmentation KW - 3D analysis KW - Computertomographie KW - Bildsegmentierung KW - Dreidimensionale Bildverarbeitung Y1 - 2018 U6 - https://doi.org/10.1186/s12891-018-1975-0 VL - 19 SP - 1 EP - 8 PB - Springer Nature ER - TY - CHAP A1 - Maier, Johannes A1 - Huber, Michaela A1 - Katzky, Uwe A1 - Perret, Jerome A1 - Wittenberg, Thomas A1 - Palm, Christoph T1 - Force-Feedback-assisted Bone Drilling Simulation Based on CT Data T2 - Bildverarbeitung für die Medizin 2018; Algorithmen - Systeme - Anwendungen; Proceedings des Workshops vom 11. bis 13. März 2018 in Erlangen N2 - In order to fix a fracture using minimally invasive surgery approaches, surgeons are drilling complex and tiny bones with a 2 dimensional X-ray as single imaging modality in the operating room. Our novel haptic force-feedback and visual assisted training system will potentially help hand surgeons to learn the drilling procedure in a realistic visual environment. Within the simulation, the collision detection as well as the interaction between virtual drill, bone voxels and surfaces are important. In this work, the chai3d collision detection and force calculation algorithms are combined with a physics engine to simulate the bone drilling process. The chosen Bullet-Physics-Engine provides a stable simulation of rigid bodies, if the collision model of the drill and the tool holder is generated as a compound shape. Three haptic points are added to the K-wire tip for removing single voxels from the bone. For the drilling process three modes are proposed to emulate the different phases of drilling in restricting the movement of a haptic device. KW - Handchirurgie KW - Osteosynthese KW - Simulation KW - Lernprogramm Y1 - 2018 U6 - https://doi.org/10.1007/978-3-662-56537-7_78 SP - 291 EP - 296 PB - Springer CY - Berlin ER - TY - JOUR A1 - Graßmann, Felix A1 - Mengelkamp, Judith A1 - Brandl, Caroline A1 - Harsch, Sebastian A1 - Zimmermann, Martina E. A1 - Linkohr, Birgit A1 - Peters, Annette A1 - Heid, Iris M. A1 - Palm, Christoph A1 - Weber, Bernhard H. F. T1 - A Deep Learning Algorithm for Prediction of Age-Related Eye Disease Study Severity Scale for Age-Related Macular Degeneration from Color Fundus Photography JF - Ophtalmology N2 - Purpose Age-related macular degeneration (AMD) is a common threat to vision. While classification of disease stages is critical to understanding disease risk and progression, several systems based on color fundus photographs are known. Most of these require in-depth and time-consuming analysis of fundus images. Herein, we present an automated computer-based classification algorithm. Design Algorithm development for AMD classification based on a large collection of color fundus images. Validation is performed on a cross-sectional, population-based study. Participants. We included 120 656 manually graded color fundus images from 3654 Age-Related Eye Disease Study (AREDS) participants. AREDS participants were >55 years of age, and non-AMD sight-threatening diseases were excluded at recruitment. In addition, performance of our algorithm was evaluated in 5555 fundus images from the population-based Kooperative Gesundheitsforschung in der Region Augsburg (KORA; Cooperative Health Research in the Region of Augsburg) study. Methods. We defined 13 classes (9 AREDS steps, 3 late AMD stages, and 1 for ungradable images) and trained several convolution deep learning architectures. An ensemble of network architectures improved prediction accuracy. An independent dataset was used to evaluate the performance of our algorithm in a population-based study. Main Outcome Measures. κ Statistics and accuracy to evaluate the concordance between predicted and expert human grader classification. Results. A network ensemble of 6 different neural net architectures predicted the 13 classes in the AREDS test set with a quadratic weighted κ of 92% (95% confidence interval, 89%–92%) and an overall accuracy of 63.3%. In the independent KORA dataset, images wrongly classified as AMD were mainly the result of a macular reflex observed in young individuals. By restricting the KORA analysis to individuals >55 years of age and prior exclusion of other retinopathies, the weighted and unweighted κ increased to 50% and 63%, respectively. Importantly, the algorithm detected 84.2% of all fundus images with definite signs of early or late AMD. Overall, 94.3% of healthy fundus images were classified correctly. Conclusions Our deep learning algoritm revealed a weighted κ outperforming human graders in the AREDS study and is suitable to classify AMD fundus images in other datasets using individuals >55 years of age. KW - Senile Makuladegeneration KW - Krankheitsverlauf KW - Mustererkennung KW - Maschinelles Lernen Y1 - 2018 U6 - https://doi.org/10.1016/j.ophtha.2018.02.037 N1 - Corresponding authors: Bernhard H. F. Weber, University of Regensburg, and Christoph Palm VL - 125 IS - 9 SP - 1410 EP - 1420 PB - Elsevier ER - TY - JOUR A1 - Souza Jr., Luis Antonio de A1 - Palm, Christoph A1 - Mendel, Robert A1 - Hook, Christian A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Weber, Silke A. T. A1 - Papa, João Paulo T1 - A survey on Barrett's esophagus analysis using machine learning JF - Computers in Biology and Medicine N2 - This work presents a systematic review concerning recent studies and technologies of machine learning for Barrett's esophagus (BE) diagnosis and treatment. The use of artificial intelligence is a brand new and promising way to evaluate such disease. We compile some works published at some well-established databases, such as Science Direct, IEEEXplore, PubMed, Plos One, Multidisciplinary Digital Publishing Institute (MDPI), Association for Computing Machinery (ACM), Springer, and Hindawi Publishing Corporation. Each selected work has been analyzed to present its objective, methodology, and results. The BE progression to dysplasia or adenocarcinoma shows a complex pattern to be detected during endoscopic surveillance. Therefore, it is valuable to assist its diagnosis and automatic identification using computer analysis. The evaluation of the BE dysplasia can be performed through manual or automated segmentation through machine learning techniques. Finally, in this survey, we reviewed recent studies focused on the automatic detection of the neoplastic region for classification purposes using machine learning methods. KW - Speiseröhrenkrankheit KW - Diagnose KW - Mustererkennung KW - Maschinelles Lernen KW - Literaturbericht KW - Barrett's esophagus KW - Machine learning KW - Adenocarcinoma KW - Image processing KW - Pattern recognition KW - Computer-aided diagnosis Y1 - 2018 U6 - https://doi.org/10.1016/j.compbiomed.2018.03.014 VL - 96 SP - 203 EP - 213 PB - Elsevier ER - TY - JOUR A1 - Maier, Johannes A1 - Weiherer, Maximilian A1 - Huber, Michaela A1 - Palm, Christoph T1 - Imitating human soft tissue on basis of a dual-material 3D print using a support-filled metamaterial to provide bimanual haptic for a hand surgery training system JF - Quantitative Imaging in Medicine and Surgery N2 - Background: 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. Methods: The goal of this experiment is to imitate human soft tissue with its haptic and elasticity for a realistic hand phantom fabrication, using only a dual-material 3D printer and support-material-filled metamaterial between skin and bone. We present our workflow to generate lattice structures between hard bone and soft skin with iterative cube edge (CE) or cube face (CF) unit cells. Cuboid and finger shaped sample prints with and without inner hard bone in different lattice thickness are constructed and 3D printed. Results: The most elastic available rubber-like material is too firm to imitate soft tissue. By reducing the amount of rubber in the inner volume through support material (SUP), objects become significantly softer. Without metamaterial, after disintegration, the SUP can be shifted through the volume and thus the body loses its original shape. Although the CE design increases the elasticity, it cannot restore the fabric form. In contrast to CE, the CF design increases not only the elasticity but also guarantees a local limitation of the SUP. Therefore, the body retains its shape and internal bones remain in its intended place. Various unit cell sizes, lattice thickening and skin thickness regulate the rubber material and SUP ratio. Test prints with higher SUP and lower rubber material percentage appear softer and vice versa. This was confirmed by an expert surgeon evaluation. Subjects adjudged pure rubber-like material as too firm and samples only filled with SUP or lattice structure in CE design as not suitable for imitating tissue. 3D-printed finger samples in CF design were rated as realistic compared to the haptic of human tissue with a good palpable bone structure. Conclusions: We developed a new dual-material 3D print technique to imitate soft tissue of the human hand with its haptic properties. Blowy SUP is trapped within a lattice structure to soften rubber-like 3D print material, which makes it possible to reproduce a realistic replica of human hand soft tissue. KW - Dual-material 3D printing KW - Hand surgery training KW - Metamaterial KW - Support material KW - Tissue-imitating hand phantom KW - Handchirurgie KW - 3D-Druck KW - Biomaterial KW - Lernprogramm Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:898-opus4-979 N1 - Corresponding author: Christoph Palm VL - 9 IS - 1 SP - 30 EP - 42 PB - AME Publishing Company ER - TY - JOUR A1 - Maier, Johannes A1 - Perret, Jerome A1 - Simon, Martina A1 - Schmitt-Rüth, Stephanie A1 - Wittenberg, Thomas A1 - Palm, Christoph T1 - Force-feedback assisted and virtual fixtures based K-wire drilling simulation JF - Computers in Biology and Medicine N2 - One common method to fix fractures of the human hand after an accident is an osteosynthesis with Kirschner wires (K-wires) to stabilize the bone fragments. The insertion of K-wires is a delicate minimally invasive surgery, because surgeons operate almost without a sight. Since realistic training methods are time consuming, costly and insufficient, a virtual-reality (VR) based training system for the placement of K-wires was developed. As part of this, the current work deals with the real-time bone drilling simulation using a haptic force-feedback device. To simulate the drilling, we introduce a virtual fixture based force-feedback drilling approach. By decomposition of the drilling task into individual phases, each phase can be handled individually to perfectly control the drilling procedure. We report about the related finite state machine (FSM), describe the haptic feedback of each state and explain, how to avoid jerking of the haptic force-feedback during state transition. The usage of the virtual fixture approach results in a good haptic performance and a stable drilling behavior. This was confirmed by 26 expert surgeons, who evaluated the virtual drilling on the simulator and rated it as very realistic. To make the system even more convincing, we determined real drilling feed rates through experimental pig bone drilling and transferred them to our system. Due to a constant simulation thread we can guarantee a precise drilling motion. Virtual fixtures based force-feedback calculation is able to simulate force-feedback assisted bone drilling with high quality and, thus, will have a great potential in developing medical applications. KW - Handchirurgie KW - Osteosynthese KW - Operationstechnik KW - Lernprogramm KW - Virtuelle Realität KW - Medical training system KW - Virtual fixtures KW - Virtual reality KW - Force-feedback haptic KW - Minimally invasive hand surgery KW - K-wire drilling Y1 - 2019 U6 - https://doi.org/10.1016/j.compbiomed.2019.103473 N1 - Corresponding author: Christoph Palm VL - 114 SP - 1 EP - 10 PB - Elsevier ER - TY - CHAP A1 - Middel, Luise A1 - Palm, Christoph A1 - Erdt, Marius T1 - Synthesis of Medical Images Using GANs T2 - Uncertainty for safe utilization of machine learning in medical imaging and clinical image-based procedures. First International Workshop, UNSURE 2019, and 8th International Workshop, CLIP 2019, held in conjunction with MICCAI 2019, Shenzhen, China, October 17, 2019 N2 - The success of artificial intelligence in medicine is based on the need for large amounts of high quality training data. Sharing of medical image data, however, is often restricted by laws such as doctor-patient confidentiality. Although there are publicly available medical datasets, their quality and quantity are often low. Moreover, datasets are often imbalanced and only represent a fraction of the images generated in hospitals or clinics and can thus usually only be used as training data for specific problems. The introduction of generative adversarial networks (GANs) provides a mean to generate artificial images by training two convolutional networks. This paper proposes a method which uses GANs trained on medical images in order to generate a large number of artificial images that could be used to train other artificial intelligence algorithms. This work is a first step towards alleviating data privacy concerns and being able to publicly share data that still contains a substantial amount of the information in the original private data. The method has been evaluated on several public datasets and quantitative and qualitative tests showing promising results. KW - Neuronale Netze KW - Deep Learning KW - Generative adversarial networks KW - Machine Learning KW - Artificial Intelligence KW - Data privacy KW - Deep Learning KW - Bilderzeugung KW - Datenschutz Y1 - 2019 SN - 978-3-030-32688-3 U6 - https://doi.org/10.1007/978-3-030-32689-0_13 SN - 0302-9743 SP - 125 EP - 134 PB - Springer Nature CY - Cham ER - TY - JOUR A1 - Brown, Peter A1 - Consortium, RELISH A1 - Zhou, Yaoqi A1 - Palm, Christoph T1 - Large expert-curated database for benchmarking document similarity detection in biomedical literature search JF - Database N2 - Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research. KW - Information Retrieval KW - Indexierung KW - Literaturdatenbank KW - Dokument KW - Ähnlichkeitssuche KW - Suchmaschine Y1 - 2019 U6 - https://doi.org/10.1093/database/baz085 VL - 2019 SP - 1 EP - 66 PB - Oxford University Pres ER - TY - JOUR A1 - Ebigbo, Alanna A1 - Mendel, Robert A1 - Probst, Andreas A1 - Manzeneder, Johannes A1 - Souza Jr., Luis Antonio de A1 - Papa, João Paulo A1 - Palm, Christoph A1 - Messmann, Helmut T1 - Computer-aided diagnosis using deep learning in the evaluation of early oesophageal adenocarcinoma JF - GuT N2 - Computer-aided diagnosis using deep learning (CAD-DL) may be an instrument to improve endoscopic assessment of Barrett’s oesophagus (BE) and early oesophageal adenocarcinoma (EAC). Based on still images from two databases, the diagnosis of EAC by CAD-DL reached sensitivities/specificities of 97%/88% (Augsburg data) and 92%/100% (Medical Image Computing and Computer-Assisted Intervention [MICCAI] data) for white light (WL) images and 94%/80% for narrow band images (NBI) (Augsburg data), respectively. Tumour margins delineated by experts into images were detected satisfactorily with a Dice coefficient (D) of 0.72. This could be a first step towards CAD-DL for BE assessment. If developed further, it could become a useful adjunctive tool for patient management. KW - Speiseröhrenkrebs KW - Diagnose KW - Computerunterstütztes Verfahren KW - Maschinelles Lernen Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:898-opus4-68 N1 - Corresponding authors: Alanna Ebigbo and Christoph Palm VL - 68 IS - 7 SP - 1143 EP - 1145 PB - British Society of Gastroenterology ER - TY - GEN A1 - Ebigbo, Alanna A1 - Mendel, Robert A1 - Probst, Andreas A1 - Manzeneder, Johannes A1 - Souza Jr., Luis Antonio de A1 - Papa, João Paulo A1 - Palm, Christoph A1 - Messmann, Helmut T1 - Artificial Intelligence in Early Barrett's Cancer: The Segmentation Task T2 - Endoscopy N2 - Aims: The delineation of outer margins of early Barrett's cancer can be challenging even for experienced endoscopists. Artificial intelligence (AI) could assist endoscopists faced with this task. As of date, there is very limited experience in this domain. In this study, we demonstrate the measure of overlap (Dice coefficient = D) between highly experienced Barrett endoscopists and an AI system in the delineation of cancer margins (segmentation task). Methods: An AI system with a deep convolutional neural network (CNN) was trained and tested on high-definition endoscopic images of early Barrett's cancer (n = 33) and normal Barrett's mucosa (n = 41). The reference standard for the segmentation task were the manual delineations of tumor margins by three highly experienced Barrett endoscopists. Training of the AI system included patch generation, patch augmentation and adjustment of the CNN weights. Then, the segmentation results from patch classification and thresholding of the class probabilities. Segmentation results were evaluated using the Dice coefficient (D). Results: The Dice coefficient (D) which can range between 0 (no overlap) and 1 (complete overlap) was computed only for images correctly classified by the AI-system as cancerous. At a threshold of t = 0.5, a mean value of D = 0.72 was computed. Conclusions: AI with CNN performed reasonably well in the segmentation of the tumor region in Barrett's cancer, at least when compared with expert Barrett's endoscopists. AI holds a lot of promise as a tool for better visualization of tumor margins but may need further improvement and enhancement especially in real-time settings. KW - Speiseröhrenkrankheit KW - Maschinelles Lernen KW - Barrett's esphagus KW - Deep Learning KW - Segmentation Y1 - 2019 U6 - https://doi.org/10.1055/s-0039-1681187 VL - 51 IS - 04 SP - 6 PB - Georg Thieme Verlag CY - Stuttgart ER - TY - JOUR A1 - Ebigbo, Alanna A1 - Palm, Christoph A1 - Probst, Andreas A1 - Mendel, Robert A1 - Manzeneder, Johannes A1 - Prinz, Friederike A1 - Souza Jr., Luis Antonio de A1 - Papa, João Paulo A1 - Siersema, Peter A1 - Messmann, Helmut T1 - A technical review of artificial intelligence as applied to gastrointestinal endoscopy: clarifying the terminology JF - Endoscopy International Open N2 - The growing number of publications on the application of artificial intelligence (AI) in medicine underlines the enormous importance and potential of this emerging field of research. In gastrointestinal endoscopy, AI has been applied to all segments of the gastrointestinal tract most importantly in the detection and characterization of colorectal polyps. However, AI research has been published also in the stomach and esophagus for both neoplastic and non-neoplastic disorders. The various technical as well as medical aspects of AI, however, remain confusing especially for non-expert physicians. This physician-engineer co-authored review explains the basic technical aspects of AI and provides a comprehensive overview of recent publications on AI in gastrointestinal endoscopy. Finally, a basic insight is offered into understanding publications on AI in gastrointestinal endoscopy. KW - Diagnose KW - Maschinelles Lernen KW - Gastroenterologie KW - Künstliche Intelligenz KW - Barrett's esophagus KW - Deep learning Y1 - 2019 U6 - https://doi.org/10.1055/a-1010-5705 VL - 07 IS - 12 SP - 1616 EP - 1623 PB - Georg Thieme Verlag CY - Stuttgart 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 - JOUR A1 - Hartmann, Robin A1 - Weiherer, Maximilian A1 - Schiltz, Daniel A1 - Seitz, Stephan A1 - Lotter, Luisa A1 - Anker, Alexandra A1 - Palm, Christoph A1 - Prantl, Lukas A1 - Brébant, Vanessa T1 - A Novel Method of Outcome Assessment in Breast Reconstruction Surgery: Comparison of Autologous and Alloplastic Techniques Using Three-Dimensional Surface Imaging JF - Aesthetic Plastic Surgery N2 - Background Breast reconstruction is an important coping tool for patients undergoing a mastectomy. There are numerous surgical techniques in breast reconstruction surgery (BRS). Regardless of the technique used, creating a symmetric outcome is crucial for patients and plastic surgeons. Three-dimensional surface imaging enables surgeons and patients to assess the outcome’s symmetry in BRS. To discriminate between autologous and alloplastic techniques, we analyzed both techniques using objective optical computerized symmetry analysis. Software was developed that enables clinicians to assess optical breast symmetry using three-dimensional surface imaging. Methods Twenty-seven patients who had undergone autologous (n = 12) or alloplastic (n = 15) BRS received three-dimensional surface imaging. Anthropomorphic data were collected digitally using semiautomatic measurements and automatic measurements. Automatic measurements were taken using the newly developed software. To quantify symmetry, a Symmetry Index is proposed. Results Statistical analysis revealed that there is no dif- ference in the outcome symmetry between the two groups (t test for independent samples; p = 0.48, two-tailed). Conclusion This study’s findings provide a foundation for qualitative symmetry assessment in BRS using automatized digital anthropometry. In the present trial, no difference in the outcomes’ optical symmetry was detected between autologous and alloplastic approaches. KW - Breast reconstruction KW - Breast symmetry KW - Digital anthropometry KW - Mammoplastik KW - Dreidimensionale Bildverarbeitung KW - Autogene Transplantation KW - Alloplastik Y1 - 2020 U6 - https://doi.org/10.1007/s00266-020-01749-4 VL - 44 SP - 1980 EP - 1987 PB - Springer CY - Heidelberg ER - TY - CHAP A1 - Weiherer, Maximilian A1 - Zorn, Martin A1 - Wittenberg, Thomas A1 - Palm, Christoph ED - Tolxdorff, Thomas ED - Deserno, Thomas M. ED - Handels, Heinz ED - Maier, Andreas ED - Maier-Hein, Klaus H. ED - Palm, Christoph T1 - Retrospective Color Shading Correction for Endoscopic Images T2 - Bildverarbeitung für die Medizin 2020. Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 15. bis 17. März 2020 in Berlin N2 - In this paper, we address the problem of retrospective color shading correction. An extension of the established gray-level shading correction algorithm based on signal envelope (SE) estimation to color images is developed using principal color components. Compared to the probably most general shading correction algorithm based on entropy minimization, SE estimation does not need any computationally expensive optimization and thus can be implemented more effciently. We tested our new shading correction scheme on artificial as well as real endoscopic images and observed promising results. Additionally, an indepth analysis of the stop criterion used in the SE estimation algorithm is provided leading to the conclusion that a fixed, user-defined threshold is generally not feasible. Thus, we present new ideas how to develop a non-parametric version of the SE estimation algorithm using entropy. KW - Endoskopie KW - Bildgebendes Verfahren KW - Farbenraum KW - Graustufe Y1 - 2020 SN - 978-3-658-29266-9 U6 - https://doi.org/10.1007/978-3-658-29267-6 SP - 14 EP - 19 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Ott, Tankred A1 - Palm, Christoph A1 - Vogt, Robert A1 - Oberprieler, Christoph T1 - GinJinn: An object-detection pipeline for automated feature extraction from herbarium specimens JF - Applications in Plant Sciences N2 - PREMISE: The generation of morphological data in evolutionary, taxonomic, and ecological studies of plants using herbarium material has traditionally been a labor-intensive task. Recent progress in machine learning using deep artificial neural networks (deep learning) for image classification and object detection has facilitated the establishment of a pipeline for the automatic recognition and extraction of relevant structures in images of herbarium specimens. METHODS AND RESULTS: We implemented an extendable pipeline based on state-of-the-art deep-learning object-detection methods to collect leaf images from herbarium specimens of two species of the genus Leucanthemum. Using 183 specimens as the training data set, our pipeline extracted one or more intact leaves in 95% of the 61 test images. CONCLUSIONS: We establish GinJinn as a deep-learning object-detection tool for the automatic recognition and extraction of individual leaves or other structures from herbarium specimens. Our pipeline offers greater flexibility and a lower entrance barrier than previous image-processing approaches based on hand-crafted features. KW - Deep Learning KW - herbarium specimens KW - object detection KW - visual recognition KW - Deep Learning KW - Objekterkennung KW - Maschinelles Sehen KW - Pflanzen Y1 - 2020 U6 - https://doi.org/10.1002/aps3.11351 SN - 2168-0450 VL - 8 IS - 6 SP - e11351 PB - Wiley, Botanical Society of America ER - TY - JOUR A1 - Maier, Johannes A1 - Weiherer, Maximilian A1 - Huber, Michaela A1 - Palm, Christoph T1 - Optically tracked and 3D printed haptic phantom hand for surgical training system JF - Quantitative Imaging in Medicine and Surgery N2 - Background: For surgical fixation of bone fractures of the human hand, so-called Kirschner-wires (K-wires) are drilled through bone fragments. Due to the minimally invasive drilling procedures without a view of risk structures like vessels and nerves, a thorough training of young surgeons is necessary. For the development of a virtual reality (VR) based training system, a three-dimensional (3D) printed phantom hand is required. To ensure an intuitive operation, this phantom hand has to be realistic in both, its position relative to the driller as well as in its haptic features. The softest 3D printing material available on the market, however, is too hard to imitate human soft tissue. Therefore, a support-material (SUP) filled metamaterial is used to soften the raw material. Realistic haptic features are important to palpate protrusions of the bone to determine the drilling starting point and angle. An optical real-time tracking is used to transfer position and rotation to the training system. Methods: A metamaterial already developed in previous work is further improved by use of a new unit cell. Thus, the amount of SUP within the volume can be increased and the tissue is softened further. In addition, the human anatomy is transferred to the entire hand model. A subcutaneous fat layer and penetration of air through pores into the volume simulate shiftability of skin layers. For optical tracking, a rotationally symmetrical marker attached to the phantom hand with corresponding reference marker is developed. In order to ensure trouble-free position transmission, various types of marker point applications are tested. Results: Several cuboid and forearm sample prints lead to a final 30 centimeter long hand model. The whole haptic phantom could be printed faultless within about 17 hours. The metamaterial consisting of the new unit cell results in an increased SUP share of 4.32%. Validated by an expert surgeon study, this allows in combination with a displacement of the uppermost skin layer a good palpability of the bones. Tracking of the hand marker in dodecahedron design works trouble-free in conjunction with a reference marker attached to the worktop of the training system. Conclusions: In this work, an optically tracked and haptically correct phantom hand was developed using dual-material 3D printing, which can be easily integrated into a surgical training system. KW - Handchirurgie KW - 3D-Druck KW - Lernprogramm KW - Zielverfolgung KW - HaptiVisT KW - Dual-material 3D printing KW - hand surgery training KW - metamaterial KW - tissue imitating phantom hand Y1 - 2020 U6 - https://doi.org/10.21037/qims.2019.12.03 N1 - Corresponding author: Christoph Palm VL - 10 IS - 02 SP - 340 EP - 455 PB - AME Publishing Company CY - Hong Kong, China ER - TY - CHAP A1 - Chang, Ching-Sheng A1 - Lin, Jin-Fa A1 - Lee, Ming-Ching A1 - Palm, Christoph ED - Tolxdorff, Thomas ED - Deserno, Thomas M. ED - Handels, Heinz ED - Maier, Andreas ED - Maier-Hein, Klaus H. ED - Palm, Christoph T1 - Semantic Lung Segmentation Using Convolutional Neural Networks T2 - Bildverarbeitung für die Medizin 2020. Algorithmen - Systeme - Anwendungen. Proceedings des Workshops vom 15. bis 17. März 2020 in Berlin N2 - Chest X-Ray (CXR) images as part of a non-invasive diagnosis method are commonly used in today’s medical workflow. In traditional methods, physicians usually use their experience to interpret CXR images, however, there is a large interobserver variance. Computer vision may be used as a standard for assisted diagnosis. In this study, we applied an encoder-decoder neural network architecture for automatic lung region detection. We compared a three-class approach (left lung, right lung, background) and a two-class approach (lung, background). The differentiation of left and right lungs as direct result of a semantic segmentation on basis of neural nets rather than post-processing a lung-background segmentation is done here for the first time. Our evaluation was done on the NIH Chest X-ray dataset, from which 1736 images were extracted and manually annotated. We achieved 94:9% mIoU and 92% mIoU as segmentation quality measures for the two-class-model and the three-class-model, respectively. This result is very promising for the segmentation of lung regions having the simultaneous classification of left and right lung in mind. KW - Neuronales Netz KW - Segmentierung KW - Brustkorb KW - Deep Learning KW - Encoder-Decoder Network KW - Chest X-Ray Y1 - 2020 SN - 978-3-658-29266-9 U6 - https://doi.org/10.1007/978-3-658-29267-6_17 SP - 75 EP - 80 PB - Springer Vieweg CY - Wiesbaden ER - TY - GEN A1 - Ebigbo, Alanna A1 - Mendel, Robert A1 - Tziatzios, Georgios A1 - Probst, Andreas A1 - Palm, Christoph A1 - Messmann, Helmut T1 - Real-Time Diagnosis of an Early Barrett's Carcinoma using Artificial Intelligence (AI) - Video Case Demonstration T2 - Endoscopy N2 - Introduction We present a clinical case showing the real-time detection, characterization and delineation of an early Barrett’s cancer using AI. Patients and methods A 70-year old patient with a long-segment Barrett’s esophagus (C5M7) was assessed with an AI algorithm. Results The AI system detected a 10 mm focal lesion and AI characterization predicted cancer with a probability of >90%. After ESD resection, histopathology showed mucosal adenocarcinoma (T1a (m), R0) confirming AI diagnosis. Conclusion We demonstrate the real-time AI detection, characterization and delineation of a small and early mucosal Barrett’s cancer. KW - Artificial Intelligence KW - Barrett's Carcinoma KW - Speiseröhrenkrebs KW - Künstliche Intelligenz KW - Diagnose Y1 - 2020 U6 - https://doi.org/10.1055/s-0040-1704075 VL - 52 IS - S 01 PB - Thieme ER - TY - JOUR A1 - Ebigbo, Alanna A1 - Mendel, Robert A1 - Probst, Andreas A1 - Manzeneder, Johannes A1 - Prinz, Friederike A1 - Souza Jr., Luis Antonio de A1 - Papa, João Paulo A1 - Palm, Christoph A1 - Messmann, Helmut T1 - Real-time use of artificial intelligence in the evaluation of cancer in Barrett’s oesophagus JF - Gut N2 - Based on previous work by our group with manual annotation of visible Barrett oesophagus (BE) cancer images, a real-time deep learning artificial intelligence (AI) system was developed. While an expert endoscopist conducts the endoscopic assessment of BE, our AI system captures random images from the real-time camera livestream and provides a global prediction (classification), as well as a dense prediction (segmentation) differentiating accurately between normal BE and early oesophageal adenocarcinoma (EAC). The AI system showed an accuracy of 89.9% on 14 cases with neoplastic BE. KW - Speiseröhrenkrankheit KW - Diagnose KW - Maschinelles Lernen KW - Barrett's esophagus KW - Deep learning KW - real-time Y1 - 2020 U6 - https://doi.org/10.1136/gutjnl-2019-319460 VL - 69 IS - 4 SP - 615 EP - 616 PB - BMJ CY - London ER - TY - CHAP A1 - Mendel, Robert A1 - Souza Jr., Luis Antonio de A1 - Rauber, David A1 - Papa, João Paulo A1 - Palm, Christoph T1 - Semi-supervised Segmentation Based on Error-Correcting Supervision T2 - Computer vision - ECCV 2020: 16th European conference, Glasgow, UK, August 23-28, 2020, Proceedings, Part XXIX 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. The secondary correction network learns on the labeled data to optimally spot correct predictions, as well as to amend incorrect ones. As auxiliary regularization term, the corrector directly influences the supervised training of the segmentation network. On unlabeled data, the output of the correction network is essential to create a proxy for the unknown truth. The corrector’s output is combined with the segmentation network’s prediction to form the new target. We propose a loss function that incorporates both the pseudo-labels as well as the predictive certainty of the correction network. Our approach can easily be added to supervised segmentation models. We show consistent improvements over a supervised baseline on experiments on both the Pascal VOC 2012 and the Cityscapes datasets with varying amounts of labeled data. KW - Semi-Supervised Learning KW - Machine Learning Y1 - 2020 SN - 978-3-030-58525-9 U6 - https://doi.org/10.1007/978-3-030-58526-6_9 SP - 141 EP - 157 PB - Springer CY - Cham ER - TY - JOUR A1 - Souza Jr., Luis Antonio de A1 - Passos, Leandro A. A1 - Mendel, Robert A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Palm, Christoph A1 - Papa, João Paulo T1 - Assisting Barrett's esophagus identification using endoscopic data augmentation based on Generative Adversarial Networks JF - Computers in Biology and Medicine N2 - Barrett's esophagus figured a swift rise in the number of cases in the past years. Although traditional diagnosis methods offered a vital role in early-stage treatment, they are generally time- and resource-consuming. In this context, computer-aided approaches for automatic diagnosis emerged in the literature since early detection is intrinsically related to remission probabilities. However, they still suffer from drawbacks because of the lack of available data for machine learning purposes, thus implying reduced recognition rates. This work introduces Generative Adversarial Networks to generate high-quality endoscopic images, thereby identifying Barrett's esophagus and adenocarcinoma more precisely. Further, Convolution Neural Networks are used for feature extraction and classification purposes. The proposed approach is validated over two datasets of endoscopic images, with the experiments conducted over the full and patch-split images. The application of Deep Convolutional Generative Adversarial Networks for the data augmentation step and LeNet-5 and AlexNet for the classification step allowed us to validate the proposed methodology over an extensive set of datasets (based on original and augmented sets), reaching results of 90% of accuracy for the patch-based approach and 85% for the image-based approach. Both results are based on augmented datasets and are statistically different from the ones obtained in the original datasets of the same kind. Moreover, the impact of data augmentation was evaluated in the context of image description and classification, and the results obtained using synthetic images outperformed the ones over the original datasets, as well as other recent approaches from the literature. Such results suggest promising insights related to the importance of proper data for the accurate classification concerning computer-assisted Barrett's esophagus and adenocarcinoma detection. KW - Maschinelles Lernen KW - Barrett's esophagus KW - Machine learning KW - Adenocarcinoma KW - Generative adversarial networks KW - Neuronales Netz KW - Adenocarcinom KW - Speiseröhrenkrebs KW - Diagnose Y1 - 2020 U6 - https://doi.org/10.1016/j.compbiomed.2020.104029 VL - 126 IS - November PB - Elsevier 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 - Arribas, Julia A1 - Antonelli, Giulio A1 - Frazzoni, Leonardo A1 - Fuccio, Lorenzo A1 - Ebigbo, Alanna A1 - van der Sommen, Fons A1 - Ghatwary, Noha A1 - Palm, Christoph A1 - Coimbra, Miguel A1 - Renna, Francesco A1 - Bergman, Jacques J.G.H.M. A1 - Sharma, Prateek A1 - Messmann, Helmut A1 - Hassan, Cesare A1 - Dinis-Ribeiro, Mario J. T1 - Standalone performance of artificial intelligence for upper GI neoplasia: a meta-analysis JF - Gut N2 - Objective: Artificial intelligence (AI) may reduce underdiagnosed or overlooked upper GI (UGI) neoplastic and preneoplastic conditions, due to subtle appearance and low disease prevalence. Only disease-specific AI performances have been reported, generating uncertainty on its clinical value. Design: We searched PubMed, Embase and Scopus until July 2020, for studies on the diagnostic performance of AI in detection and characterisation of UGI lesions. Primary outcomes were pooled diagnostic accuracy, sensitivity and specificity of AI. Secondary outcomes were pooled positive (PPV) and negative (NPV) predictive values. We calculated pooled proportion rates (%), designed summary receiving operating characteristic curves with respective area under the curves (AUCs) and performed metaregression and sensitivity analysis. Results: Overall, 19 studies on detection of oesophageal squamous cell neoplasia (ESCN) or Barrett's esophagus-related neoplasia (BERN) or gastric adenocarcinoma (GCA) were included with 218, 445, 453 patients and 7976, 2340, 13 562 images, respectively. AI-sensitivity/specificity/PPV/NPV/positive likelihood ratio/negative likelihood ratio for UGI neoplasia detection were 90% (CI 85% to 94%)/89% (CI 85% to 92%)/87% (CI 83% to 91%)/91% (CI 87% to 94%)/8.2 (CI 5.7 to 11.7)/0.111 (CI 0.071 to 0.175), respectively, with an overall AUC of 0.95 (CI 0.93 to 0.97). No difference in AI performance across ESCN, BERN and GCA was found, AUC being 0.94 (CI 0.52 to 0.99), 0.96 (CI 0.95 to 0.98), 0.93 (CI 0.83 to 0.99), respectively. Overall, study quality was low, with high risk of selection bias. No significant publication bias was found. Conclusion: We found a high overall AI accuracy for the diagnosis of any neoplastic lesion of the UGI tract that was independent of the underlying condition. This may be expected to substantially reduce the miss rate of precancerous lesions and early cancer when implemented in clinical practice. KW - Artificial Intelligence Y1 - 2021 U6 - https://doi.org/10.1136/gutjnl-2020-321922 VL - 70 IS - 8 SP - 1458 EP - 1468 PB - BMJ CY - London ER - TY - JOUR A1 - Hartmann, Robin A1 - Weiherer, Maximilian A1 - Schiltz, Daniel A1 - Baringer, Magnus A1 - Noisser, Vivien A1 - Hösl, Vanessa A1 - Eigenberger, Andreas A1 - Seitz, Stefan A1 - Palm, Christoph A1 - Prantl, Lukas A1 - Brébant, Vanessa T1 - New aspects in digital breast assessment: further refinement of a method for automated digital anthropometry JF - Archives of Gynecology and Obstetrics N2 - Purpose: In this trial, we used a previously developed prototype software to assess aesthetic results after reconstructive surgery for congenital breast asymmetry using automated anthropometry. To prove the consensus between the manual and automatic digital measurements, we evaluated the software by comparing the manual and automatic measurements of 46 breasts. Methods: Twenty-three patients who underwent reconstructive surgery for congenital breast asymmetry at our institution were examined and underwent 3D surface imaging. Per patient, 14 manual and 14 computer-based anthropometric measurements were obtained according to a standardized protocol. Manual and automatic measurements, as well as the previously proposed Symmetry Index (SI), were compared. Results: The Wilcoxon signed-rank test revealed no significant differences in six of the seven measurements between the automatic and manual assessments. The SI showed robust agreement between the automatic and manual methods. Conclusion: The present trial validates our method for digital anthropometry. Despite the discrepancy in one measurement, all remaining measurements, including the SI, showed high agreement between the manual and automatic methods. The proposed data bring us one step closer to the long-term goal of establishing robust instruments to evaluate the results of breast surgery. KW - digital anthropometry KW - reconstructive surgery KW - 3D surface imaging Y1 - 2021 U6 - https://doi.org/10.1007/s00404-020-05862-2 SN - 1432-0711 VL - 303 SP - 721 EP - 728 PB - Springer Nature CY - Heidelberg ER - TY - GEN A1 - Römmele, Christoph A1 - Mendel, Robert A1 - Rauber, David A1 - Rückert, Tobias A1 - Byrne, Michael F. A1 - Palm, Christoph A1 - Messmann, Helmut A1 - Ebigbo, Alanna T1 - Endoscopic Diagnosis of Eosinophilic Esophagitis Using a deep Learning Algorithm T2 - Endoscopy N2 - Aims Eosinophilic esophagitis (EoE) is easily missed during endoscopy, either because physicians are not familiar with its endoscopic features or the morphologic changes are too subtle. In this preliminary paper, we present the first attempt to detect EoE in endoscopic white light (WL) images using a deep learning network (EoE-AI). Methods 401 WL images of eosinophilic esophagitis and 871 WL images of normal esophageal mucosa were evaluated. All images were assessed for the Endoscopic Reference score (EREFS) (edema, rings, exudates, furrows, strictures). Images with strictures were excluded. EoE was defined as the presence of at least 15 eosinophils per high power field on biopsy. A convolutional neural network based on the ResNet architecture with several five-fold cross-validation runs was used. Adding auxiliary EREFS-classification branches to the neural network allowed the inclusion of the scores as optimization criteria during training. EoE-AI was evaluated for sensitivity, specificity, and F1-score. In addition, two human endoscopists evaluated the images. Results EoE-AI showed a mean sensitivity, specificity, and F1 of 0.759, 0.976, and 0.834 respectively, averaged over the five distinct cross-validation runs. With the EREFS-augmented architecture, a mean sensitivity, specificity, and F1-score of 0.848, 0.945, and 0.861 could be demonstrated respectively. In comparison, the two human endoscopists had an average sensitivity, specificity, and F1-score of 0.718, 0.958, and 0.793. Conclusions To the best of our knowledge, this is the first application of deep learning to endoscopic images of EoE which were also assessed after augmentation with the EREFS-score. The next step is the evaluation of EoE-AI using an external dataset. We then plan to assess the EoE-AI tool on endoscopic videos, and also in real-time. This preliminary work is encouraging regarding the ability for AI to enhance physician detection of EoE, and potentially to do a true “optical biopsy” but more work is needed. KW - Eosinophilic Esophagitis KW - Endoscopy KW - Deep Learning Y1 - 2021 U6 - https://doi.org/10.1055/s-0041-1724274 VL - 53 IS - S 01 PB - Georg Thieme Verlag CY - Stuttgart ER - TY - GEN A1 - Scheppach, Markus W. A1 - Rauber, David A1 - Mendel, Robert A1 - Palm, Christoph A1 - Byrne, Michael F. A1 - Messmann, Helmut A1 - Ebigbo, Alanna T1 - Detection Of Celiac Disease Using A Deep Learning Algorithm T2 - Endoscopy N2 - Aims Celiac disease (CD) is a complex condition caused by an autoimmune reaction to ingested gluten. Due to its polymorphic manifestation and subtle endoscopic presentation, the diagnosis is difficult and thus the disorder is underreported. We aimed to use deep learning to identify celiac disease on endoscopic images of the small bowel. Methods Patients with small intestinal histology compatible with CD (MARSH classification I-III) were extracted retrospectively from the database of Augsburg University hospital. They were compared to patients with no clinical signs of CD and histologically normal small intestinal mucosa. In a first step MARSH III and normal small intestinal mucosa were differentiated with the help of a deep learning algorithm. For this, the endoscopic white light images were divided into five equal-sized subsets. We avoided splitting the images of one patient into several subsets. A ResNet-50 model was trained with the images from four subsets and then validated with the remaining subset. This process was repeated for each subset, such that each subset was validated once. Sensitivity, specificity, and harmonic mean (F1) of the algorithm were determined. Results The algorithm showed values of 0.83, 0.88, and 0.84 for sensitivity, specificity, and F1, respectively. Further data showing a comparison between the detection rate of the AI model and that of experienced endoscopists will be available at the time of the upcoming conference. Conclusions We present the first clinical report on the use of a deep learning algorithm for the detection of celiac disease using endoscopic images. Further evaluation on an external data set, as well as in the detection of CD in real-time, will follow. However, this work at least suggests that AI can assist endoscopists in the endoscopic diagnosis of CD, and ultimately may be able to do a true optical biopsy in live-time. KW - Celiac Disease KW - Deep Learning Y1 - 2021 U6 - https://doi.org/10.1055/s-0041-1724970 N1 - Digital poster exhibition VL - 53 IS - S 01 PB - Georg Thieme Verlag CY - Stuttgart ER - TY - CHAP A1 - Souza Jr., Luis Antonio de A1 - Passos, Leandro A. A1 - Mendel, Robert A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Palm, Christoph A1 - Papa, João Paulo T1 - Fine-tuning Generative Adversarial Networks using Metaheuristics BT - A Case Study on Barrett's Esophagus Identification T2 - Bildverarbeitung für die Medizin 2021. Proceedings, German Workshop on Medical Image Computing, Regensburg, March 7-9, 2021 N2 - Barrett's esophagus denotes a disorder in the digestive system that affects the esophagus' mucosal cells, causing reflux, and showing potential convergence to esophageal adenocarcinoma if not treated in initial stages. Thus, fast and reliable computer-aided diagnosis becomes considerably welcome. Nevertheless, such approaches usually suffer from imbalanced datasets, which can be addressed through Generative Adversarial Networks (GANs). Such techniques generate realistic images based on observed samples, even though at the cost of a proper selection of its hyperparameters. Many works employed a class of nature-inspired algorithms called metaheuristics to tackle the problem considering distinct deep learning approaches. Therefore, this paper's main contribution is to introduce metaheuristic techniques to fine-tune GANs in the context of Barrett's esophagus identification, as well as to investigate the feasibility of generating high-quality synthetic images for early-cancer assisted identification. KW - Endoskopie KW - Computerunterstützte Medizin KW - Deep Learning Y1 - 2021 SN - 978-3-658-33197-9 U6 - https://doi.org/10.1007/978-3-658-33198-6_50 SP - 205 EP - 210 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Souza Jr., Luis Antonio de A1 - Mendel, Robert A1 - Strasser, Sophia A1 - Ebigbo, Alanna A1 - Probst, Andreas A1 - Messmann, Helmut A1 - Papa, João Paulo A1 - Palm, Christoph T1 - Convolutional Neural Networks for the evaluation of cancer in Barrett’s esophagus: Explainable AI to lighten up the black-box JF - Computers in Biology and Medicine N2 - Even though artificial intelligence and machine learning have demonstrated remarkable performances in medical image computing, their level of accountability and transparency must be provided in such evaluations. The reliability related to machine learning predictions must be explained and interpreted, especially if diagnosis support is addressed. For this task, the black-box nature of deep learning techniques must be lightened up to transfer its promising results into clinical practice. Hence, we aim to investigate the use of explainable artificial intelligence techniques to quantitatively highlight discriminative regions during the classification of earlycancerous tissues in Barrett’s esophagus-diagnosed patients. Four Convolutional Neural Network models (AlexNet, SqueezeNet, ResNet50, and VGG16) were analyzed using five different interpretation techniques (saliency, guided backpropagation, integrated gradients, input × gradients, and DeepLIFT) to compare their agreement with experts’ previous annotations of cancerous tissue. We could show that saliency attributes match best with the manual experts’ delineations. Moreover, there is moderate to high correlation between the sensitivity of a model and the human-and-computer agreement. The results also lightened that the higher the model’s sensitivity, the stronger the correlation of human and computational segmentation agreement. We observed a relevant relation between computational learning and experts’ insights, demonstrating how human knowledge may influence the correct computational learning. KW - Deep Learning KW - Künstliche Intelligenz KW - Computerunterstützte Medizin KW - Barrett's esophagus KW - Adenocarcinoma KW - Machine learning KW - Explainable artificial intelligence KW - Computer-aided diagnosis Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:898-opus4-20126 SN - 0010-4825 VL - 135 SP - 1 EP - 14 PB - Elsevier ER - TY - JOUR A1 - Ebigbo, Alanna A1 - Mendel, Robert A1 - Rückert, Tobias A1 - Schuster, Laurin A1 - Probst, Andreas A1 - Manzeneder, Johannes A1 - Prinz, Friederike A1 - Mende, Matthias A1 - Steinbrück, Ingo A1 - Faiss, Siegbert A1 - Rauber, David A1 - Souza Jr., Luis Antonio de A1 - Papa, João Paulo A1 - Deprez, Pierre A1 - Oyama, Tsuneo A1 - Takahashi, Akiko A1 - Seewald, Stefan A1 - Sharma, Prateek A1 - Byrne, Michael F. A1 - Palm, Christoph A1 - Messmann, Helmut T1 - Endoscopic prediction of submucosal invasion in Barrett’s cancer with the use of Artificial Intelligence: A pilot Study JF - Endoscopy N2 - Background and aims: The accurate differentiation between T1a and T1b Barrett’s cancer has both therapeutic and prognostic implications but is challenging even for experienced physicians. We trained an Artificial Intelligence (AI) system on the basis of deep artificial neural networks (deep learning) to differentiate between T1a and T1b Barrett’s cancer white-light images. Methods: Endoscopic images from three tertiary care centres in Germany were collected retrospectively. A deep learning system was trained and tested using the principles of cross-validation. A total of 230 white-light endoscopic images (108 T1a and 122 T1b) was evaluated with the AI-system. For comparison, the images were also classified by experts specialized in endoscopic diagnosis and treatment of Barrett’s cancer. Results: The sensitivity, specificity, F1 and accuracy of the AI-system in the differentiation between T1a and T1b cancer lesions was 0.77, 0.64, 0.73 and 0.71, respectively. There was no statistically significant difference between the performance of the AI-system and that of human experts with sensitivity, specificity, F1 and accuracy of 0.63, 0.78, 0.67 and 0.70 respectively. Conclusion: This pilot study demonstrates the first multicenter application of an AI-based system in the prediction of submucosal invasion in endoscopic images of Barrett’s cancer. AI scored equal to international experts in the field, but more work is necessary to improve the system and apply it to video sequences and in a real-life setting. Nevertheless, the correct prediction of submucosal invasion in Barret´s cancer remains challenging for both experts and AI. KW - Maschinelles Lernen KW - Neuronales Netz KW - Speiseröhrenkrebs KW - Diagnose KW - Artificial Intelligence KW - Machine learning KW - Adenocarcinoma KW - Barrett’s cancer KW - submucosal invasion Y1 - 2021 U6 - https://doi.org/10.1055/a-1311-8570 VL - 53 IS - 09 SP - 878 EP - 883 PB - Thieme CY - Stuttgart ER - TY - CHAP A1 - Weber Nunes, Danilo A1 - Hammer, Michael A1 - Hammer, Simone A1 - Uller, Wibke A1 - Palm, Christoph T1 - Classification of Vascular Malformations Based on T2 STIR Magnetic Resonance Imaging T2 - Bildverarbeitung für die Medizin 2022: Proceedings, German Workshop on Medical Image Computing, Heidelberg, June 26-28, 2022 N2 - Vascular malformations (VMs) are a rare condition. They can be categorized into high-flow and low-flow VMs, which is a challenging task for radiologists. In this work, a very heterogeneous set of MRI images with only rough annotations are used for classification with a convolutional neural network. The main focus is to describe the challenging data set and strategies to deal with such data in terms of preprocessing, annotation usage and choice of the network architecture. We achieved a classification result of 89.47 % F1-score with a 3D ResNet 18. KW - Deep Learning KW - Magnetic Resonance Imaging KW - Vascular Malformations Y1 - 2022 U6 - https://doi.org/10.1007/978-3-658-36932-3_57 SP - 267 EP - 272 PB - Springer Vieweg CY - Wiesbaden ER - TY - JOUR A1 - Knoedler, Leonard A1 - Baecher, Helena A1 - Kauke-Navarro, Martin A1 - Prantl, Lukas A1 - Machens, Hans-Günther A1 - Scheuermann, Philipp A1 - Palm, Christoph A1 - Baumann, Raphael A1 - Kehrer, Andreas A1 - Panayi, Adriana C. A1 - Knoedler, Samuel T1 - Towards a Reliable and Rapid Automated Grading System in Facial Palsy Patients: Facial Palsy Surgery Meets Computer Science JF - Journal of Clinical Medicine N2 - Background: Reliable, time- and cost-effective, and clinician-friendly diagnostic tools are cornerstones in facial palsy (FP) patient management. Different automated FP grading systems have been developed but revealed persisting downsides such as insufficient accuracy and cost-intensive hardware. We aimed to overcome these barriers and programmed an automated grading system for FP patients utilizing the House and Brackmann scale (HBS). Methods: Image datasets of 86 patients seen at the Department of Plastic, Hand, and Reconstructive Surgery at the University Hospital Regensburg, Germany, between June 2017 and May 2021, were used to train the neural network and evaluate its accuracy. Nine facial poses per patient were analyzed by the algorithm. Results: The algorithm showed an accuracy of 100%. Oversampling did not result in altered outcomes, while the direct form displayed superior accuracy levels when compared to the modular classification form (n = 86; 100% vs. 99%). The Early Fusion technique was linked to improved accuracy outcomes in comparison to the Late Fusion and sequential method (n = 86; 100% vs. 96% vs. 97%). Conclusions: Our automated FP grading system combines high-level accuracy with cost- and time-effectiveness. Our algorithm may accelerate the grading process in FP patients and facilitate the FP surgeon’s workflow. Y1 - 2022 U6 - https://doi.org/10.3390/jcm11174998 VL - 11 IS - 17 PB - MDPI CY - Basel ER - TY - GEN A1 - Scheppach, Markus W. A1 - Mendel, Robert A1 - Probst, Andreas A1 - Meinikheim, Michael A1 - Palm, Christoph A1 - Messmann, Helmut A1 - Ebigbo, Alanna T1 - Artificial Intelligence (AI) – assisted vessel and tissue recognition during third space endoscopy (Smart ESD) T2 - Zeitschrift für Gastroenterologie N2 - Clinical setting  Third space procedures such as endoscopic submucosal dissection (ESD) and peroral endoscopic myotomy (POEM) are complex minimally invasive techniques with an elevated risk for operator-dependent adverse events such as bleeding and perforation. This risk arises from accidental dissection into the muscle layer or through submucosal blood vessels as the submucosal cutting plane within the expanding resection site is not always apparent. Deep learning algorithms have shown considerable potential for the detection and characterization of gastrointestinal lesions. So-called AI – clinical decision support solutions (AI-CDSS) are commercially available for polyp detection during colonoscopy. Until now, these computer programs have concentrated on diagnostics whereas an AI-CDSS for interventional endoscopy has not yet been introduced. We aimed to develop an AI-CDSS („Smart ESD“) for real-time intra-procedural detection and delineation of blood vessels, tissue structures and endoscopic instruments during third-space endoscopic procedures. Characteristics of Smart ESD  An AI-CDSS was invented that delineates blood vessels, tissue structures and endoscopic instruments during third-space endoscopy in real-time. The output can be displayed by an overlay over the endoscopic image with different modes of visualization, such as a color-coded semitransparent area overlay, or border tracing (demonstration video). Hereby the optimal layer for dissection can be visualized, which is close above or directly at the muscle layer, depending on the applied technique (ESD or POEM). Furthermore, relevant blood vessels (thickness> 1mm) are delineated. Spatial proximity between the electrosurgical knife and a blood vessel triggers a warning signal. By this guidance system, inadvertent dissection through blood vessels could be averted. Technical specifications  A DeepLabv3+ neural network architecture with KSAC and a 101-layer ResNeSt backbone was used for the development of Smart ESD. It was trained and validated with 2565 annotated still images from 27 full length third-space endoscopic videos. The annotation classes were blood vessel, submucosal layer, muscle layer, electrosurgical knife and endoscopic instrument shaft. A test on a separate data set yielded an intersection over union (IoU) of 68%, a Dice Score of 80% and a pixel accuracy of 87%, demonstrating a high overlap between expert and AI segmentation. Further experiments on standardized video clips showed a mean vessel detection rate (VDR) of 85% with values of 92%, 70% and 95% for POEM, rectal ESD and esophageal ESD respectively. False positive measurements occurred 0.75 times per minute. 7 out of 9 vessels which caused intraprocedural bleeding were caught by the algorithm, as well as both vessels which required hemostasis via hemostatic forceps. Future perspectives  Smart ESD performed well for vessel and tissue detection and delineation on still images, as well as on video clips. During a live demonstration in the endoscopy suite, clinical applicability of the innovation was examined. The lag time for processing of the live endoscopic image was too short to be visually detectable for the interventionist. Even though the algorithm could not be applied during actual dissection by the interventionist, Smart ESD appeared readily deployable during visual assessment by ESD experts. Therefore, we plan to conduct a clinical trial in order to obtain CE-certification of the algorithm. This new technology may improve procedural safety and speed, as well as training of modern minimally invasive endoscopic resection techniques. KW - Artificial Intelligence KW - Medical Image Computing KW - Endoscopy KW - Bildgebendes Verfahren KW - Medizin KW - Künstliche Intelligenz KW - Endoskopie Y1 - 2022 U6 - https://doi.org/10.1055/s-0042-1755110 VL - 60 IS - 08 PB - Georg Thieme Verlag CY - Stuttgart ER - TY - GEN A1 - Meinikheim, Michael A1 - Mendel, Robert A1 - Scheppach, Markus W. A1 - Probst, Andreas A1 - Prinz, Friederike A1 - Schwamberger, Tanja A1 - Schlottmann, Jakob A1 - Gölder, Stefan Karl A1 - Walter, Benjamin A1 - Steinbrück, Ingo A1 - Palm, Christoph A1 - Messmann, Helmut A1 - Ebigbo, Alanna T1 - INFLUENCE OF AN ARTIFICIAL INTELLIGENCE (AI) BASED DECISION SUPPORT SYSTEM (DSS) ON THE DIAGNOSTIC PERFORMANCE OF NON-EXPERTS IN BARRETT´S ESOPHAGUS RELATED NEOPLASIA (BERN) T2 - Endoscopy N2 - Aims Barrett´s esophagus related neoplasia (BERN) is difficult to detect and characterize during endoscopy, even for expert endoscopists. We aimed to assess the add-on effect of an Artificial Intelligence (AI) algorithm (Barrett-Ampel) as a decision support system (DSS) for non-expert endoscopists in the evaluation of Barrett’s esophagus (BE) and BERN. Methods Twelve videos with multimodal imaging white light (WL), narrow-band imaging (NBI), texture and color enhanced imaging (TXI) of histologically confirmed BE and BERN were assessed by expert and non-expert endoscopists. For each video, endoscopists were asked to identify the area of BERN and decide on the biopsy spot. Videos were assessed by the AI algorithm and regions of BERN were highlighted in real-time by a transparent overlay. Finally, endoscopists were shown the AI videos and asked to either confirm or change their initial decision based on the AI support. Results Barrett-Ampel correctly identified all areas of BERN, irrespective of the imaging modality (WL, NBI, TXI), but misinterpreted two inflammatory lesions (Accuracy=75%). Expert endoscopists had a similar performance (Accuracy=70,8%), while non-experts had an accuracy of 58.3%. When AI was implemented as a DSS, non-expert endoscopists improved their diagnostic accuracy to 75%. Conclusions AI may have the potential to support non-expert endoscopists in the assessment of videos of BE and BERN. Limitations of this study include the low number of videos used. Randomized clinical trials in a real-life setting should be performed to confirm these results. KW - Artificial Intelligence KW - Barrett's Esophagus KW - Speiseröhrenkrankheit KW - Künstliche Intelligenz KW - Diagnose Y1 - 2022 U6 - https://doi.org/10.1055/s-00000012 VL - 54 IS - S 01 SP - S39 PB - Thieme ER -