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Technical Note: Feasibility of translating 3.0T-trained Deep-Learning Segmentation Models Out-of-the-Box on Low-Field MRI 0.55T Knee-MRI of Healthy Controls

arXiv

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arXiv 2023年

作者： Rupsa, Bhattacharjee Zehra, Akkaya Johanna, Luitjens Pan, Su Yang, Yang Valentina, Pedoia Sharmila, Majumdar Department of Radiology & Biomedical Imaging University of California San Francisco United States Siemens Medical Solutions USA Inc. MalvernPA United States Image Analysis and Visualization Group Altos Labs San Francisco United States

In the current study, our purpose is to evaluate the feasibility of applyingdeep learning (DL) enabled algorithms to quantify bilateral knee biomarkers inhealthy controls scanned at 0.55T and compared with 3.0T. The current studyassesses the performance of standard in-practice bone, and cartilagesegmentation algorithms at 0.55T, both qualitatively and quantitatively, interms of comparing segmentation performance, areas of improvement, andcompartment-wise cartilage thickness values between 0.55T vs. 3.0T. Initialresults demonstrate a usable to good technical feasibility of translatingexisting quantitative deep-learning-based image segmentation techniques,trained on 3.0T, out of 0.55T for knee MRI, in a multi-vendor acquisitionenvironment. Especially in terms of segmenting cartilage compartments, themodels perform almost equivalent to 3.0T in terms of Likert ranking. The 0.55Tlow-field sustainable and easy-to-install MRI, as demonstrated, thus, can beutilized for evaluating knee cartilage thickness and bone segmentations aidedby established DL algorithms trained at higher-field strengths out-of-the-boxinitially. This could be utilized at the far-spread point-of-care locationswith a lack of radiologists available to manually segment low-field images, atleast till a decent base of low-field data pool is collated. With furtherfine-tuning with manual labeling of low-field data or utilizing synthesizedhigher SNR images from low-field images, OA biomarker quantificationperformance is potentially guaranteed to be further improved. © 2023, CC BY-NC-ND.

关键词： Magnetic resonance imaging

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LYSTO: The Lymphocyte Assessment Hackathon and Benchmark Dataset

arXiv

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arXiv 2023年

作者： Jiao, Yiping van der Laak, Jeroen Albarqouni, Shadi Li, Zhang Tan, Tao Bhalerao, Abhir Ma, Jiabo Sun, Jiamei Pocock, Johnathan Pluim, Josien P.W. Koohbanani, Navid Alemi Bashir, Raja Muhammad Saad Raza, Shan E Ahmed Liu, Sibo Graham, Simon Wetstein, Suzanne Khurram, Syed Ali Watson, Thomas Rajpoot, Nasir Veta, Mitko Ciompi, Francesco Department of Pathology Radboud University Medical Center Nijmegen Netherlands School of Artificial Intelligence Nanjing University of Information Science Technology China Center for Medical Image Science and Visualization Linköping University Linköping Sweden Helmholtz AI Helmholtz Zentrum München Nuerherberg 85764 Germany Faculty of Informatics Technical University of Munich Garching85748 Germany College of Aerospace Science and Engineering National University of Defense Technology China Hunan Provincial Key Laboratory of Image Measurement and Vision Navigation China Macao Polytechnic University China Department of Computer Science University of Warwick Coventry United Kingdom Huazhong University of Science and Technology China Singapore Medical Image Analysis Group Department of Biomedical Engineering Eindhoven University of Technology Eindhoven Netherlands School of Clinical Dentistry University of Sheffield Sheffield United Kingdom United Kingdom

We introduce LYSTO, the Lymphocyte Assessment Hackathon, which was held in conjunction with the MICCAI 2019 Conference in Shenzen (China). The competition required participants to automatically assess the number of lymphocytes, in particular T-cells, in histopathological images of colon, breast, and prostate cancer stained with CD3 and CD8 immunohistochemistry. Differently from other challenges setup in medical image analysis, LYSTO participants were solely given a few hours to address this problem. In this paper, we describe the goal and the multi-phase organization of the hackathon;we describe the proposed methods and the on-site results. Additionally, we present post-competition results where we show how the presented methods perform on an independent set of lung cancer slides, which was not part of the initial competition, as well as a comparison on lymphocyte assessment between presented methods and a panel of pathologists. We show that some of the participants were capable to achieve pathologist-level performance at lymphocyte assessment. After the hackathon, LYSTO was left as a lightweight plug-and-play benchmark dataset on grand-challenge website, together with an automatic evaluation platform. LYSTO has supported a number of research in lymphocyte assessment in oncology. LYSTO will be a long-lasting educational challenge for deep learning and digital pathology, it is available at https://***/.MSC Codes 68T07 © 2023, CC BY.

关键词： Pathology

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Quantifying the effects of data augmentation and stain color normalization in convolutional neural networks for computational pathology

arXiv

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arXiv 2019年

作者： Tellez, David Litjens, Geert Bándi, Péter Bulten, Wouter Bokhorst, John-Melle Ciompi, Francesco van der Laak, Jeroen Diagnostic Image Analysis Group Department of Pathology Radboud University Medical Center Nijmegen Netherlands Center for Medical Image Science and Visualization Linköping University Linköping Sweden

Stain variation is a phenomenon observed when distinct pathology laboratories stain tissue slides that exhibit similar but not identical color appearance. Due to this color shift between laboratories, convolutional neural networks (CNNs) trained with images from one lab often underperform on unseen images from the other lab. Several techniques have been proposed to reduce the generalization error, mainly grouped into two categories: stain color augmentation and stain color normalization. The former simulates a wide variety of realistic stain variations during training, producing stain-invariant CNNs. The latter aims to match training and test color distributions in order to reduce stain variation. For the first time, we compared some of these techniques and quantified their effect on CNN classification performance using a heterogeneous dataset of hematoxylin and eosin histopathology images from 4 organs and 9 pathology laboratories. Additionally, we propose a novel unsupervised method to perform stain color normalization using a neural network. Based on our experimental results, we provide practical guidelines on how to use stain color augmentation and stain color normalization in future computational pathology applications. Copyright © 2019, The Authors. All rights reserved.

关键词： Pathology

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Biomedical image analysis competitions: The state of current participation practice

arXiv

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arXiv 2022年

作者： Eisenmann, Matthias Reinke, Annika Weru, Vivienn Tizabi, Minu Dietlinde Isensee, Fabian Adler, Tim J. Godau, Patrick Cheplygina, Veronika Kozubek, Michal Maier-Hein, Klaus Jäger, Paul F. Kopp-Schneider, Annette Maier-Hein, Lena Ali, Sharib Gupta, Anubha Kybic, Jan Noble, Alison de Solórzano, Carlos Ortiz Pachade, Samiksha Petitjean, Caroline Sage, Daniel Wei, Donglai Wilden, Elizabeth Alapatt, Deepak Andrearczyk, Vincent Baid, Ujjwal Bakas, Spyridon Balu, Niranjan Bano, Sophia Bawa, Vivek Singh Bernal, Jorge Bodenstedt, Sebastian Casella, Alessandro Choi, Jinwook Commowick, Olivier Daum, Marie Depeursinge, Adrien Dorent, Reuben Egger, Jan Eichhorn, Hannah Engelhardt, Sandy Ganz, Melanie Girard, Gabriel Hansen, Lasse Heinrich, Mattias Heller, Nicholas Hering, Alessa Huaulmé, Arnaud Kim, Hyunjeong Li, Hongwei Bran Landman, Bennett Li, Jianning Ma, Jun Martel, Anne Martín-Isla, Carlos Menze, Bjoern Nwoye, Chinedu Innocent Oreiller, Valentin Padoy, Nicolas Pati, Sarthak Payette, Kelly Sudre, Carole van Wijnen, Kimberlin Vardazaryan, Armine Vercauteren, Tom Wagner, Martin Wang, Chuanbo Yap, Moi Hoon Yu, Zeyun Yuan, Chun Zenk, Maximilian Zia, Aneeq Zimmerer, David Bao, Rina Choi, Chanyeol Cohen, Andrew Dzyubachyk, Oleh Galdran, Adrian Gan, Tianyuan Guo, Tianqi Gupta, Pradyumna Haithami, Mahmood Ho, Edward Jang, Ikbeom Li, Zhili Luo, Zhengbo Lux, Filip Makrogiannis, Sokratis Müller, Dominik Oh, Young-Tack Pang, Subeen Pape, Constantin Polat, Gorkem Reed, Charlotte Rosalie Ryu, Kanghyun Scherr, Tim Thambawita, Vajira Wang, Haoyu Wang, Xinliang Xu, Kele Yeh, Hung Yeo, Doyeob Yuan, Yixuan Zeng, Yan Zhao, Xin Abbing, Julian Adam, Jannes Adluru, Nagesh Agethen, Niklas Ahmed, Salman Al Khalil, Yasmina Alenyà, Mireia Alhoniemi, Esa An, Chengyang Arega, Tewodros Weldebirhan Avisdris, Netanell Aydogan, Dogu Baran Bai, Yingbin Calisto, Maria Baldeon Basaran, Berke Doga Beetz, Marcel Bian, Hao Blansit, Kevin Bloch, Louise Bohnsack, Robert Bosticardo, Sara Breen, Jack Brudfors, Mikael Brüngel, Raphael Cabezas, Mariano Cacciola, Alb Heidelberg Division of Intelligent Medical Systems Germany Heidelberg HI Helmholtz Imaging Germany Faculty of Mathematics and Computer Science Heidelberg University Heidelberg Germany Heidelberg Division of Biostatistics Germany Heidelberg Division of Medical Image Computing Germany Heidelberg HI Applied Vision Lab Germany IT University of Copenhagen Copenhagen Denmark Centre for Biomedical Image Analysis Masaryk University Brno Czech Republic Heidelberg Interactive Machine Learning Group Germany Faculty of Mathematics and Computer Science and Medical Faculty Heidelberg University Heidelberg Germany NCT Heidelberg DKFZ University Hospital Heidelberg Germany School of Computing University of Leeds Leeds United Kingdom SBILab Department of ECE IIIT-Delhi India Faculty of Electrical Engineering Czech Technical University Prague Czech Republic Institute of Biomedical Engineering University of Oxford United Kingdom Center for Applied Medical Research Pamplona Spain Shri Guru Gobind Singhji Institute of Engineering and Technology Maharashtra Nanded India Université de Rouen Normandie France Lausanne Switzerland School of Engineering and Applied Science Harvard University United States ICube University of Strasbourg CNRS France Institute of Informatics School of Management HES-SO Valais-Wallis University of Applied Sciences and Arts Western Switzerland Techno-Pôle 3 Sierre3960 Switzerland Department of Nuclear Medicine and Molecular Imaging Lausanne University Hospital Rue du Bugnon 46 LausanneCH-1011 Switzerland University of Pennsylvania PhiladelphiaPA United States Department of Radiology University of Washington United States Wellcome EPSRC Centre for Interventional and Surgical Sciences University College London London United Kingdom Visual Artificial Intelligence Lab Oxford Brookes University Oxford United Kingdom Universitat Autònoma de Barcelona & Computer Vision Center Spain Dresden Fetscherstraße 74 PF 64 Dresden01307 Germany

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps. © 2022, CC BY.

关键词： Benchmarking

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The Brain Tumor Sequence Registration (BraTS-Reg) Challenge: Establishing Correspondence Between Pre-Operative and Follow-up MRI Scans of Diffuse Glioma Patients

arXiv

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arXiv 2021年

作者： Baheti, Bhakti Chakrabarty, Satrajit Akbari, Hamed Bilello, Michel Wiestler, Benedikt Schwarting, Julian Calabrese, Evan Rudie, Jeffrey Abidi, Syed Mousa, Mina Villanueva-Meyer, Javier Fields, Brandon K.K. Kofler, Florian Shinohara, Russell Takeshi Iglesias, Juan Eugenio Mok, Tony C.W. Chung, Albert C.S. Wodzinski, Marek Jurgas, Artur Marini, Niccolò Atzori, Manfredo Müller, Henning Grosbröhmer, Christoph Siebert, Hanna Hansen, Lasse Heinrich, Mattias P. Canalini, Luca Klein, Jan Gerken, Annika Heldmann, Stefan Hering, Alessa Hahn, Horst K. Meng, Mingyuan Bi, Lei Feng, Dagan Kim, Jinman Zeineldinal, Ramy A. Karar, Mohamed E. Mathis-Ullrich, Franziska Burgert, Oliver Abderezaei, Javid Pionteck, Aymeric Chopra, Agamdeep Kurt, Mehmet Yan, Kewei Yan, Yonghong Tang, Zhe Ma, Jianqiang Nasser, Sahar Almahfouz Kurian, Nikhil Cherian Meena, Mohit Shamsi, Saqib Sethi, Amit Tustison, Nicholas J. Avants, Brian B. Cook, Philip Gee, James C. Tian, Lin Greer, Hastings Niethammer, Marc Hoopesar, Andrew Hoffmannas, Malte Dalcaar, Adrian V. Christodoulidis, Stergios Estiene, Théo Vakalopoulou, Maria Paragios, Nikos Marcus, Daniel S. Davatzikos, Christos Sotiras, Aristeidis Menze, Bjoern Bakas, Spyridon Waldmannstetter, Diana Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Electrical and Systems Engineering Washington University in St. Louis St. LouisMO United States GE HealthCare San RamonCA United States University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Mallinckrodt Institute of Radiology Washington University School of Medicine St. LouisMO United States Institute for Informatics Data Science & Biostatistics Washington University School of Medicine St. LouisMO United States Department of Bioengineering Santa Clara University Santa ClaraCA United States Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Department of Computer Science TUM School of Computation Information and Technology Technical University of Munich Munich Germany Department of Diagnostic and Interventional Neuroradiology School of Medicine Klinikum rechts der Isar Technical University of Munich Munich Germany Department of Nuclear Medicine University Hospital Regensburg Regensburg Germany University Hospital Regensburg Regensburg Germany Department of Radiology & Biomedical Imaging University of California San FranciscoCA United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Radiology University of California San DiegoCA United States Helmholtz AI Helmholtz Munich Neuherberg Germany Penn Statistics in Imaging and Visualization Center Department of Biostatistics Epidemiology and Informatics University of Pennsylvania Philadelphia United States Massachusetts General Hospital Harvard Medical School United States Centre for Medical Imaging Computing University College London United Kingdom The Hong Kong University of Science and Technology Hong Kong University of Applied Sciences West

Registration of longitudinal brain Magnetic Resonance Imaging (MRI) scans containing pathologies is challenging due to dramatic changes in tissue appearance. Although there has been considerable progress in developing general-purpose medical image registration techniques, they have not yet attained the requisite precision and reliability for this task, highlighting its inherent complexity. Here we describe the Brain Tumor Sequence Registration (BraTS-Reg) challenge, as the first public benchmark environment for deformable registration algorithms focusing on estimating correspondences between pre-operative and follow-up scans of the same patient diagnosed with a diffuse brain glioma. The challenge was conducted in conjunction with both the IEEE International Symposium on Biomedical Imaging (ISBI) 2022 and the International Conference on medical image Computing and Computer-Assisted Intervention (MICCAI) 2022. The BraTS-Reg data comprise de-identified multi-institutional multi-parametric MRI (mpMRI) scans, curated for size and resolution according to a canonical anatomical template, and divided into training, validation, and testing sets. Clinical experts annotated ground truth (GT) landmark points of anatomical locations distinct across the temporal domain. The training data with their GT annotations, were publicly released to enable the development of registration algorithms. The validation data, without their GT annotations, were also released to allow for algorithmic evaluation prior to the testing phase, which only allowed submission of containerized algorithms for evaluation on hidden hold-out testing data. Quantitative evaluation and ranking was based on the Median Euclidean Error (MEE), Robustness, and the determinant of the Jacobian of the displacement field. The top-ranked methodologies yielded similar performance across all evaluation metrics and shared several methodological commonalities, including pre-alignment, deep neural networks, inverse consistency

关键词： Magnetic resonance imaging

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Flowing crossfade of endoscopic images for the generation of a mosaic 1

引用

Workshops Bildverarbeitung fur die Medizin: Algorithmen - Systeme - Anwendungen, BVM 2005 - Workshop on image Processing for Medicine: Algorithms - Systems - Applications, BVM 2005

作者： Wald, Diana Reeff, Mireille Székely, Gabor Cattin, Philippe Paulus, Dietrich Medical Image Analysis and Visualization Group Computer Vision Laboratory Swiss Federal Institute of Technology Sternwartstr. 7 CH-8092 Zurich Switzerland Institut für Computervisualistik Universitätsstr. 1 D-56070 Koblenz Germany

ISBN: (数字)9783540264316

ISBN: (纸本)3540250522

Im Beitrag wird ein neues Verfahren zum fließenden Überblenden von Endoskopiebildern vorgestellt. Spezielles Augenmerk wird dabei auf die Erhaltung von feinsten Details in den Aufnahmen und einen guten visuellen Gesamteindruck gelegt. Die Bilder werden zunächst in ihrer Intensität angeglichen. Die Überlappungsbereiche werden anschließend mit dem neuen Verfahren überblendet.

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Information Processing in medical Imaging 1

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丛书名： Lecture Notes in Computer Science

1000年

作者： Gábor Székely Horst K. Hahn

ISBN: (数字)9783642220920

ISBN: (纸本)9783642220913

This book constitutes the refereed proceedings of the 22nd International Conference on Information Processing in medical Imaging, IPMI 2011, held at Kloster Irsee, Germany, in July 2011. The 24 full papers and 39 poster papers included in this volume were carefully reviewed and selected from 224 submissions. The papers are organized in topical sections on segmentation, statistical methods, shape analysis, registration, diffusion imaging, disease progression modeling, and computer aided diagnosis. The poster sessions deal with segmentation, shape analysis, statistical methods, image reconstruction, microscopic image analysis, computer aided diagnosis, diffusion imaging, functional brain analysis, registration and other related topics.

关键词： image Processing and Computer Vision Pattern Recognition Artificial Intelligence Computer Graphics Health Informatics Imaging / Radiology

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