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Iterative Deep Convolutional Encoder-Decoder Network for Medical image Segmentation

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arXiv 2017年

作者： Kim, Jung Uk Kim, Hak Gu Ro, Yong Man Image and Video Systems Lab School of Electrical Engineering Korea Advanced Institute of Science and Technology Korea Republic of

In this paper, we propose a novel medical image segmentation using iterative deep learning framework. We have combined an iterative learning approach and an encoder-decoder network to improve segmentation results, which enables to precisely localize the regions of interest (ROIs) including complex shapes or detailed textures of medical images in an iterative manner. The proposed iterative deep convolutional encoder-decoder network consists of two main paths: convolutional encoder path and convolutional decoder path with iterative learning. Experimental results show that the proposed iterative deep learning framework is able to yield excellent medical image segmentation performances for various medical images. The effectiveness of the proposed method has been proved by comparing with other state-of-the-art medical image segmentation methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Textures

Comparative validation of machine learning algorithms for surgical workflow and skill analysis with the heichole benchmark

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arXiv 2021年

作者： Wagner, Martin Müller-Stich, Beat-Peter Kisilenko, Anna Tran, Duc Heger, Patrick Mündermann, Lars Lubotsky, David M. Müller, Benjamin Davitashvili, Tornike Capek, Manuela Reinke, Annika Yu, Tong Vardazaryan, Armine Innocent Nwoye, Chinedu Padoy, Nicolas Liu, Xinyang Lee, Eung-Joo Disch, Constantin Meine, Hans Xia, Tong Jia, Fucang Kondo, Satoshi Reiter, Wolfgang Jin, Yueming Long, Yonghao Jiang, Meirui Dou, Qi Heng, Pheng Ann Twick, Isabell Kirtac, Kadir Hosgor, Enes Bolmgren, Jon Lindström Stenzel, Michael von Siemens, Björn Kenngott, Hannes G. Nickel, Felix von Frankenberg, Moritz Mathis-Ullrich, Franziska Maier-Hein, Lena Speidel, Stefanie Bodenstedt, Sebastian Department for General Visceral and Transplantation Surgery Heidelberg University Hospital Im Neuenheimer Feld 420 Heidelberg69120 Germany Heidelberg Im Neuenheimer Feld 460 Heidelberg69120 Germany Data Assisted Solutions Corporate Research & Technology KARL STORZ SE & Co. KG Dr. Karl-Storz-Str. 34 Tuttlingen78332 Germany Im Neuenheimer Feld 223 Heidelberg69120 Germany Im Neuenheimer Feld 223 Heidelberg69120 Germany Faculty of Mathematics and Computer Science Heidelberg University Im Neuenheimer Feld 205 Heidelberg69120 Germany ICube University of Strasbourg CNRS France 300 bd Sébastien Brant - CS 10413 Illkirch CedexF-67412 France IHU Strasbourg France 1 Place de l'hôpital Strasbourg67000 France Sheikh Zayed Institute for Pediatric Surgical Innovation Children's National Hospital 111 Michigan Ave NW WashingtonDC20010 United States University of Maryland College Park 2405 A V Williams Building College ParkMD20742 United States Fraunhofer Institute for Digital Medicine MEVIS Max-von-Laue-Str. 2 Bremen28359 Germany University of Bremen FB3 Medical Image Computing Group ℅ Fraunhofer MEVIS Am Fallturm 1 Bremen28359 Germany Lab for Medical Imaging and Digital Surgery Shenzhen Institute of Advanced Technology Chinese Academy of Sciences Shenzhen518055 China Konika Minolta Inc. JP TOWER 2-7-2 Marunouchi Chiyoda-ku Tokyo100-7015 Japan Wintegral GmbH Ehrenbreitsteiner Str. 36 München80993 Germany Department of Computer Science and Engineering Ho Sin-Hang Engineering Building The Chinese University of Hong Kong Sha Tin NT Hong Kong Caresyntax GmbH Komturstr. 18A Berlin12099 Germany Department of Surgery Salem Hospital of the Evangelische Stadtmission Heidelberg Zeppelinstrasse 11-33 Heidelberg69121 Germany Health Robotics and Automation Laboratory Institute for Anthropomatics and Robotics Karlsruhe Institute of Technology Geb. 40.28 KIT Campus Süd Engler-Bunte-Ring 8 Karlsruhe76131 Germany Medical Faculty Heidelberg Uni

PURPOSE: Surgical workflow and skill analysis are key technologies for the next generation of cognitive surgical assistance systems. These systems could increase the safety of the operation through context-sensitive warnings and semi-autonomous robotic assistance or improve training of surgeons via data-driven feedback. In surgical workflow analysis up to 91% average precision has been reported for phase recognition on an open data single-center video dataset. In this work we investigated the generalizability of phase recognition algorithms in a multi-center setting including more difficult recognition tasks such as surgical action and surgical skill. METHODS: To achieve this goal, a dataset with 33 laparoscopic cholecystectomy videos from three surgical centers with a total operation time of 22 hours was created. labels included framewise annotation of seven surgical phases with 250 phase transitions, 5514 occurences of four surgical actions, 6980 occurences of 21 surgical instruments from seven instrument categories and 495 skill classifications in five skill dimensions. The dataset was used in the 2019 international Endoscopic Vision challenge, sub-challenge for surgical workflow and skill analysis. Here, 12 research teams trained and submitted their machine learning algorithms for recognition of phase, action, instrument and/or skill assessment. RESULTS: F1-scores were achieved for phase recognition between 23.9% and 67.7% (n=9 teams), for instrument presence detection between 38.5% and 63.8% (n=8 teams), but for action recognition only between 21.8% and 23.3% (n=5 teams). The average absolute error for skill assessment was 0.78 (n=1 team). CONCLUSION: Surgical workflow and skill analysis are promising technologies to support the surgical team, but are not solved yet, as shown by our comparison of machine learning algorithms. This novel HeiChole benchmark can be used for comparable evaluation and validation of future work. In future studies, it is of utmost impo

关键词： Learning algorithms

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 — Ex vivo imaging: added value and acquisition

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arXiv 2022年

作者： Schilling, Kurt G. Grussu, Francesco Ianus, Andrada Hansen, Brian Howard, Amy F.D. Barrett, Rachel L.C. Aggarwal, Manisha Michielse, Stijn Nasrallah, Fatima Syeda, Warda Wang, Nian Veraart, Jelle Roebroeck, Alard Bagdasarian, Andrew F. Eichner, Cornelius Sepehrband, Farshid Zimmermann, Jan Soustelle, Lucas Bowman, Christien Tendler, Benjamin C. Hertanu, Andreea Jeurissen, Ben Verhoye, Marleen Frydman, Lucio de Looij, Yohan van Hike, David Dunn, Jeff F. Miller, Karla Landman, Bennett A. Shemesh, Noam Anderson, Adam McKinnon, Emilie Farquharson, Shawna Acqua, Flavio Dell Pierpaoli, Carlo Drobnjak, Ivana Leemans, Alexander Harkins, Kevin D. Descoteaux, Maxime Xu, Duan Huang, Hao Santin, Mathieu D. Grant, Samuel C. Obenaus, Andre Kim, Gene S. Wu, Dan Le Bihan, Denis Blackband, Stephen J. Ciobanu, Luisa Fieremans, Els Bai, Ruiliang Leergaard, Trygve B. Zhang, Jiangyang Dyrby, Tim B. Allan Johnson, G. Cohen-Adad, Julien Budde, Matthew D. Jelescu, Ileana O. Radiology and Radiological Sciences Vanderbilt University Medical Center NashvilleTN United States Vanderbilt University Institute of Imaging Science Vanderbilt University NashvilleTN United States Radiomics Group Vall d’Hebron Institute of Oncology Vall d’Hebron Barcelona Hospital Campus Barcelona Spain Queen Square MS Centre Queen Square Institute of Neurology Faculty of Brain Sciences University College London London United Kingdom Champalimaud Research Champalimaud Foundation Lisbon Portugal Center of Functionally Integrative Neuroscience Aarhus University Aarhus Denmark Department of Bioengineering Imperial College London London United Kingdom FMRIB Centre Wellcome Centre for Integrative Neuroimaging Nuffield Department of Clinical Neurosciences University of Oxford Oxford United Kingdom Department of Neuroimaging Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom NatBrainLab Department of Forensics and Neurodevelopmental Sciences Institute of Psychiatry Psychology and Neuroscience King's College London London United Kingdom Russell H. Morgan Department of Radiology and Radiological Science Johns Hopkins University School of Medicine BaltimoreMD United States Maastricht University Medical Center Maastricht Netherlands The Queensland Brain Institute The University of Queensland Queensland Australia Melbourne Neuropsychiatry Centre The University of Melbourne ParkvilleVIC Australia Department of Radiology and Imaging Sciences Indiana University IN United States Stark Neurosciences Research Institute Indiana University School of Medicine IN United States Center for Biomedical Imaging NYU Grossman School of Medicine New YorkNY United States Faculty of psychology and Neuroscience Maastricht University Maastricht Netherlands Department of Chemical & Biomedical Engineering FAMU-FSU College of Engineering Florida State University TallahasseeFL United States Center for Interdisciplinary Magnetic Re

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio (SNR) and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts for improved microstructure and connectivity characterization. Another major advantage of ex vivo dMRI is the direct comparison with histological data, as a crucial methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a 3-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We first give general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge. © 2022, CC BY.

关键词： image acquisition

Smart Cloud System for Forensic Thermal image Enhancement Using Local and Global Logarithmic Transform Histogram Matching

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Smart Cloud System for Forensic Thermal Image Enhancement Us...

IEEE International Conference on Smart Cloud (SmartCloud)

作者： Viacheslav Voronin Evgenii Semenishchev Vladimir Frants Sos Agaian Lab. “Mathematical methods of image processing and intelligent computer vision systems” Don State Technical University Rostov-on-Don Russian Federation “STANKIN” Moscow State University of Technology Moscow Russian Federation Dept. of Computer Science CUNY/The College of Staten Island Staten Island New York United States

Digital images used in the investigation of a crime often undergo several concurrent enhancement operations for improved automated analysis. The challenges are related to the big size of data and complexity of the forensic image processing. Our purpose is providing a smart cloud system to image processing for PC and Smartphones with limited computation complexity. This paper presents a new thermal image enhancement algorithm based on combined local and global image processing in the frequency domain. The presented approach uses the fact that the relationship between stimulus and perception is logarithmic. The basic idea is to apply logarithmic transform histogram matching with spatial equalization approach on different image blocks. The resulting image is a weighted mean of all processing blocks. The weights for every local and global enhanced image driven through optimization of measure of enhancement (EME). Some presented experimental results illustrate the performance of the proposed cloud system on real thermal images in comparison with the traditional methods.

关键词： Histograms Transforms image enhancement Forensics Adaptive equalizers Clouds

Automatic Segmentation of Kidney and Renal Tumor in CT images Based on 3D Fully Convolutional Neural Network with Pyramid Pooling Module

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Automatic Segmentation of Kidney and Renal Tumor in CT Image...

International Conference on Pattern Recognition

作者： Guanyu Yang Guoqing Li Tan Pan Youyong Kong Jiasong Wu Huazhong Shu Limin Luo Jean-Louis Dillenseger Jean-Louis Coatrieux Lijun Tang Xiaomei Zhu Lab of Image Science and Technology Centre de Recherche en Information Biomédicale Sino-Francais (CRIBs) Nanjing China INSERM-U1099 Centre de Recherche en Information Biomédicalc Sino-Francais (CRIBs) Rennes France Department of Radiology The First Affiliated Hospital of Nanjing Medical University Nanjing China

Renal cancer is one of ten most common cancers in human beings. The laparoscopic partial nephrectomy (LPN) becomes the main therapeutic approach in treating renal cancer. Accurate kidney and tumor segmentation in CT images is a prerequisite step in the surgery planning. However, automatic and accurate kidney and renal tumor segmentation in CT images remains a challenge. In this paper, we propose a new method to perform a precise segmentation of kidney and renal tumor in CT angiography images. This method relies on a three-dimensional (3D) fully convolutional network (FCN) which combines a pyramid pooling module (PPM). The proposed network is implemented as an end-to-end learning system directly on 3D volumetric images. It can make use of the 3D spatial contextual information to improve the segmentation of the kidney as well as the tumor lesion. The experiments conducted on 140 patients show that these target structures can be segmented with a high accuracy. The resulting average dice coefficients obtained for kidney and renal tumor are equal to 0.931 and 0.802 respectively. These values are higher than those obtained from the other two neural networks.

关键词： Tumors Kidney Computed tomography image segmentation Three-dimensional displays Two dimensional displays Convolutional neural networks

Blind Visual Quality Assessment for Smart Cloud-Based Video Storage

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Blind Visual Quality Assessment for Smart Cloud-Based Video ...

IEEE International Conference on Smart Cloud (SmartCloud)

作者： Vladimir Frants Viacheslav Voronin Alexander Zelenskiy Sos Agaian Metrological lab. “Small GIC” Moscow State University of Technology “STANKIN” Moscow Russian Federation Pro-rector for Research Work and R&D Politics Moscow State University of Technology “STANKIN” Moscow Russian Federation Lab. “Mathematical methods of image processing and intelligent computer vision systems.” Don State Technical University Rostov-on-Don Russian Federation Dept. of Computer Science CUNY The College of Staten Island Staten Island New York United States

In this paper, we present a new video quality metric targeted for use within cloud-based video storage systems. Because of the limited capacity of storage solutions currently in use, it is common for stored videos to have low perceived video quality. Ability to predict the quality of coded video sequence in fully automatic fashion is crucial for optimal coding parameters selection. We have developed general quality estimation approach applicable for different kinds of video content and useful for online correction of perceived quality of stored video sequence. Proposed objective video quality metric is designed to have a high level of correlation with human-based quality assessment results. A high level of conformity of predicted video quality to perceived quality level is achieved by using a convolutional neural network trained on a large volume of video data in the framework of generative adversarial learning and combination of carefully selected regularization techniques. Evaluation of developed VQA metric on commonly used datasets shows equal or better correlation with MOS than the current state of the art approaches.

关键词： Quality assessment Measurement Video recording Video sequences Streaming media Training Visualization

An environment for sustainable research software in Germany and beyond: Current state, open challenges, and call for action

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arXiv 2020年

作者： Anzt, Hartwig Bach, Felix Druskat, Stephan Löffler, Frank Loewe, Axel Renard, Bernhard Y. Seemann, Gunnar Struck, Alexander Achhammer, Elke Aggarwal, Piush Appel, Franziska Bader, Michael Brusch, Lutz Busse, Christian Chourdakis, Gerasimos Dabrowski, Piotr W. Ebert, Peter Flemisch, Bernd Friedl, Sven Fritzsch, Bernadette Funk, Maximilian D. Gast, Volker Goth, Florian Grad, Jean-Noël Hermann, Sibylle Hohmann, Florian Janosch, Stephan Kutra, Dominik Linxweiler, Jan Muth, Thilo Peters-Kottig, Wolfgang Rack, Fabian Raters, Fabian H.C. Rave, Stephan Reina, Guido Reißig, Malte Ropinski, Timo Schaarschmidt, Joerg Seibold, Heidi Thiele, Jan P. Uekerman, Benjamin Unger, Stefan Weeber, Rudolf Germany Innovative Computing Lab University of Tennessee KnoxvilleTN United States Department of English Studies Friedrich Schiller University Jena Germany Germany Department of Computer Science Humboldt-Universität zu Berlin Germany Heinz Nixdorf Chair for Distributed Information Systems Friedrich Schiller University Jena Germany Michael Stifel Center Jena Germany Center for Computation and Technology Louisiana State University Baton Rouge United States Germany Robert Koch Institute Berlin Germany Hasso Plattner Institute Faculty of Digital Engineering University of Potsdam Germany Institute for Experimental Cardiovascular Medicine University Heart Centre Freiburg Bad Krozingen Germany Faculty of Medicine University of Freiburg Freiburg Germany Matters of Activity. Image Space Material. Cluster of Excellence at Humboldt-Universität zu Berlin Germany Technische Universität München Germany Language Technology Lab Universität Duisburg-Essen Germany Germany Department of Informatics Technical University of Munich Germany Technische Universität Dresden Germany Deutsches Krebsforschungszentrum Heidelberg Germany Scientific Computing in Computer Science Technical University Munich Germany School of Computing Communication and Business Hochschule für Technik und Wirtschaft Berlin Germany Center for Bioinformatics Saar Saarland Informatics Campus Germany Institute for Modelling Hydraulic and Environmental Systems University of Stuttgart Germany Berlin Institute of Health Germany Scientific Computing Alfred Wegener Institute Helmholtz Center for Polar and Marine Research Bremerhaven Germany Max-Planck-Gesellschaft e.V. Institut für Theoretische Physik und Astrophysik Universität Würzburg Germany Institut für Computerphysik University of Stuttgart Germany University Library University of Stuttgart Germany Universität Bremen Germany Max Planck Institute of Molecular Cell Biology and Genetics Dresden Germany European Molecular Biology Laboratory Heidelb

Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin. Copyright © 2020, The Authors. All rights reserved.

关键词： Software design

Text detection and recognition on traffic panel in roadside imagery

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Text detection and recognition on traffic panel in roadside ...

International Conference of Information and Communication technology for Embedded Systems (IC-ICTES)

作者： Sarwar Khan Somying Thainimit Itsuo Kumazawa Sanparith Marukatat Department of Electrical Engineering Kasetsart University Bangkok Thailand Imaging Science and Engineering Laboratory Tokyo Institute of Technology Tokyo Japan Image Technology Lab (IMG) NECTEC Pathumthani Thailand

ISBN: (纸本)9781509048106

Text recognition has revolutionized the world of image processing and intelligent transportation system (ITS). It opened several possibilities to traditional ITS concept. Advancement in text recognition has made it possible to implement text recognition in ITS. Traffic panel text recognition, a real time application is considered as a key addition to the revolution in modern ITS. This research aims at developing real time application for traffic panel text recognition for English and Thai. Text recognition in this paper is based on Support vector Machine (SVM), KNN and maximally stable extremal regions (MSER). Traffic panel are extracted based on visual appearance. Based on traffic panel background, color mask is applied to remove non text candidates. Multi-level MSER is used for segmentation. Raw pixel value of segmented character is used as feature vector. This system is trained for English and Thai language and then tested on roadside images of traffic panels. The results of different kernels are compared with each other to select best possible kernel for SVM. SVM results are then compared with KNN to find best classifier for this problem. The result shows that proposed system is robust and performs well in challenging environment.

关键词： Text recognition Support vector machines image color analysis image segmentation Character recognition Feature extraction Shape

L-BAND VEGETATION OPTICAL DEPTH FOR CROP PHENOLOGY MONITORING AND CROP YIELD ASSESSMENT

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L-BAND VEGETATION OPTICAL DEPTH FOR CROP PHENOLOGY MONITORIN...

IEEE International Geoscience and Remote Sensing Symposium

作者： D. Chaparro M. Piles M. Vall-llossera A. Camps A. G. Konings D. Entekhabi T. Jagdhuber Universitat Politécnica de Catalunya CommSensLab & IEEC/UPC Barcelona Spain Image Processing Lab (IPL) Universitat de Valéncia Valencia Spain Department of Earth System Science Stanford University Stanford CA United States Department of Civil and Environmental Engineering Massachusetts Institute of Technology Cambridge MA United States German Aerospace Center Microwaves and Radar Institute Wessling

Vegetation Optical Depth (VOD) at L-band is highly sensitive to the water content and above-ground biomass of vegetation. Hence, it has great potential for monitoring crop phenology and for providing crop yield forecasts. Recently, the Multi-Temporal Dual Channel Algorithm (MT-DCA) has been proposed to retrieve L-band VOD from Soil Moisture Active Passive (SMAP) measurements. In previous research, SMAP VOD has been compared to crop phenology and has been used to derive crop yield estimates. Here, we review and expand these initial research studies. In particular, we quantify the capability of VOD to detect different crop stages, and test different VOD metrics (i.e., maximum, range and integrals of VOD) to provide crop yield estimates in the United States Corn Belt. Results show that VOD captures 50% to 70% of crop changes during growing and maturing phases, and that it explains between 44% (in heterogeneous crop regions) and 74% (in homogenous croplands) of final crop yields.

关键词： Agriculture Vegetation mapping Optical sensors Optical scattering L-band Microwave measurement