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Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study

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Journal of Pathology Informatics 2023年 14卷 100308-100308页

作者： Fatemi, Michael Feng, Eric Sharma, Cyril Azher, Zarif Goel, Tarushii Ramwala, Ojas Palisoul, Scott M. Barney, Rachael E. Perreard, Laurent Kolling, Fred W. Salas, Lucas A. Christensen, Brock C. Tsongalis, Gregory J. Vaickus, Louis J. Levy, Joshua J. Department of Computer Science University of Virginia Charlottesville VA United States Thomas Jefferson High School for Science and Technology Alexandria VA United States Department of Computer Science Purdue University West Lafayette IN United States Department of Computer Science Massachusetts Institute of Technology Cambridge MA United States Department of Biomedical Informatics and Medical Education University of Washington Seattle WA United States Emerging Diagnostic and Investigative Technologies Department of Pathology and Laboratory Medicine Dartmouth Health NH United States Dartmouth Cancer Center NH United States Department of Epidemiology Dartmouth College Geisel School of Medicine Hanover NH United States Department of Molecular and Systems Biology Dartmouth College Geisel School of Medicine Hanover NH United States Integrative Neuroscience at Dartmouth (IND) graduate program Dartmouth College Geisel School of Medicine Hanover NH United States Department of Community and Family Medicine Dartmouth College Geisel School of Medicine Hanover NH United States Department of Dermatology Dartmouth Health NH United States Program in Quantitative Biomedical Sciences Dartmouth College Geisel School of Medicine Hanover NH United States

Over 150 000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50 000 individuals will die from CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. Tumor metastasis is the primary factor related to the risk of recurrence and mortality. Yet, screening for nodal and distant metastasis is costly, and invasive and incomplete resection may hamper adequate assessment. Signatures of the tumor-immune microenvironment (TIME) at the primary site can provide valuable insights into the aggressiveness of the tumor and the effectiveness of various treatment options. Spatially resolved transcriptomics technologies offer an unprecedented characterization of TIME through high multiplexing, yet their scope is constrained by cost. Meanwhile, it has long been suspected that histological, cytological, and macroarchitectural tissue characteristics correlate well with molecular information (e.g., gene expression). Thus, a method for predicting transcriptomics data through inference of RNA patterns from whole slide images (WSI) is a key step in studying metastasis at scale. In this work, we collected tissue from 4 stage-III (pT3) matched colorectal cancer patients for spatial transcriptomics profiling. The Visium spatial transcriptomics (ST) assay was used to measure transcript abundance for 17 943 genes at up to 5000 55-micron (i.e., 1–10 cells) spots per patient sampled in a honeycomb pattern, co-registered with hematoxylin and eosin (H&E) stained WSI. The Visium ST assay can measure expression at these spots through tissue permeabilization of mRNAs, which are captured through spatially (i.e., x–y positional coordinates) barcoded, gene specific oligo probes. WSI subimages were extracted around each co-registered Visium spot and were used to predict the expression at these spots using machine learning models. We prototyped and compared several convolutional, transformer, and graph convolutional neural

关键词： Colorectal cancer Deep learning Graph neural network Histomorphology Spatial transcriptomics Transformers

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Chern-Protected Flatband Edge State in Metaphotonics

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Physical Review Letters 2025年第22期134卷 223806-223806页

作者： Jianfeng Chen Yidong Zheng Shuihua Yang Andrea Alù Zhi-Yuan Li Cheng-Wei Qiu Department of Electrical and Computer Engineering National University of Singapore Singapore Singapore School of Physics and Optoelectronics South China University of Technology Guangzhou 510640 China Physics Program Graduate Center City University of New York New York New York 10016 USA Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA

Two-dimensional Dirac semimetals feature flatband edge states but a zero Chern number, while Chern insulators support one-way edge states associated with a nonzero Chern number. Here, we demonstrate a two-dimensional photonic crystal combining the response of a semimetal and of a Chern insulator, termed a Chern semimetal. This photonic semimetal is characterized by a nonzero Chern number, simultaneously hosting both a flatband edge state and a one-way edge state. We experimentally realize such a photonic Chern semimetal using a gyromagnetic photonic crystal with programmable magnetic bias, tailoring its second-neighbor coupling within each sublattice. We also verify the ability to control over the light speed while preserving topological protection. Our findings open new avenues toward exploring topological phases and their applications across fermionic and bosonic systems, providing an exciting platform for nanophotonic applications and a playground for topological physics discoveries.

关键词： Nanophotonics

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Journal of the Formosan Medical Association 2024年第2期123卷 159-178页

作者： Lee, Pei-Lin Wu, Yen-Wen Cheng, Hao-Min Wang, Cheng-Yi Chuang, Li-Pang Lin, Chou-Han Hang, Liang-Wen Yu, Chih-Chieh Hung, Chung-Lieh Liu, Ching-Lung Chou, Kun-Ta Su, Mao-Chang Cheng, Kai-Hung Huang, Chun-Yao Hou, Charles Jia-Yin Chiu, Kuo-Liang Center of Sleep Disorder National Taiwan University Hospital Taipei Taiwan School of Medicine College of Medicine National Taiwan University Taipei Taiwan Division of Cardiology Cardiovascular Medical Center Far Eastern Memorial Hospital New Taipei City Taiwan School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan Division of Faculty Development Taipei Veterans General Hospital Taipei Taiwan PhD Program of Interdisciplinary Medicine (PIM) National Yang Ming Chiao Tung University College of Medicine Taipei Taiwan Department of Internal Medicine Cardinal Tien Hospital and School of Medicine College of Medicine Fu Jen Catholic University New Taipei City Taiwan Sleep Center Department of Thoracic Medicine Chang Gung Memorial Hospital Linkou Taiwan School of Medicine Chang Gung University Tauyan Taiwan Division of Respirology Department of Internal Medicine Far Eastern Memorial Hospital New Taipei City Taiwan School of Nursing & Graduate Institute of Nursing China Medical University Taichung Taiwan Sleep Medicine Center China Medical University Hospital Taichung Taiwan Division of Cardiology Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan Cardiovascular Center MacKay Memorial Hospital Taipei Taiwan Institute of Biomedical Sciences Mackay Medical College Taipei Taiwan Division of Chest Departments of Internal Medicine MacKay Memorial Hospital Taipei Taiwan MacKay Medical College New Taipei City Taiwan Division of Clinical Respiratory Physiology Department of Chest Medicine Taipei Veterans General Hospital Taipei Taiwan Sleep Center Division of Pulmonary and Critical Care Medicine Department of Internal Medicine Kaohsiung Chang Gung Memorial Hospital Kaohsiung Taiwan Department of Respiratory Care Chang Gung University of Science and Technology Chiayi Taiwan Kao-Ho Hospital Kaohsiung Taiwan Division of Cardiology Department of Internal Medicine E-Da Hospital Kaohsiung Taiwan Division of Cardio

Sleep disordered breathing (SDB) is highly prevalent and may be linked to cardiovascular disease in a bidirectional manner. The Taiwan Society of Cardiology, Taiwan Society of Sleep Medicine and Taiwan Society of Pulmonary and Critical Care Medicine established a task force of experts to evaluate the evidence regarding the assessment and management of SDB in patients with atrial fibrillation (AF), hypertension and heart failure with reduced ejection fraction (HFrEF). The GRADE process was used to assess the evidence associated with 15 formulated questions. The task force developed recommendations and determined strength (Strong, Weak) and direction (For, Against) based on the quality of evidence, balance of benefits and harms, patient values and preferences, and resource use. The resulting 11 recommendations are intended to guide clinicians in determining which the specific patient-care strategy should be utilized by clinicians based on the needs of individual patients. © 2023 Formosan Medical Association

关键词： Atrial fibrillation Continuous positive airway pressure Heart failure Hypertension Sleep disordered breathing

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Nonreciprocal photonic topological order driven by uniform optical pumping

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Physical Review B 2020年第10期102卷 100303(R)-100303(R)页

作者： Robert Duggan Sander A. Mann Andrea Alù Department of Electrical and Computer Engineering The University of Texas at Austin Austin Texas 78712 USA Photonics Initiative CUNY Advanced Science Research Center New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10026 USA

Photonic topological insulators (PTIs) have raised significant interest in recent years, in part because of their protected edge propagation. Most PTI realizations have been based on reciprocal platforms, with protection only from symmetry-preserving defects. Nonreciprocal PTIs protect against arbitrary disorder, but their implementation requires breaking reciprocity either through a magnetic bias or complex spatiotemporal modulation schemes. Here, we demonstrate that nonreciprocal topological protection can be achieved by optically pumping a nonlinear photonic crystal with a uniform bias field, drastically simplifying the implementation of quantum-Hall-like topological protection in silicon-compatible platforms for classical and quantum optics.

关键词： Metamaterials Nonlinear optics Topological insulators

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Comparison of endoscopic third ventriculostomy versus cerebrospinal fluid shunt procedures for the treatment of pediatric hydrocephalus in Taiwan

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Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery 2024年第9期40卷 2883-2891页

作者： Shu-Mei Chen Li-Ying Chen Jiann-Her Lin Nicole Salazar Tu-Hsueh Yeh Wei-Lun Lo Tai-Ngar Lui Yi-Chen Hsieh Li-Nien Chien Department of Neurosurgery Taipei Medical University Hospital Taipei Medical University Taipei Taiwan. Department of Surgery School of Medicine Taipei Medical University Taipei Taiwan. Health Data Analytics and Statistics Center Office of Data Science Taipei Medical University Taipei Taiwan. Julius L. Chambers Biomedical/Biotechnology Institute and Department of Biological & Biomedical Sciences North Carolina Central University Durham NC USA. Department of Neurology Taipei Medical University Hospital Taipei Taipei Medical University Taipei Taiwan. Department of Neurology School of Medicine College of Medicine Taipei Medical University Taipei Taiwan. Department of Neurosurgery Shuang Ho Hospital Taipei Medical University Taipei Taiwan. The PhD Program in Medical Neuroscience College of Medical Science and Technology Taipei Medical University 250 Wu-Hsing Street Taipei Taiwan. ychsieh@tmu.edu.tw. Institute of Health and Welfare Policy College of Medicine National Yang Ming Chiao Tung University No.155 Sec. 2 Linong St. Beitou District Taipei Taiwan. linien.chien@nycu.edu.tw. Graduate Institute of Data Science College of Management Taipei Medical University Taipei Taiwan. linien.chien@nycu.edu.tw.

PURPOSE:Pediatric hydrocephalus is the most common cause of surgically treatable neurological disease in children. Controversies exist whether endoscopic third ventriculostomy (ETV) or cerebrospinal fluid (CSF) shunt placement is the most appropriate treatment for pediatric hydrocephalus. This study aimed to compare the risk of re-operation and death between the two procedures. METHODS:We performed a retrospective population-based cohort study and included patients younger than 20-years-old who underwent CSF shunt or ETV for hydrocephalus from the Taiwan National Health Insurance Research Database. RESULTS:A total of 3,555 pediatric patients from 2004 to 2017 were selected, including 2,340 (65.8%) patients that received CSF shunt placement and 1215 (34.2%) patients that underwent ETV. The incidence of all-cause death was 3.31 per 100 person-year for CSF shunt group and 2.52 per 100 person-year for ETV group, with an adjusted hazard ratio (HR) of 0.79 (95% confidence interval [CI] = 0.66-0.94, p = 0.009). The cumulative incidence competing risk for reoperation was 31.2% for the CSF shunt group and 26.4% for the ETV group, with an adjusted subdistribution HR of 0.82 (95% CI = 0.70-0.96, p = 0.015). Subgroup analysis showed that ETV was beneficial for hydrocephalus coexisting with brain or spinal tumor, central nervous system infection, and intracranial hemorrhage. CONCLUSION:Our data indicates ETV is a better operative procedure for pediatric hydrocephalus when advanced surgical techniques and instruments are available.

关键词： Cerebrospinal shunt Pediatric hydrocephalus Reoperation Third ventriculostomy

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Low-Velocity-Favored Transition Radiation

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Physical Review Letters 2023年第11期131卷 113002-113002页

作者： Jialin Chen Ruoxi Chen Fuyang Tay Zheng Gong Hao Hu Yi Yang Xinyan Zhang Chan Wang Ido Kaminer Hongsheng Chen Baile Zhang Xiao Lin Interdisciplinary Center for Quantum Information State Key Laboratory of Extreme Photonics and Instrumentation ZJU-Hangzhou Global Scientific and Technological Innovation Center College of Information Science & Electronic Engineering Zhejiang University Hangzhou 310027 China International Joint Innovation Center the Electromagnetics Academy at Zhejiang University Zhejiang University Haining 314400 China Department of Electrical and Computer Engineering Technion-Israel Institute of Technology Haifa 32000 Israel Department of Electrical and Computer Engineering Rice University Houston Texas 77005 USA Applied Physics Graduate Program Smalley-Curl Institute Rice University Houston Texas 77005 USA School of Electrical and Electronic Engineering Nanyang Technological University Singapore 639798 Singapore Department of Physics University of Hong Kong Hong Kong 999077 China Key Lab of Advanced Micro/Nano Electronic Devices & Smart Systems of Zhejiang Jinhua Institute of Zhejiang University Zhejiang University Jinhua 321099 China Shaoxing Institute of Zhejiang University Zhejiang University Shaoxing 312000 China Division of Physics and Applied Physics School of Physical and Mathematical Sciences Nanyang Technological University Singapore 637371 Singapore Centre for Disruptive Photonic Technologies Nanyang Technological University Singapore 637371 Singapore

When a charged particle penetrates through an optical interface, photon emissions emerge—a phenomenon known as transition radiation. Being paramount to fundamental physics, transition radiation has enabled many applications from high-energy particle identification to novel light sources. A rule of thumb in transition radiation is that the radiation intensity generally decreases with the decrease of particle velocity v; as a result, low-energy particles are not favored in practice. Here, we find that there exist situations where transition radiation from particles with extremely low velocities (e.g., v/c<10−3) exhibits comparable intensity as that from high-energy particles (e.g., v/c=0.999), where c is the light speed in free space. The comparable radiation intensity implies an extremely high photon extraction efficiency from low-energy particles, up to 8 orders of magnitude larger than that from high-energy particles. This exotic phenomenon of low-velocity-favored transition radiation originates from the interference of the excited Ferrell-Berreman modes in an ultrathin epsilon-near-zero slab. Our findings may provide a promising route toward the design of integrated light sources based on low-energy electrons and specialized detectors for beyond-standard-model particles.

关键词： Atom or molecule scattering from surfaces Atomic & molecular collisions Cherenkov radiation Crystal optics Electron beams & optics Light-matter interaction Optical sources & detectors Optical transient phenomena Plasmonics

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Phase-induced frequency conversion and doppler effect with time-modulated metasurfaces

arXiv

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arXiv 2021年

作者： Ramaccia, Davide Sounas, Dimitrios L. Alù, Andrea Toscano, Alessandro Bilotti, Filiberto Department of Engineering ROMA TRE University Via Vito Volterra 62 Rome00146 Italy Department of Electrical and Computer Engineering Wayne State University DetroitMI48202 United States Photonics Initiative Advanced Science Research Center Physics Program Graduate Center Department of Electrical Engineering City College City University of New York New YorkNY10031 United States

Metasurfaces consisting of electrically thin and densely packed planar arrays of subwavelength elements enable an unprecedented control of the impinging electromagnetic fields. Spatially modulated metasurfaces can efficiently tailor the spatial distribution of these fields with great flexibility. Similarly, time modulated metasurfaces can be successfully used to manipulate the frequency content and time variations of the impinging field. In this paper, we present time-modulated reflective metasurfaces that cause a frequency shift to the impinging radiation, thus realizing an artificial Doppler effect in a non-moving electrically thin structure. Starting from the theoretical analysis, we analytically derive the required time modulation of the surface admittance to achieve this effect, and present a realistic time-varying structure, based on a properly designed and dynamically tuned high-impedance surface. It is analytically and numerically demonstrated that the field emerging from the metasurface is up-/down-converted in frequency according to the modulation profile of the metasurface. The proposed metasurface concept, enabling a frequency modulation of the electromagnetic field "on-the-fly", may find application in telecommunication, radar, and sensing scenarios. Copyright © 2021, The Authors. All rights reserved.

关键词： Doppler effect

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*** as digital platform for vegetation analysis and estimation of carbon stock in KEHATI aqua park

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AIP Conference Proceedings 2024年第1期3026卷

作者： Nanda Satya Nugraha Dian Pratama Putra Mohammad Prasanto Bimantio Amallia Ferhat Rama Zakaria Rudi Nirwantono Teddy Suparyanto Bens Pardamean Faculty of Forestry Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agriculture Institute of Agriculture STIPER Yogyakarta Indonesia 55282 Faculty of Agricultural Technology Institute of Agriculture STIPER Yogyakarta Indonesia 55282 PT. Tirta Investama Pabrik Klaten Klaten Central Java Indonesia 57474 Bioinformatics & Data Science Research Center Bina Nusantara University Jakarta Indonesia 1148 Biotechnology Department Faculty of Engineering Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program - Master of Computer Science Program Bina Nusantara University Jakarta Indonesia 11480

KEHATI AQUA Park is one of the green areas managed by PT. Tirta Investama Klaten (Klaten Factory). This area is located in Wangen and Ponggok Villages, Polanharjo District, Klaten Regency, Central Java, and is an integral part of the company’s seriousness in carbon reduction movement. When maintenance of the area is important for the sustainability of the park, there is however no data on the trees inventory in the area. Therefore, this study aims to invent the trees at KEHATI AQUA Park and evaluate the potential of the area to become a carbon sink using *** application. This study was conducted at the KEHATI AQUA Park. The census method was performed to collect tree data, and the result was recorded in *** application. The carbon stock calculation was estimated using the application according to the tree data submitted in the application. The study included a total of 1048 plantation spots in 51 tree species. From those numbers, about 738 trees existed, and the remaining spots were blank spaces. Based on the condition of the trees, those were 660 good trees, 17 dry trees, and 61 under pest infection. The carbon stock estimation at KEHATI AQUA Park Klaten in the next five years (2026) is around 40 tons of carbon. Therefore, it can be concluded that the park is valuable as an area to preserve biodiversity and as a carbon sink.

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Application of Deep Artificial Neural Network to Model Characteristic Fluctuation of Multi-Channel Gate-All-Around Silicon Nanosheet and Nanofin MOSFETs Induced by Random Nanosized Metal Grains

Application of Deep Artificial Neural Network to Model Chara...

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IEEE Electron Devices Technology and Manufacturing Conference (EDTM)

作者： Sagarika Dash Yiming Li Wen-Li Sung Parallel and Scientific Computing Laboratory National Yang-Ming Chiao Tung University Hsinchu Taiwan Electrical Engineering and Computer Science International Graduate Program National Yang-Ming Chiao Tung University Hsinchu Taiwan Institute of Communications Engineering National Yang-Ming Chiao Tung University Hsinchu Taiwan Department of Electronics and Electrical Engineering National Yang-Ming Chiao Tung University Hsinchu Taiwan Institute of Biomedical Engineering National Yang-Ming Chiao Tung University Hsinchu Taiwan Center for mm Wave Smart Radar System and Technologies National Yang-Ming Chiao Tung University Hsinchu Taiwan

In this work, we propose a deep artificial neural network (D-ANN) to estimate the work function fluctuation (WKF) on 4-channel stacked gate-all-around (GAA) silicon (Si) nanosheet (NS) and nanofin (NF) MOSFET devices for the first time. The 2-layered simple deep model can well predict the transfer characteristics for both NS/NF FET with a large number of (128) input features, utilizing considerably lesser (1100 samples) data uniformly. The resultant model is evaluated by the $\mathrm{R}^{2}$ score and RMSE to witness its competency and the average error is $< 4\%$ . We do also discuss the circuit simulation possibility by applying the ANN approach.

关键词： Semiconductor device modeling MOSFET Gallium arsenide Artificial neural networks Predictive models Logic gates Silicon

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Global Wheat Head Detection 2021:An Improved Dataset for Benchmarking Wheat Head Detection Methods

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Plant Phenomics 2021年第1期3卷 277-285页

作者： Etienne David Mario Serouart Daniel Smith Simon Madec Kaaviya Velumani Shouyang Liu Xu Wang Francisco Pinto Shahameh Shafiee Izzat SATahir Hisashi Tsujimoto Shuhei Nasuda Bangyou Zheng Norbert Kirchgessner Helge Aasen Andreas Hund Pouria Sadhegi-Tehran Koichi Nagasawa Goro Ishikawa Sébastien Dandrifosse Alexis Carlier Benjamin Dumont Benoit Mercatoris Byron Evers Ken Kuroki Haozhou Wang Masanori Ishii Minhajul ABadhon Curtis Pozniak David Shaner LeBauer Morten Lillemo Jesse Poland Scott Chapman Benoit de Solan Frédéric Baret Ian Stavness Wei Guo Arvalis Institut du Végétal3 Rue Joseph et Marie Hackin75116 ParisFrance UMR1114 EMMAH INRAECentre PACABâtiment ClimatDomaine Saint-Paul228 Route de l’AérodromeCS 4050984914 Avignon CedexFrance School of Food and Agricultural Sciences The University of QueenslandGatton4343 QLDAustralia Hiphen SAS 120 Rue Jean DaussetAgroparcBâtiment Technicité84140 AvignonFrance Plant Phenomics Research Center Nanjing Agricultural UniversityNanjingChina Wheat Genetics Resource Center Dep.of Plant PathologyKansas State Univ.4024 Throckmorton Plant Sciences CenterManhattanKansasUSA Global Wheat Program International Maize and Wheat Improvement Centre(CIMMYT)MexicoD.F.Mexico Faculty of Biosciences Norwegian University of Life SciencesP.O.Box 5003NO-1432ÅsNorway Agricultural Research Corporation Wheat Research ProgramP.O.Box 126Wad MedaniSudan Arid Land Research Center Tottori UniversityTottori 680-0001Japan Laboratories of Plant Genetics and Plant Breeding Graduate School of AgricultureKyoto UniversityJapan CSIRO Agriculture and Food Queensland Biosciences Precinct306 Carmody RoadSt Lucia4067 QLDAustralia Institute of Agricultural Sciences ETH ZurichUniversitätstrasse 28092 ZurichSwitzerland Plant Sciences Department Rothamsted ResearchHarpendenUK Institute of Crop Science National Agriculture and Food Research OrganizationJapan Hokkaido Agricultural Research Center National Agriculture and Food Research OrganizationJapan Biosystems Dynamics and Exchanges TERRA Teaching and Research CenterGembloux Agro-Bio TechUniversity of Liège5030 GemblouxBelgium Plant Sciences TERRA Teaching and Research CenterGembloux Agro-Bio TechUniversity of Liège5030 GemblouxBelgium Graduate School of Agricultural and Life Sciences The University of Tokyo1-1-1 Midori-choNishitokyo CityTokyoJapan Department of Computer Science University of SaskatchewanCanada Department of Plant Sciences University of SaskatchewanCanada College of Agriculture and Life Sciences University of ArizonaTucsonArizona

The Global Wheat Head Detection(GWHD)dataset was created in 2020 and has assembled 193,634 labelled wheat heads from 4700 RGB images acquired from various acquisition platforms and 7 countries/*** an associated competition hosted in Kaggle,GWHD_2020 has successfully attracted attention from both the computer vision and agricultural science *** this first experience,a few avenues for improvements have been identified regarding data size,head diversity,and label *** address these issues,the 2020 dataset has been reexamined,relabeled,and complemented by adding 1722 images from 5 additional countries,allowing for 81,553 additional wheat *** now release in 2021 a new version of the Global Wheat Head Detection dataset,which is bigger,more diverse,and less noisy than the GWHD_2020 version.

关键词： Wheat adding release

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