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Analyzing Nitrogen Effects on Rice Panicle Development by Panicle Detection and Time-Series Tracking

Plant Phenomics 2023年第2期5卷 253-267页

作者： Qinyang Zhou Wei Guo Na Chen Ze Wang Ganghua Li Yanfeng Ding seishi ninomiya Yue Mu College of Agriculture Academy for Advanced Interdisciplinary StudiesCollaborative Innovation Center for Modern Crop Production co-sponsored by Province and MinistryNanjing Agricultural UniversityNanjing 210095China Graduate School of Agricultural and Life Sciences The University of Tokyo1-1-1 Midori-choNishi-TokyoTokyo 188-0002Japan

Detailed observation of the phenotypic changes in rice panicle substantially helps us to understand the yield formation.In recent studies,phenotyping of rice panicles during the heading–flowering stage still lacks comprehensive analysis,especially of panicle development under different nitrogen treatments.In this work,we proposed a pipeline to automatically acquire the detailed panicle traits based on time-series images by using the YOLO v5,ResNet50,and DeepSORT models.Combined with field observation data,the proposed method was used to test whether it has an ability to identify subtle differences in panicle developments under different nitrogen treatments.The result shows that panicle counting throughout the heading–flowering stage achieved high accuracy(R^(2)=0.96 and RMSE=1.73),and heading date was estimated with an absolute error of 0.25 days.In addition,by identical panicle tracking based on the time-series images,we analyzed detailed flowering phenotypic changes of a single panicle,such as flowering duration and individual panicle flowering time.For rice population,with an increase in the nitrogen application:panicle number increased,heading date changed little,but the duration was slightly extended;cumulative flowering panicle number increased,rice flowering initiation date arrived earlier while the ending date was later;thus,the flowering duration became longer.For a single panicle,identical panicle tracking revealed that higher nitrogen application led to earlier flowering initiation date,significantly longer flowering days,and significantly longer total duration from vigorous flowering beginning to the end(total DBE).However,the vigorous flowering beginning time showed no significant differences and there was a slight decrease in daily DBE.

关键词： heading identical flowering

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Next-generation regenerative therapy for ischemic stroke using peripheral blood mononuclear cells

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Neural Regeneration Research 2024年第11期19卷 2341-2342页

作者： Masato Kanazawa Itaru ninomiya Yutaka Otsu Masahiro Hatakeyama Department of Neurology Brain Research InstituteNiigata UniversityNiigataJapan

Stroke is the second leading cause of death and the third leading cause of disability worldwide after heart disease.Researchers predict that stroke deaths and permanent disabilities will increase worldwide by the year 2050.Single-target therapies may be insufficient,because ischemic cerebral injury involves several mechanisms.Cell-mediated therapies are ideal,because they target multiple cell types to enhance protection and recovery.

关键词： ischemic death cerebral

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Plant Phenomics:Emerging Transdisciplinary Science

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Plant Phenomics 2019年第1期1卷 39-41页

作者： seishi ninomiya Frédéric Baret Zong-Ming(Max)Cheng University of Tokyo TokyoJapan French National Institute of Agricultural Research ParisFrance Nanjing Agricultural University NanjingChina University of Tennessee TNUSA

Humankind is facing an unprecedented challenge to produce enough food for the coming decades because of population growth and increase in the average demand per capita,changes in climate conditions,and limitations in arable land area,as well as pressure on the water and resources.Two main avenues should be concurrently taken to increase crop productivity:improving genetics to get more efficient and resilient crops and developing optimal crop management practices.The description and understanding of crop functioning will therefore be instrumental both for genetic improvement and crop management.It will help to associate functional traits with the genome which will accelerate genetic progress by having more efficient techniques to design ideotypes adapted to particular pedoclimatic and crop management conditions and create them from the available genetic diversity.

关键词： crops Plant adapted

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How Useful Is Image-Based Active Learning for Plant Organ Segmentation?

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Plant Phenomics 2022年第1期4卷 384-394页

作者： Shivangana Rawat Akshay L.Chandra Sai Vikas Desai Vineeth N.Balasubramanian seishi ninomiya Wei Guo Department of Computer Science and Engineering Indian Institute of TechnologyHyderabadIndia Department of Computer Science University of FreiburgGermany Graduate School of Agricultural and Life Sciences The University of TokyoJapan

Training deep learning models typically requires a huge amount of labeled data which is expensive to acquire,especially in dense prediction tasks such as semantic segmentation.Moreover,plant phenotyping datasets pose additional challenges of heavy occlusion and varied lighting conditions which makes annotations more time-consuming to obtain.Active learning helps in reducing the annotation cost by selecting samples for labeling which are most informative to the model,thus improving model performance with fewer annotations.Active learning for semantic segmentation has been well studied on datasets such as PASCAL VOC and Cityscapes.However,its effectiveness on plant datasets has not received much importance.To bridge this gap,we empirically study and benchmark the effectiveness of four uncertainty-based active learning strategies on three natural plant organ segmentation datasets.We also study their behaviour in response to variations in training configurations in terms of augmentations used,the scale of training images,active learning batch sizes,and train-validation set splits.

关键词： consuming lighting sizes

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Superficial femoral artery pseudoaneurysm at implantation site of drug eluting stent discovered due to bacteremia:A case report

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World Journal of Clinical Cases 2024年第17期12卷 3194-3199页

作者： Takafumi Akai Shintarou ninomiya Takanori Kaneko Department of Vascular Surgery Asahi General HospitalChibaAsahi 289-2511Japan

BACKGROUND Drug-eluting stents(DES)are used to treat lower extremity arterial disease.During DES treatment,aneurysmal degeneration occasionally occurs,especially with fluoropolymer-based DES.However,the incidence of pseudoaneurysms after DES placement is rarely reported in the lower extremity region,although there have been several reports on pseudoaneurysm formation after DES placement in the coronary artery region.CASE SUMMARY We report the case of a 64-year-old man who presented with fever and pain in his left hand after dialysis.Bacteremia was diagnosed by blood culture,and after admission,he developed pain on the medial side of the right thigh.A pseudoaneurysm was observed in the right superficial femoral artery(SFA)at the proximal end of a previously placed DES.The bacteremia was thought to have been caused by a pseudoaneurysm of the left superficial brachial artery,and the pseudoaneurysm of the left superficial brachial artery was removed after antibiotic treatment.The pseudoaneurysm of the right SFA rapidly expanded after admission,but the expansion rate was reduced after infection control.Seven months after the first admission,the pseudoaneurysm of the left SFA was re-moved and in situ revascularization performed using a rifampicin-soaked Dacron graft.CONCLUSION Although pseudoaneurysm after DES placement in the lower extremity region is rare,it must be considered in patients with bacteremia.

关键词： Pseudoaneurysm Drug eluting stent Superficial femoral artery Bacteremia Revascularization Case report

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Immunotherapy for esophageal cancer:Where are we now and where can we go

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World Journal of Gastroenterology 2024年第19期30卷 2496-2501页

作者： Yoshiaki Shoji Kazuo Koyanagi Kohei Kanamori Kohei Tajima Mika Ogimi Yamato ninomiya Miho Yamamoto Akihito Kazuno Kazuhito Nabeshima Takayuki Nishi Masaki Mori Department of Gastroenterological Surgery Tokai University School of MedicineKanagawa 259-1193Japan

Immune checkpoint inhibitor therapy has dramatically improved patient prognosis,and thereby transformed the treatment in various cancer types including esophageal squamous cell carcinoma(ESCC)in the past decade.Monoclonal antibodies that selectively inhibit programmed cell death-1(PD-1)activity has now become standard of care in the treatment of ESCC in metastatic settings,and has a high expectation to provide clinical benefit during perioperative period.Further,anti-cytotoxic T-lymphocyte–associated protein 4(CTLA-4)monoclonal antibody has also been approved in the treatment of recurrent/metastatic ESCC in combination with anti-PD-1 antibody.Well understanding of the existing evidence of immune-based treatments for ESCC,as well as recent clinical trials on various combinations with chemotherapy for different clinical settings including neoadjuvant,adjuvant,and metastatic diseases,may provide future prospects of ESCC treatment for better patient outcomes.

关键词： Esophageal cancer Immunotherapy Immune checkpoint inhibitor Programmed cell death-1 Anti-cytotoxic T-lymphocyte-associated protein 4 Neoadjuvant therapy Adjuvant therapy Clinical trials Combination therapy

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Easy MPE:Extraction of Quality Microplot Images for UAV-Based High-Throughput Field Phenotyping

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Plant Phenomics 2019年第1期1卷 30-38页

作者： Léa Tresch Yue Mu Atsushi Itoh Akito Kaga Kazunori Taguchi Masayuki Hirafuji seishi ninomiya Wei Guo International Field Phenomics Research Laboratory Institute for Sustainable Agro-Ecosystem ServicesGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan 2Montpellier SupAgroMontpellierFrance 3Plant Phenomics Research CenterNanjing Agricultural UniversityNanjingChina 4Memuro Upland Farming Research StationHokkaido Agricultural Research CenterNational Agriculture and Food Research OrganizationHokkaidoJapan 5Institute of Crop ScienceNational Agriculture and Food Research OrganizationTsukuba CityIbarakiJapan

Microplot extraction(PE)is a necessary image processing step in unmanned aerial vehicle-(UAV-)based research on breeding fields.At present,it is manually using ArcGIS,QGIS,or other GIS-based software,but achieving the desired accuracy is timeconsuming.We therefore developed an intuitive,easy-to-use semiautomatic program for MPE called Easy MPE to enable researchers and others to access reliable plot data UAV images of whole fields under variable field conditions.The program uses four major steps:(1)binary segmentation,(2)microplot extraction,(3)production of∗.shp files to enable further file manipulation,and(4)projection of individual microplots generated from the orthomosaic back onto the raw aerial UAV images to preserve the image quality.Crop rows were successfully identified in all trial fields.The performance of the proposed method was evaluated by calculating the intersection-over-union(IOU)ratio between microplots determined manually and by Easy MPE:the average IOU(±SD)of all trials was 91%(±3).

关键词： enable image union

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Characterization of peach tree crown by using high-resolution images from an unmanned aerial vehicle

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Horticulture Research 2018年第1期5卷 22-31页

作者： Yue Mu Yuichiro Fujii Daisuke Takata Bangyou Zheng Koji Noshita Kiyoshi Honda seishi ninomiya Wei Guo International Field Phenomics Research Laboratory Institute for Sustainable Agro-ecosystem ServicesThe University of Tokyo1-1-1 Midori-choNishi-TokyoTokyo188-0002Japan Research Institute for Agriculture Okayama Prefectural Technology Center for AgricultureForestry and Fisheries1174-1 KodaokiAkaiwaOkayama709-0801Japan Fukushima University 1 KanayagawaFukushimaFukushima960-1248Japan CSIRO Agriculture and Food Queensland Bioscience Precinct306 Carmody RoadSt.LuciaQLD4067Australia JST PRESTO Kawaguchi Center Building4-1-8 HonchoKawaguchiSaitama332-0012Japan Graduate School of Agricultural and Life Sciences The University of Tokyo1-1-1 YayoiBunkyoTokyo113-8657Japan International Digital Earth Applied Science Research Center Chubu University1200 MatsumotochoKasugaiAichi-ken487-8501Japan

In orchards, measuring crown characteristics is essential for monitoring the dynamics of tree growth and optimizing farm management. However, it lacks a rapid and reliable method of extracting the features of trees with an irregular crown shape such as trained peach trees. Here, we propose an efficient method of segmenting the individual trees and measuring the crown width and crown projection area (CPA) of peach trees with time-series information, based on gathered images. The images of peach trees were collected by unmanned aerial vehicles in an orchard in Okayama, Japan, and then the digital surface model was generated by using a Structure from Motion (SfM) and Multi-View Stereo (MVS) based software. After individual trees were identified through the use of an adaptive threshold and marker-controlled watershed segmentation in the digital surface model, the crown widths and CPA were calculated, and the accuracy was evaluated against manual delineation and field measurement, respectively. Taking manual delineation of 12 trees as reference, the root-mean-square errors of the proposed method were 0.08 m (R^(2) = 0.99) and 0.15 m (R^(2) = 0.93) for the two orthogonal crown widths, and 3.87 m2 for CPA (R^(2) = 0.89), while those taking field measurement of 44 trees as reference were 0.47 m (R^(2) = 0.91), 0.51 m (R^(2) = 0.74), and 4.96 m2 (R^(2) = 0.88). The change of growth rate of CPA showed that the peach trees grew faster from May to July than from July to September, with a wide variation in relative growth rates among trees. Not only can this method save labour by replacing field measurement, but also it can allow farmers to monitor the growth of orchard trees dynamically.

关键词： crown tree watershed

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The Japanese agricultural case-base InformationRetrieval System using Semi-Discrete MatrixDecomposition

The Japanese agricultural case-base InformationRetrieval Sys...

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国际农业工程大会

作者： seishi ninomiya HeadNetwork Computing Lab. Dept. Information Science ＆ Technology National Agriculture Research Center 3-1-1 Kannondai Tsukuba City Ibaraki 305-8666 Japan

＜正＞ In this paper, we present a Japanese document retrieval system that uses a new method of matrix decomposition.In order to improve the precision and recall ratio in the document retrieval system, a mathematical ...

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A Weakly Supervised Deep Learning Framework for Sorghum Head Detection and Counting

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Plant Phenomics 2019年第1期1卷 1-14页

作者： Sambuddha Ghosal Bangyou Zheng Scott CChapman Andries BPotgieter David RJordan Xuemin Wang Asheesh KSingh Arti Singh Masayuki Hirafuji seishi ninomiya Baskar Ganapathysubramanian Soumik Sarkar Wei Guo Department of Mechanical Engineering Iowa State UniversityAmesIAUSA 2Department of Computer ScienceIowa State UniversityAmesIAUSA 3CSIRO Agriculture and FoodSt.LuciaQLDAustralia 4School of Agriculture and Food SciencesThe University of QueenslandGattonQLD 4343Australia 5Queensland Alliance for Agriculture and Food Innovation(QAAFI)The University of QueenslandGattonQLDAustralia 6Queensland Alliance for Agriculture and Food Innovation(QAAFI)The University of QueenslandWarwickQLDAustralia 7Department of AgronomyIowa State UniversityAmesIAUSA 8International Field Phenomics Research LaboratoryInstitute for Sustainable Agro-Ecosystem Services

The yield of cereal crops such as sorghum(Sorghum bicolor L.Moench)depends on the distribution of crop-heads in varying branching arrangements.Therefore,counting the head number per unit area is critical for plant breeders to correlate with the genotypic variation in a specific breeding field.However,measuring such phenotypic traitsmanually is an extremely labor-intensive process and suffers from low efficiency and human errors.Moreover,the process is almost infeasible for large-scale breeding plantations or experiments.Machine learning-based approaches like deep convolutional neural network(CNN)based object detectors are promising tools for efficient object detection and counting.However,a significant limitation of such deep learningbased approaches is that they typically require a massive amount of hand-labeled images for training,which is still a tedious process.Here,we propose an active learning inspired weakly supervised deep learning framework for sorghum head detection and counting from UAV-based images.We demonstrate that it is possible to significantly reduce human labeling effort without compromising final model performance(𝑅2 between human count and machine count is 0.88)by using a semitrained CNN model(i.e.,trained with limited labeled data)to perform synthetic annotation.In addition,we also visualize key features that the network learns.This improves trustworthiness by enabling users to better understand and trust the decisions that the trained deep learning model makes.

关键词： Deep breeding network

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