A Multi-Organ Nucleus Segmentation Challenge.

Journal: IEEE transactions on medical imaging
Published Date: Oct 23, 2019

Abstract

Generalized nucleus segmentation techniques can contribute greatly to reducing the time to develop and validate visual biomarkers for new digital pathology datasets. We summarize the results of MoNuSeg 2018 Challenge whose objective was to develop generalizable nuclei segmentation techniques in digital pathology. The challenge was an official satellite event of the MICCAI 2018 conference in which 32 teams with more than 80 participants from geographically diverse institutes participated. Contestants were given a training set with 30 images from seven organs with annotations of 21,623 individual nuclei. A test dataset with 14 images taken from seven organs, including two organs that did not appear in the training set was released without annotations. Entries were evaluated based on average aggregated Jaccard index (AJI) on the test set to prioritize accurate instance segmentation as opposed to mere semantic segmentation. More than half the teams that completed the challenge outperformed a previous baseline. Among the trends observed that contributed to increased accuracy were the use of color normalization as well as heavy data augmentation. Additionally, fully convolutional networks inspired by variants of U-Net, FCN, and Mask-RCNN were popularly used, typically based on ResNet or VGG base architectures. Watershed segmentation on predicted semantic segmentation maps was a popular post-processing strategy. Several of the top techniques compared favorably to an individual human annotator and can be used with confidence for nuclear morphometrics.

Authors

  • Neeraj Kumar
  • Ruchika Verma
  • Deepak Anand
  • Yanning Zhou
  • Omer Fahri Onder
  • Efstratios Tsougenis
  • Hao Chen
    The First School of Medicine, Wenzhou Medical University, Wenzhou, China.
  • Pheng-Ann Heng
  • Jiahui Li
    College of Communication Engineering, Jilin University, Changchun, Jilin China.
  • Zhiqiang Hu
  • Yunzhi Wang
    School of Electrical and Computer Engineering, University of Oklahoma, Norman, OK, USA.
  • Navid Alemi Koohbanani
  • Mostafa Jahanifar
  • Neda Zamani Tajeddin
  • Ali Gooya
    Department of Electronic and Electrical Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK.
  • Nasir Rajpoot
    Department of Computer Science, University of Warwick, Coventry, UK.
  • Xuhua Ren
    School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, China.
  • Sihang Zhou
    Department of Radiology and BRIC, University of North Carolina at Chapel Hill, NC, USA; School of Computer, National University of Defense Technology, Changsha, China.
  • Qian Wang
    Department of Radiation Oncology, China-Japan Union Hospital of Jilin University, Changchun, China.
  • Dinggang Shen
    School of Biomedical Engineering, ShanghaiTech University, Shanghai, China.
  • Cheng-Kun Yang
  • Chi-Hung Weng
  • Wei-Hsiang Yu
  • Chao-Yuan Yeh
  • Shuang Yang
    Key Laboratory of Grain and Oil Processing and Food Safety of Sichuan Province, College of Food and Bioengineering, Xihua University Chengdu 610039 China xingyage1@163.com.
  • Shuoyu Xu
  • Pak Hei Yeung
  • Peng Sun
    Department of Microelectronics, Nankai University, Tianjin, 300350, PR China.
  • Amirreza Mahbod
  • Gerald Schaefer
  • Isabella Ellinger
  • Rupert Ecker
  • Orjan Smedby
  • Chunliang Wang
    School of Technology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
  • Benjamin Chidester
    Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
  • That-Vinh Ton
  • Minh-Triet Tran
  • Jian Ma
  • Minh N Do
    University of Illinois, Department of Electrical and Computer Engineering, Computational Imaging Group, Coordinated Science Laboratory, Urbana-Champaign, Illinois, United States.
  • Simon Graham
    Mathematics for Real World Systems Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK; Department of Computer Science, University of Warwick, UK. Electronic address: s.graham.1@warwick.ac.uk.
  • Quoc Dang Vu
    Department of Computer Science and Engineering, Sejong University, 209 Neungdong-ro, Gwangjin-gu, Seoul 05006, Korea.
  • Jin Tae Kwak
    Center for Interventional Oncology, National Institutes of Health, Bethesda, MD, 20892, USA.
  • Akshaykumar Gunda
  • Raviteja Chunduri
  • Corey Hu
  • Xiaoyang Zhou
  • Dariush Lotfi
  • Reza Safdari
    Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran. Electronic address: rsafdari@tums.ac.ir.
  • Antanas Kascenas
  • Alison O'Neil
  • Dennis Eschweiler
  • Johannes Stegmaier
    Institute for Applied Computer Science, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.
  • Yanping Cui
  • Baocai Yin
    iFLYTEK Research, Hefei, China.
  • Kailin Chen
  • Xinmei Tian
  • Philipp Gruening
  • Erhardt Barth
  • Elad Arbel
  • Itay Remer
  • Amir Ben-Dor
  • Ekaterina Sirazitdinova
  • Matthias Kohl
    Konica Minolta Laboratory Europe, Munich, Germany.
  • Stefan Braunewell
    Konica Minolta Laboratory Europe, Munich, Germany.
  • Yuexiang Li
    Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.
  • Xinpeng Xie
    Computer Vision Institute, College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China.
  • Linlin Shen
  • Jun Ma
    State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090, China.
  • Krishanu Das Baksi
  • Mohammad Azam Khan
  • Jaegul Choo
  • Adrian Colomer
  • Valery Naranjo
    Instituto de Investigación e Innovación en Bioingeniería, I3B, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
  • Linmin Pei
  • Khan M Iftekharuddin
  • Kaushiki Roy
    Department of Computer Science and Engineering, Jadavpur University, Kolkata-32, India. Electronic address: kaushiki.cse@gmail.com.
  • Debotosh Bhattacharjee
    ∥Department of Computer Science and Engineering, Jadavpur University, Kolkata-700032, West Bengal, India.
  • Anibal Pedraza
  • Maria Gloria Bueno
  • Sabarinathan Devanathan
  • Saravanan Radhakrishnan
  • Praveen Koduganty
  • Zihan Wu
  • Guanyu Cai
  • Xiaojie Liu
    * College of Applied Sciences, Beijing University of Technology, Beijing 100124, P. R. China.
  • Yuqin Wang
  • Amit Sethi

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