A Multi-Organ Nucleus Segmentation Challenge

Neeraj Kumar, Ruchika Verma, Deepak Anand, Yanning Zhou, Omer Fahri Onder, Efstratios Tsougenis, Hao Chen, Pheng Ann Heng, Jiahui Li, Zhiqiang Hu, Yunzhi Wang, Navid Alemi Koohbanani, Mostafa Jahanifar, Neda Zamani Tajeddin, Ali Gooya, Nasir Rajpoot, Xuhua Ren, Sihang Zhou, Qian Wang, Dinggang ShenCheng Kun Yang, Chi Hung Weng, Wei Hsiang Yu, Chao Yuan Yeh, Shuang Yang, Shuoyu Xu, Pak Hei Yeung, Peng Sun, Amirreza Mahbod, Gerald Schaefer, Isabella Ellinger, Rupert Ecker, Orjan Smedby, Chunliang Wang, Benjamin Chidester, That Vinh Ton, Minh Triet Tran, Jian Ma, Minh N. Do, Simon Graham, Quoc Dang Vu, Jin Tae Kwak, Akshaykumar Gunda, Raviteja Chunduri, Corey Hu, Xiaoyang Zhou, Dariush Lotfi, Reza Safdari, Antanas Kascenas, Alison O'Neil, Dennis Eschweiler, Johannes Stegmaier, Yanping Cui, Baocai Yin, Kailin Chen, Xinmei Tian, Philipp Gruening, Erhardt Barth, Elad Arbel, Itay Remer, Amir Ben-Dor, Ekaterina Sirazitdinova, Matthias Kohl, Stefan Braunewell, Yuexiang Li, Xinpeng Xie, Linlin Shen, Jun Ma, Krishanu Das Baksi, Mohammad Azam Khan, Jaegul Choo, Adrian Colomer, Valery Naranjo, Linmin Pei, Khan M. Iftekharuddin, Kaushiki Roy, Debotosh Bhattacharjee, Anibal Pedraza, Maria Gloria Bueno, Sabarinathan Devanathan, Saravanan Radhakrishnan, Praveen Koduganty, Zihan Wu, Guanyu Cai, Xiaojie Liu, Yuqin Wang, Amit Sethi

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number8880654
Pages (from-to)1380-1391
Number of pages12
JournalIEEE transactions on medical imaging
Volume39
Issue number5
DOIs
StatePublished - May 2020

Keywords

  • Multi-organ
  • aggregated Jaccard index
  • digital pathology
  • instance segmentation
  • nucleus segmentation

ASJC Scopus subject areas

  • Software
  • Radiological and Ultrasound Technology
  • Computer Science Applications
  • Electrical and Electronic Engineering

Fingerprint Dive into the research topics of 'A Multi-Organ Nucleus Segmentation Challenge'. Together they form a unique fingerprint.

  • Cite this

    Kumar, N., Verma, R., Anand, D., Zhou, Y., Onder, O. F., Tsougenis, E., Chen, H., Heng, P. A., Li, J., Hu, Z., Wang, Y., Koohbanani, N. A., Jahanifar, M., Tajeddin, N. Z., Gooya, A., Rajpoot, N., Ren, X., Zhou, S., Wang, Q., ... Sethi, A. (2020). A Multi-Organ Nucleus Segmentation Challenge. IEEE transactions on medical imaging, 39(5), 1380-1391. [8880654]. https://doi.org/10.1109/TMI.2019.2947628