Structured crowdsourcing enables convolutional segmentation of histology images

Mohamed Amgad, Habiba Elfandy, Hagar Hussein, Lamees A. Atteya, Mai A.T. Elsebaie, Lamia S. Abo Elnasr, Rokia A. Sakr, Hazem S.E. Salem, Ahmed F. Ismail, Anas M. Saad, Joumana Ahmed, Maha A.T. Elsebaie, Mustafijur Rahman, Inas A. Ruhban, Nada M. Elgazar, Yahya Alagha, Mohamed H. Osman, Ahmed M. Alhusseiny, Mariam M. Khalaf, Abo Alela F. YounesAli Abdulkarim, Duaa M. Younes, Ahmed M. Gadallah, Ahmad M. Elkashash, Salma Y. Fala, Basma M. Zaki, Jonathan Beezley, Deepak R. Chittajallu, David Manthey, David A. Gutman, Lee A.D. Cooper*, Robert Murphy

*Corresponding author for this work

Research output: Contribution to journalArticle

7 Scopus citations

Abstract

While deep-learning algorithms have demonstrated outstanding performance in semantic image segmentation tasks, large annotation datasets are needed to create accurate models. Annotation of histology images is challenging due to the effort and experience required to carefully delineate tissue structures, and difficulties related to sharing and markup of whole-slide images. Results: We recruited 25 participants, ranging in experience from senior pathologists to medical students, to delineate tissue regions in 151 breast cancer slides using the Digital Slide Archive. Inter-participant discordance was systematically evaluated, revealing low discordance for tumor and stroma, and higher discordance for more subjectively defined or rare tissue classes. Feedback provided by senior participants enabled the generation and curation of 20 000+ annotated tissue regions. Fully convolutional networks trained using these annotations were highly accurate (mean AUC=0.945), and the scale of annotation data provided notable improvements in image classification accuracy. Availability and Implementation: Dataset is freely available at: https://goo.gl/cNM4EL. Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)3461-3467
Number of pages7
JournalBioinformatics
Volume35
Issue number18
DOIs
StatePublished - Sep 15 2019
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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    Amgad, M., Elfandy, H., Hussein, H., Atteya, L. A., Elsebaie, M. A. T., Abo Elnasr, L. S., Sakr, R. A., Salem, H. S. E., Ismail, A. F., Saad, A. M., Ahmed, J., Elsebaie, M. A. T., Rahman, M., Ruhban, I. A., Elgazar, N. M., Alagha, Y., Osman, M. H., Alhusseiny, A. M., Khalaf, M. M., ... Murphy, R. (2019). Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics, 35(18), 3461-3467. https://doi.org/10.1093/bioinformatics/btz083