A deep-learning model for transforming the style of tissue images from cryosectioned to formalin-fixed and paraffin-embedded.

Journal: Nature biomedical engineering
PMID: 36564629

Abstract

Histological artefacts in cryosectioned tissue can hinder rapid diagnostic assessments during surgery. Formalin-fixed and paraffin-embedded (FFPE) tissue provides higher quality slides, but the process for obtaining them is laborious (typically lasting 12-48 h) and hence unsuitable for intra-operative use. Here we report the development and performance of a deep-learning model that improves the quality of cryosectioned whole-slide images by transforming them into the style of whole-slide FFPE tissue within minutes. The model consists of a generative adversarial network incorporating an attention mechanism that rectifies cryosection artefacts and a self-regularization constraint between the cryosectioned and FFPE images for the preservation of clinically relevant features. Transformed FFPE-style images of gliomas and of non-small-cell lung cancers from a dataset independent from that used to train the model improved the rates of accurate tumour subtyping by pathologists.

Authors

  • Kutsev Bengisu Ozyoruk
    Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey.
  • Sermet Can
    Department of Computer Engineering, Bogazici University, Istanbul, Turkey.
  • Berkan Darbaz
    Department of Computer Engineering, Bogazici University, Istanbul, Turkey.
  • Kayhan Başak
  • Derya Demir
    Faculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey.
  • Guliz Irem Gokceler
    Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey.
  • Gurdeniz Serin
    Faculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey.
  • Uguray Payam Hacisalihoglu
    Pathology Department, Istanbul Yeni Yuzyil University Medical Faculty, Gaziosmanpasa Hospital, Izmir, Turkey.
  • Emirhan Kurtuluş
    Stanford University, Stanford, CA, USA.
  • Ming Y Lu
    Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
  • Tiffany Y Chen
    Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
  • Drew F K Williamson
    Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
  • Funda Yılmaz
    Faculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey.
  • Faisal Mahmood
    Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. faisalmahmood@bwh.harvard.edu.
  • Mehmet Turan
    Institute of Biomedical Engineering, Bogazici University, Istanbul, Turkey. Electronic address: mehmet.turan@boun.edu.tr.

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