Evidence map›Paper›PMID 36564629›Full record

ArticleNature biomedical engineering2022

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

Kutsev Bengisu Ozyoruk, Sermet Can, Berkan Darbaz, Kayhan Başak, Derya Demir, Guliz Irem Gokceler, Gurdeniz Serin, Uguray Payam Hacisalihoglu, Emirhan Kurtuluş, Ming Y Lu and 5 more

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Article in Nature biomedical engineering, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
38citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

38 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  6. Diagnosis of Lung Diseases in the Artificial Intelligence Era.International journal of molecular sciences · 2026
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Kutsev Bengisu OzyorukDepartment of Computer Engineering, Bogazici University, Istanbul, Turkey.
Sermet CanDepartment of Computer Engineering, Bogazici University, Istanbul, Turkey.
Berkan DarbazDepartment of Computer Engineering, Bogazici University, Istanbul, Turkey.ORCID http://orcid.org/0000-0002-4699-6849
Kayhan BaşakDepartment of Pathology, Sağlık Bilimleri University, Kartal Dr.Lütfi Kırdar City Hospital, Istanbul, Turkey.ORCID http://orcid.org/0000-0003-1960-8924
Derya DemirFaculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey.
Guliz Irem GokcelerDepartment of Computer Engineering, Bogazici University, Istanbul, Turkey.
Gurdeniz SerinFaculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey.
Uguray Payam HacisalihogluPathology Department, Istanbul Yeni Yuzyil University Medical Faculty, Gaziosmanpasa Hospital, Izmir, Turkey.
Emirhan KurtuluşStanford University, Stanford, CA, USA.
Ming Y LuDepartment of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-0009-9699
Tiffany Y ChenDepartment of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-2546-2941
Drew F K WilliamsonDepartment of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0003-1745-8846
Funda YılmazFaculty of Medicine, Department of Pathology, Ege University, Izmir, Turkey.ORCID http://orcid.org/0000-0003-1837-6498
Faisal Mahmood *Department of Pathology, Brigham and Women's Hospital and Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. faisalmahmood@bwh.harvard.edu.ORCID http://orcid.org/0000-0001-7587-1562
Mehmet Turan *Department of Computer Engineering, Bogazici University, Istanbul, Turkey. mehmet.turan@boun.edu.tr.ORCID http://orcid.org/0000-0002-0913-2531

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Carcinoma, Non-Small-Cell LungDeep LearningLung NeoplasmsFormaldehydeHumansParaffin EmbeddingFormaldehyde

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.