Deep learning-based transformation of H&E stained tissues into special stains

Kevin de Haan, Yijie Zhang, Jonathan E. Zuckerman, Tairan Liu, Anthony E. Sisk, Miguel F.P. Diaz, Kuang Yu Jen, Alexander Nobori, Sofia Liou, Sarah Zhang, Rana Riahi, Yair Rivenson, W. Dean Wallace, Aydogan Ozcan

Research output: Contribution to journalArticlepeer-review

5 Scopus citations


Pathology is practiced by visual inspection of histochemically stained tissue slides. While the hematoxylin and eosin (H&E) stain is most commonly used, special stains can provide additional contrast to different tissue components. Here, we demonstrate the utility of supervised learning-based computational stain transformation from H&E to special stains (Masson’s Trichrome, periodic acid-Schiff and Jones silver stain) using kidney needle core biopsy tissue sections. Based on the evaluation by three renal pathologists, followed by adjudication by a fourth pathologist, we show that the generation of virtual special stains from existing H&E images improves the diagnosis of several non-neoplastic kidney diseases, sampled from 58 unique subjects (P = 0.0095). A second study found that the quality of the computationally generated special stains was statistically equivalent to those which were histochemically stained. This stain-to-stain transformation framework can improve preliminary diagnoses when additional special stains are needed, also providing significant savings in time and cost.

Original languageEnglish (US)
Article number4884
JournalNature communications
Issue number1
StatePublished - Dec 2021
Externally publishedYes

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


Dive into the research topics of 'Deep learning-based transformation of H&E stained tissues into special stains'. Together they form a unique fingerprint.

Cite this