| BRÁZDIL, Tomáš, Matej GALLO, Rudolf NENUTIL, Andrej KUBANDA, Martin TOUFAR and Petr HOLUB. Automated annotations of epithelial cells and stroma in hematoxylin–eosin-stained whole-slide images using cytokeratin re-staining. The Journal of Pathology: Clinical Research. 2022, vol. 8, No 2, p. 129-142. ISSN 2056-4538. Available from: https://dx.doi.org/10.1002/cjp2.249. |
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@article{1801217,
author = {Brázdil, Tomáš and Gallo, Matej and Nenutil, Rudolf and Kubanda, Andrej and Toufar, Martin and Holub, Petr},
article_number = {2},
doi = {http://dx.doi.org/10.1002/cjp2.249},
keywords = {U-Net; artificial intelligence; digital pathology; H&E; immunohistochemistry; deep learning; tissue registration},
language = {eng},
issn = {2056-4538},
journal = {The Journal of Pathology: Clinical Research},
title = {Automated annotations of epithelial cells and stroma in hematoxylin–eosin-stained whole-slide images using cytokeratin re-staining},
url = {https://onlinelibrary.wiley.com/doi/10.1002/cjp2.249},
volume = {8},
year = {2022}
}
TY - JOUR
ID - 1801217
AU - Brázdil, Tomáš - Gallo, Matej - Nenutil, Rudolf - Kubanda, Andrej - Toufar, Martin - Holub, Petr
PY - 2022
TI - Automated annotations of epithelial cells and stroma in hematoxylin–eosin-stained whole-slide images using cytokeratin re-staining
JF - The Journal of Pathology: Clinical Research
VL - 8
IS - 2
SP - 129-142
EP - 129-142
SN - 20564538
KW - U-Net
KW - artificial intelligence
KW - digital pathology
KW - H&E
KW - immunohistochemistry
KW - deep learning
KW - tissue registration
UR - https://onlinelibrary.wiley.com/doi/10.1002/cjp2.249
N2 - The diagnosis of solid tumors of epithelial origin (carcinomas) represents a major part of the workload in clinical histopathology. Distinguishing stroma from epithelium is a critical component of artificial intelligence (AI) methods developed to detect and analyze carcinomas. In this paper, we propose a novel automated workflow that enables large-scale guidance of AI methods to identify the epithelial component. The workflow is based on re-staining existing hematoxylin and eosin (H&E) formalin-fixed paraffin-embedded (FFPE) slides by immunohistochemistry for cytokeratins - cytoskeleton components specific to epithelial cells. We also demonstrate how the automatically generated masks can be used to train modern AI image segmentation based on U-Net, resulting in reliable detection of epithelial regions in previously unseen H&E slides.
ER -
BRÁZDIL, Tomáš, Matej GALLO, Rudolf NENUTIL, Andrej KUBANDA, Martin TOUFAR and Petr HOLUB. Automated annotations of epithelial cells and stroma in hematoxylin–eosin-stained whole-slide images using cytokeratin re-staining. \textit{The Journal of Pathology: Clinical Research}. 2022, vol.~8, No~2, p.~129-142. ISSN~2056-4538. Available from: https://dx.doi.org/10.1002/cjp2.249.
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