Optical super-resolution histology of formalin-fixed paraffin-embedded tissue samples: challenges and opportunities

Luis E. Villegas-Hernández, Vishesh K. Dubey, Ganesh Acharya and Balpreet Singh Ahluwalia ()
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Luis E. Villegas-Hernández: UiT The Arctic University of Norway
Vishesh K. Dubey: UiT The Arctic University of Norway
Ganesh Acharya: Karolinska Institute
Balpreet Singh Ahluwalia: UiT The Arctic University of Norway

Nature Communications, 2025, vol. 16, issue 1, 1-11

Abstract: Abstract This review covers the advancements of optical super-resolution microscopy (SRM) on formalin-fixed paraffin-embedded (FFPE) histological samples. We cover the implementation of various SRM strategies in histology, including wide field methods such as structured illumination microscopy, single-molecule localization microscopy and fluorescence fluctuations-based SRM, as well as the point-scanning stimulated emission depletion microscopy. We also cover the recent developments in FFPE-based expansion microscopy. The review highlights the advantages and challenges of these SRM methods in FFPE histology, and provides insights into emerging optical and computational techniques that can potentially open avenues for understanding disease mechanisms, tailoring treatments, and advancing personalized medicine across disciplines. This review article is intended for a broad audience, including histopathologists, biologists, physiologists, and physicists.

Date: 2025
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DOI: 10.1038/s41467-025-64626-1

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