Beyond slides: The era of 3D histology

Zihang He

Yingying Li

Lixue Shi

1,2,*

*Correspondence to: Lixue Shi, Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China. E-mail: shilixue@fudan.edu.cn

EXO. 2026;1:202622. 10.70401/EXO.2026.0021

Received: June 03, 2026Accepted: September 30, 2026Published: September 30, 2026

This manuscript is made available in its unedited form to allow early access to the reported findings. Further editing will be completed before final publication. As such, the content may include errors, and standard legal disclaimers are applicable.

Abstract

Histology has long served as the foundation of tissue diagnosis, yet its reliance on thin 2D sections incompletely captures the spatial continuity, volumetric heterogeneity, and multicellular architecture of biological tissues. Recent advances in volumetric imaging, spatial omics, label-free optical pathology, and artificial intelligence are enabling tissue analysis beyond the conventional glass slide. In this Perspective, we discuss the emergence of 3D histology and the technological developments driving the transition from planar sampling to volumetric tissue analysis. We highlight how the added spatial dimension can reveal diagnostically relevant features that are only partially represented in conventional sections, and discuss efforts to extend molecular profiling into intact tissues through multiplexed imaging and volumetric spatial omics. We further examine the growing role of label-free modalities, particularly stimulated Raman scattering microscopy, for rapid and minimally destructive pathology. Finally, we consider the computational foundations required to reconstruct, align and interpret volumetric data, including emerging applications in virtual histology and molecular prediction. Together, these developments suggest that 3D histology is evolving into a broader framework for integrating tissue morphology, molecular state, and function within intact spatial contexts, with emerging opportunities for biological discovery and precision medicine.

Keywords

3D histopathology, non-destructive histology, molecular histology, label-free imaging, virtual staining

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