Three-dimensional virtual H&E staining of label-free colon cancer tissue using holotomography and deep learning

In standard histopathology, hematoxylin and eosin (H&E) staining stands as a pivotal tool for cancer tissue analysis. However, this method is limited to two-dimensional (2D) analysis or requires labor-intensive preparation for three-dimensional (3D) inspection of cancer tissues. In this study, we present a method for 3D virtual H&E staining of label-free colon cancer tissues, employing holotomography and deep learning. Holotomography is used to measure the 3D refractive index (RI) distribution of the label-free colon cancer slides. A deep learning-based image-to-image translation framework is integrated into the resulting 3D RI distribution, enabling virtual H&E staining in 3D. Our method has been applied to colon cancer tissue slides with thicknesses up to 20 um, with conventional chemical H&E staining providing a direct validation for the method. This framework not only bypasses the conventional staining process but also provides 3D structures of glands, lumens, and individual nuclei. The results demonstrate enhancement in histopathological efficiency and the extension of the standard histopathology into the 3D realm. ### Competing Interest Statement D.R., D.A., H.C., H.-s.M. and Y.K.P. have financial interests in Tomocube, a company that commercializes holotomography and quantitative phase imaging instruments. All other authors declare no competing interests.