The X-ray images were acquired at the Hereon research facility P05 at DESY in Hamburg, where high-intensity X-rays make biological and medical samples visible at high resolution. Credit: Hereon/Torben Fischer

Histology is one of the foundations of modern diagnostics. When physicians want to determine whether tissue is pathologically altered, they rely on microscopic tissue analysis: They cut the tissue into ultrathin sections, stain it with special dyes, and examine it under a light microscope. In this manner, physicians can identify whether a tumor is present and, if so, what kind of tumor it is—thereby enabling informed therapeutic decisions. In addition, doctors often assess during surgery whether all altered tissue has already been removed or further intervention is required.

However, the procedure is labor-intensive: The tissue must be either frozen or fixed and embedded in wax, then cut and stained—a time-consuming process that divides the sample into many slices and tears apart its spatial context. "You cannot view the tissue in its full 3D context, for example, to follow the path of blood vessels or determine where exactly the tumor ends," explains Dominik John, researcher at the Hereon Institute of Materials Physics and first author of the study published in Advanced Science.

This is why experts are working on what is known as virtual histology—3D X-ray imaging with micrometer-scale resolution. Unlike visible light, X-rays can penetrate samples several centimeters in thickness while providing data on the entire tissue volume. Instead of the analysis being limited to only a few selected tissue regions, any area can be examined from any desired direction. But one problem remained unsolved: X-ray images are black and white. This meant that the dyes used in classical histology to color cell nuclei or specific tissue types could not be distinguished from the surrounding tissue in X-ray images.

The X-ray beam originates from a bending magnet source (MCT) or an undulator (P05) and is set to the desired energy using a double multi-layer monochromator. After a distance 𝑠 , the beam impinges upon the modulator, which introduces a phase shift in regular intervals across the wavefront. The sample is positioned at a distance 𝑙 from the modulator, and the detector is at a distance Δ from the sample. Credit: Advanced Science (2026). DOI: 10.1002/advs.202519783

X-ray imaging with color information

This is where the innovative method developed by John together with an international team of researchers from Hamburg, Munich, and Melbourne comes into play. The approach combines high-resolution X-ray computed tomography with a special phase-contrast technique and a new evaluation algorithm. This algorithm simultaneously uses two distinct measurements: how strongly the tissue attenuates the X-rays and how much it refracts them.

The latter becomes visible through a fine grid placed in the X-ray beam, which projects a dot pattern onto the sample. "This allows the method to compute two separate 3D images," John explains. "One shows only the tissue, the other only the dye."

As a demonstration, the researchers examined kidneys from mice and rats treated with the dye hematein. A lead atom was attached to the dye to enhance X-ray contrast. The team conducted their measurements at the PETRA III X-ray source at DESY in Hamburg and at the Australian Synchrotron in Melbourne. The result: the method not only shows where the dye is located—it also quantifies its amount.

"We can determine the exact dye concentration for each region of the tissue sample," says John. "This is valuable information for research." To compare their X-ray images with conventional histological images, the team prepared tissue sections from the same sample—and found good agreement.

The method is still complex because it depends on large-scale research facilities. The experts therefore aim to make it more accessible through modern laboratory X-ray sources. "Initially, it could serve as a tool for scientific studies, for example in cancer research," says John. "But if we can find a way to improve the resolution further, it would also become highly relevant for clinical diagnostics."

In medicine, diseased tissue could be analyzed in its full spatial context—for instance, to better assess tumor spread, completeness of surgical removal, or therapeutic effects. For patients, this would be a tangible benefit: more precise diagnoses, better-informed treatment decisions, and potentially less invasive procedures.

Publication details

Dominik John et al, Quantitative Stain Mapping in X‐Ray Virtual Histology, Advanced Science (2026). DOI: 10.1002/advs.202519783

Journal information: Advanced Science

Citation: Virtual histography: From tissue section to 3D image (2026, January 21) retrieved 21 January 2026 from https://medicalxpress.com/news/2026-01-virtual-histography-tissue-section-3d.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.