Artificial Intelligence Translates Raw Micro CT Scans Into 3D Virtual Stains

Rudolf Virchow fundamentally changed medicine when he formulated his cell theory of disease in the 19^th century: diseases do not arise inexplicably within the organism, but rather in specific cells and tissues. To this day, pathology – the study of disease processes – is essentially based on the time-consuming examination of thin tissue sections, which are stained and then viewed under a microscope.

Now an international research team at the Paul Scherrer Institute PSI has managed to overcome this two-dimensional limitation. Using high-resolution micro-computed tomography (µCT) and artificial intelligence, a group led by physicist Goran Lovric from the PSI Center for Photon Science generated virtual stains of tissue samples, so-called histological stains. This could potentially eliminate the need to prepare and stain ultrathin, delicate sections.

We have shown for the first time that a CT-based virtual stain can deliver results similar to conventional laboratory histology. This could open up a wealth of clinical and scientific applications."

Goran Lovric, Physicist, Paul Scherrer Institute

Familiar Color Markers of Histology

The researchers combined high-resolution phase-contrast micro-CT (PCµCT) with machine learning methods. The platform is called VISTACT – short for virtual staining of micro-computed tomography. While conventional computed tomography primarily measures differences in X-ray density, phase-contrast micro-CT utilizes additional X-ray information, thereby achieving significantly better visualization of soft tissue. This allows three-dimensional visualization of fine anatomical structures on the micrometer scale – so far, however, only in greyscale. In pathology, however, specialists are trained to interpret the typical color contrasts of conventional histological stains: cell nuclei appear blue-violet, collagen pink, and elastic fibres dark. Many of these visual reference points are lost in greyscale CT datasets.

"We therefore wanted to carry over the familiar color world of histology to three-dimensional CT data," explains Lovric. To achieve this, the researchers trained a specialized AI model using pairs of real histological sections and their corresponding CT scans. In this way the AI model learned which microscopic patterns typically receive which staining. It then was able to virtually stain new CT data – essentially an automatic translation between two image worlds.

More Precise Localization

One crucial technical step was precise mapping of the images. Histological sections are only a few micrometers thick and can easily become distorted during sectioning or mounting. In addition, it is essential to determine exactly where each section is located within the three-dimensional CT dataset. Lovric's research group developed a multi-stage process that automatically identifies the corresponding layer and compares it with the histology data. According to the researchers, this spatial mapping is significantly more precise than previous standard methods.

To carry out the virtual staining, researchers used a so-called conditional generative adversarial network – a specialized AI model for image-to-image translation. With greyscale images from micro-CT scans as input, the model generated virtual histological specimens. Remarkably, the AI produced not merely coarse color areas but rather plausibly differentiated tissue components of various types: blood in the fine vessels appeared yellowish, collagen structures pink, and surfaces in the lungs grey to violet.

Lung Tissue Test Provides Proof of Concept

The researchers tested their new method on lung tissue taken from individuals with pulmonary hypertension. This condition involves pathological remodelling of the pulmonary vessels. "We were able to map the altered vascular regions in three dimensions," says Cristina Almagro-Pérez. She is the first author of the new publication and worked in Goran Lovric's group during her master's thesis. She is now doing research in the USA.

The new technique can be automated and can work significantly faster than the current method. However, it is not yet ready for routine use in hospitals: the necessary phase-contrast imaging was performed at the TOMCAT beamline of the Swiss Light Source SLS, one of the large research facilities at PSI. The resulting volumes of data were enormous, and the resolution was often insufficient to depict individual cell nuclei reliably.

Furthermore, virtual histology remains a statistical reconstruction: the AI platform does not generate actual histological information, but rather plausible predictions based on the training data. Almagro-Pérez and Lovric emphasize that the procedure has not yet reached routine diagnostic quality. However, the "proof of concept" has been established, and the method is, in principle, applicable to the examination of various diseases. Particularly in examining tumors, vascular lesions, or complex tissue architectures, this form of non-destructive 3-D pathology has the potential to accelerate research into disease biomarkers and thus to open up new diagnostic perspectives in the long term.

More than 150 years after the advent of Virchow's cellular pathology, histology might again be on the verge of a fundamental transformation.