3D histology enables exploration of tissue structures and pathologies in their natural spatial context, providing more comprehensive view to the tissue environment. However, visualization of 3D stacks of high resolution whole slide images is challenging.
We developed a virtual reality application for visualization of 3D histology from sparse serial sectioned stacks. The VR application, called SparStVR, enables modeling whole sample from sample masks and embedding multimodal measurements from heatmaps. The application generates textured 3D models and generates embedded measurements from a stack of histology whole slide images and associated masks for sample and object level.
New view on 3D histology
The benefit of VR is the immersive and interactive experience for user. Instead of browsing 2D sections one by one, or 3D rendering with pre-defined view, the user can explore the 3D reconstruction both outside and inside the volume with free angle and unlimited movement within the VR space.
Further, the application enables detailed inspection of predefined structures within the sample volume, for example, glands or lesions, like the tumor in figure below. These objects can be grabbed, rotated, and explored section by section, providing a truly interactive experience for the user - and allowing inspection of the spatial context of the sample in an unprecedented manner.
The VR application presents the tissue as textured objects, with the available stains representing the texture appearance, providing the opportunity to switch views between multiple stainings or even GAN-based virtual stains.
One potential use case for the VR application is visualization regions of interest or spatial hotspots through extracting relevant features from the stack and exploring them in detail within VR, providing a novel tool for discoveries in, e.g., cancer research.
SparStVR - improved VR technology
Virtual reality has been around for a while, and its use in various biomedical applications have been proposed. However, VR for 3D histology has received limited interest, with the massive high resolution image stacks posing a challenge for practical applications. In our earlier work, we presented a preliminary version of using VR for visualizing 3D histology with limited support for interaction and feature space visualization (Liimatainen et al. BMC Cancer, 2021).
In the current SparStVR application (Liimatainen et al. Communications Engineering, 2026), improvements to the earlier are numerous, including on-the-fly feature computation, improved support for interactions and more advanced point cloud based feature visualization. Spectator view and screenshot functionality facilitate collaborative use, e.g., in teaching and enable documentation while exploring the histology in 3D. The application is implemented with Unreal Engine 5 (UE5) by Epic Games with OpenXR framework and UE5 VR Template as starting point.
Next steps
Novel visualization tools for 3D histology enable exploration of tissue in its natural spatial context. Immersive user experience using VR glasses, enabling interaction within the application, engages the user and creates a game-like experience. This provides an opportunity for teaching use, which we have already piloted at two Finnish universities. Feedback from students is positive, encouraging use of SparStVR application for teaching 3D histology.
We hope our work sparks interest towards novel ways to visualize histology and 3D samples. Our own future work aims to continue using modern technology to advance biomedical research, including new tools for visualization of 3D histology.
References
Liimatainen, K., Latonen, L., & Ruusuvuori, P. (2026). SparStVR - Exploring sparse 3D histology data in virtual reality. Communications Engineering, 2026.
https://doi.org/10.1038/s44172-026-00634-3
Liimatainen, K., Latonen, L., Valkonen, M., Kartasalo, K., & Ruusuvuori, P. (2021). Virtual reality for 3D histology: multi-scale visualization of organs with interactive feature exploration. BMC cancer, 21(1), 1133.