Abstract
BackgroundVirtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data. Here, we use VR for visualization of 3D histology data, creating a novel interface for digital pathology to aid cancer research.MethodsOur contribution includes 3D modeling of a whole organ and embedded objects of interest, fusing the models with associated quantitative features and full resolution serial section patches, and implementing the virtual reality application. Our VR application is multi-scale in nature, covering two object levels representing different ranges of detail, namely organ level and sub-organ level. In addition, the application includes several data layers, including the measured histology image layer and multiple representations of quantitative features computed from the histology.ResultsIn our interactive VR application, the user can set visualization properties, select different samples and features, and interact with various objects, which is not possible in the traditional 2D-image view used in digital pathology. In this work, we used whole mouse prostates (organ level) with prostate cancer tumors (sub-organ objects of interest) as example cases, and included quantitative histological features relevant for tumor biology in the VR model.ConclusionsOur application enables a novel way for exploration of high-resolution, multidimensional data for biomedical research purposes, and can also be used in teaching and researcher training. Due to automated processing of the histology data, our application can be easily adopted to visualize other organs and pathologies from various origins.
Highlights
Virtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data
Applicability of 3D imaging modalities depends on the physical sample size and such measurement devices are not always available, while manual modeling from histology data is time-consuming and subjective
With our use-case, we show how the organ level view in the VR application enables detection of cancer growth pattern differences, validated in the detailed histology level view, and explored for the associated quantitative details
Summary
Virtual reality (VR) enables data visualization in an immersive and engaging manner, and it can be used for creating ways to explore scientific data. We use VR for visualization of 3D histology data, creating a novel interface for digital pathology to aid cancer research. In addition to modeling the tissue based on histological sections only, fusion models of histological serial sections and native 3D imaging modalities such as micro-computed tomography (μCT) [4,5,6,7,8,9,10] or magnetic resonance imaging (MRI) [11,12,13] are possible. Even manually created 3D models representing epithelium with textures acquired from histological samples have been made for teaching purposes [14]. Applicability of 3D imaging modalities depends on the physical sample size and such measurement devices are not always available, while manual modeling from histology data is time-consuming and subjective. Unlike non destructive 3D imaging, modeling based on serial sections is possible for already sectioned and processed samples. Archived clinical sample sets could be accessed to enable retrospective clinical studies holding the potential to advance histopathology and to open up new research areas
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