QuST: QuPath Extension for Integrative Whole Slide Image and Spatial Transcriptomics Analysis

Recently, various technologies have been introduced into digital pathology, including artificial intelligence (AI) driven methods, in both areas of pathological whole slide image (WSI) analysis and spatial transcriptomics (ST) analysis. AI-driven WSI analysis utilizes the power of deep learning (DL), expands the field of view for histopathological image analysis. On the other hand, ST bridges the gap between tissue spatial analysis and biological signals, offering the possibility to understand the spatial biology. However, a major bottleneck in DL-based WSI analysis is the preparation of training patterns, as hematoxylin \& eosin (H\&E) staining does not provide direct biological evidence, such as gene expression, for determining the category of a biological component. On the other hand, as of now, the resolution in ST is far beyond that of WSI, resulting the challenge of further spatial analysis. Although various WSI analysis tools, including QuPath, have cited the use of WSI analysis tools in the context of ST analysis, its usage is primarily focused on initial image analysis, with other tools being utilized for more detailed transcriptomic analysis. As a result, the information hidden beneath WSI has not yet been fully utilized to support ST analysis. To bridge this gap, we introduce QuST, a QuPath extension designed to bridge the gap between H\&E WSI and ST analyzing tasks. In this paper, we highlight the importance of integrating DL-based WSI analysis and ST analysis in understanding disease biology and the challenges in integrating these modalities due to differences in data formats and analytical methods. The QuST source code is hosted on GitHub and documentation is available at https://github.com/huangch/qust.