Abstract
Understanding spatial dynamics within tissue microenvironments is crucial for deciphering cellular interactions and molecular signaling in living systems. These spatial characteristics govern cell distribution, extracellular matrix components, and signaling molecules, influencing local biochemical and biophysical conditions. Despite significant progress in analyzing digital pathology images, current methods for capturing spatial relationships are limited. They often rely on specific spatial features that only partially describe the complex spatial distributions of cells and are frequently tied to particular outcomes within predefined model frameworks. Furthermore, these methods are typically limited to field of view analysis, which restricts their capacity to capture spatial patterns across whole-slide images, thereby limiting their ability to fully address the complexities of tissue architecture. To address these limitations, we present SpatialQPFs (Spatial Quantitative Pathology Features), an R package designed to extract interpretable spatial features from cell imaging data using spatial statistical methodologies. Leveraging segmented cell information, our package offers a comprehensive toolkit for applying a range of spatial statistical methods within a stochastic process framework, including analyses of point process data, areal data, and geostatistical data. By decoupling feature extraction from specific outcome models, SpatialQPFs enables thorough large-scale spatial analyses applicable across diverse clinical and biological contexts. This approach enhances the depth and accuracy of spatial insights derived from tissue data, empowering researchers to conduct comprehensive spatial analyses efficiently and reproducibly. By providing a flexible and robust framework for spatial feature extraction, SpatialQPFs facilitates advanced spatial analyses, paving the way for new discoveries in tissue biology and pathology. SpatialQPFs code and documentation are publicly available at https://github.com/Genentech/SpatialQPFs .