PySpatial: A High-Speed Whole Slide Image Pathomics Toolkit

Whole Slide Image (WSI) analysis plays a crucial role in modern digital pathology, enabling large-scale feature extraction from tissue samples[1]. However, traditional feature extraction pipelines based on tools like CellProfiler[2] often involve lengthy workflows, requiring WSI segmentation into patches, feature extraction at the patch level, and subsequent mapping back to the original WSI[4]. To address these challenges, we present PySpatial, a high-speed pathomics toolkit specifically designed for WSI-level analysis. PySpatial streamlines the conventional pipeline by directly operating on computational regions of interest, reducing redundant processing steps. Utilizing rtree-based spatial indexing and matrix-based computation, PySpatial efficiently maps and processes computational regions, significantly accelerating feature extraction while maintaining high accuracy. Our experiments on two datasets-Perivascular Epithelioid Cell (PEC) and data from the Kidney Precision Medicine Project (KPMP) [13]-demonstrate substantial performance improvements. For smaller and sparse objects in PEC datasets, PySpatial achieves nearly a 10-fold speedup compared to standard CellProfiler pipelines. For larger objects, such as glomeruli and arteries in KPMP datasets, PySpatial achieves a 2-fold speedup. These results highlight PySpatial's potential to handle large-scale WSI analysis with enhanced efficiency and accuracy, paving the way for broader applications in digital pathology.