CAESAR.Suite - CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation

Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types.