Characterizing cell-type spatial relationships across length scales in spatially resolved omics data

This seminar was delivered on 13 April 2026. For more information: https://spds.sydney.edu.au/ Speaker: Rafael dos Santos Peixoto, Johns Hopkins University Abstract: Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we present CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package. To demonstrate the utility of such multi-scale characterization, recapitulate expected cell-type spatial relationships, and evaluate against other cell-type spatial analyses, we apply CRAWDAD to various simulated and real SRO datasets across diverse tissues and SRO technologies. We further demonstrate how such multi-scale characterization, enabled by CRAWDAD, can be used to compare cell-type spatial relationships across multiple samples. Finally, we apply CRAWDAD to SRO datasets of the human spleen to identify consistent as well as patient and sample-specific cell-type spatial relationships. In general, we anticipate that such multi-scale analysis of SRO data enabled by CRAWDAD will provide useful quantitative metrics to facilitate the identification, characterization, and comparison of cell-type spatial relationships across axes of interest. About the speaker: Rafael is a PhD candidate in Biomedical Engineering at Johns Hopkins University. Under the supervision of Jean Fan, he develops software to analyze spatial omics data. His first project was CRAWDAD, an R package to analyze cell-type spatial relationships. Now, he is investigating the molecular differences in acute kidney injury. Outside of the lab, he enjoys playing and watching sports. He is from Brazil, and hopes they will win this World Cup!