Multi-class instance segmentation of renal structures in highly multiplexed immunofluorescence microscopy images

Lupus nephritis (LN) is a severe manifestation of systemic lupus erythematosus, with up to 30% of LN patients progressing to end-stage kidney disease within ten years of diagnosis. Spatial relationships between specific types of immune cells and kidney structures hold valuable information clinically and biologically. Thus, we develop a modular computational pipeline to analyze the spatially resolved molecular features from high-plex immunofluorescence imaging data. Here, we present three modules of the pipeline, with the goal of achieving multiclass segmentation of renal cells and structures.