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Advanced segementation and analysis of spatial data using Ilastik and Spectre

1. Cell segmentation

Advanced multicut boundary segmentation with Ilastik

Some IMC images contain extremely dense collections of cells, where cytoplasmic (and sometimes) nuclear signal from one cell is difficult to distinguish from another. In this protocol we describe boundary-based segmentation using the 'multi-cut' workflow in Ilastik. Additional cell type and region masks can be included, which dramatically enhances analysis.


2. Spatial analysis

Advanced spatial analysis in R using Spectre (including region masks)

A more advanced workflow in Spectre, incorporating cell type and region masks for enhanced spatial analysis.