Visualizing levels of gene expression in Squidpy with MERFISH data

Hi everyone,

When analysing MERFISH data in Squidpy, is it possible to color cells based on their quantified expression of an individual gene similar to using ImageFeaturePlot() in Seurat ?



hi @wdg118 unfortunately not yet, but we will support it in the future. I’d suggest to check out GitHub - ckmah/bento-tools: A Python toolkit for subcellular analysis of spatial transcriptomics data if you want a tool that uses the same data structure as scverse.