Visualizing levels of gene expression in Squidpy with MERFISH data

Help squidpy
1

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 ?

Thanks,

Will

2

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.