Remove dots below certain expression level threshold

[hndyilm]

Hi everyone,

I analyzed Visium spatial transcriptomics data using squidpy.
When using "spatial_scatter", is it possible to not show specific dots with a gene expression leven below a certain threshold. This would be super helpful as one would be able to see the underlying histology picture better.

Thanks in advance for your help!! Hande

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[LLehner]

Hi @hndyilm, thank you for your interest in squidpy. This is indeed functionality that we want to add. However we are likely going to implement it as part of the spatialdata-plot package.

I will update here once this has been implemented and also show an example.