How to Subset CellScopes Objects with Metadata from Seurat or stLearn

[YuxiZhang-0113]

Hi,

I've been testing CellScopes with various spatial transcriptomics datasets and find its capabilities very impressive. However, I encountered an issue when trying to subset CellScopes objects.

I often use metadata from objects processed with Seurat or stLearn and integrate this metadata into a processed CellScopes object for visualization. Sometimes, the metadata I have does not cover all the spots in the CellScopes object, leading to mismatches.

I also attempted to convert Seurat's visium object to a CellScopes object using cs.from_seurat. However, this approach does not allow me to use cs.add_visium_img to add the original Tiff file. The error I received is:

MethodError: no method matching add_visium_img(::CellScopes.VisiumObject, ::String) Closest candidates are: add_visium_img(::CellScopes.VisiumObject; img_path) at ~/.julia/packages/CellScopes/mRlqf/src/spatial/sp_processing.jl:251

Stacktrace: [1] top-level scope @ In[5]:1

Therefore, I would appreciate any guidance on how to subset CellScopes objects for various spatial transcriptomics and single-cell data.

Thank you for your assistance!

Best regards