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ckmah / bento-tools

A Python toolkit for subcellular analysis of spatial transcriptomics data
https://bento-tools.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
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Can I use Bento in NGS-based ST data？（Stereo-seq or VisimHD） #118

Closed zhoutianrui-tongji closed 3 months ago

zhoutianrui-tongji commented 5 months ago

Dear author, this is a handy work. I want to ask you about it. All the ST data used in this paper are FISH-based, I wonder if it is possible to use ST data with subcellular resolution. Like Stereo-seq or 10X VisimHD?

And it would be nice if you could give a tutorial on using your personal data. I look forward to hearing from you.

ckmah commented 5 months ago

@zhoutianrui-tongji, we have not tested our methods against spatially-binned count data i.e. Stereo-seq, Visium HD, Curio etc., but I invite you to take a look at SpatialData's supported platforms. How are you currently analyzing slide-based data, especially at the subcellular resolution?

And yes we are working hard to release our refactor from AnnData to SpatialData, enabling access to public/custom ST datasets. Check back soon!

zhoutianrui-tongji commented 4 months ago

Thank u very much, I check SpatialData's supported platforms, and it contains 10X VisiumHD, I think it similar to Stereo-seq.