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TrigosTeam / SPIAT

https://trigosteam.github.io/SPIAT/
Artistic License 2.0
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Convert spatialExperiment object into Seurat object #24

Closed JessicaP94 closed 8 months ago

JessicaP94 commented 1 year ago

Firstly, thank you for the amazing package!

I was wondering how I could convert the SpatialExperiment object generated from format_image_to_spe into a Seurat object. I have data from QuPath but it would be nice to know how to do it also for inForm.

Thank you

fuerzhou commented 1 year ago

Thank you for your interest in our tool. Unfortunately I am not aware of any function to convert SPE objects to Seurat objects. Seurat has the function to read 10x Visium data as Seurat objects but I'm not sure about their functionalities around spatial proteomics data. Perhaps raise the issue with them?

RoshanJalal commented 1 year ago

Great package and excited to try it out. Would it be possible to define the phenotype of the cells based on absence of a marker and presence of another as a combination?

Thank you