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Czh3 / iSpatial

infer whole genome spatial transcriptome by integrating single cell RNAseq and spatial transcriptome
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Imputing spatial information of scRNA genes #3

Open michellemlin opened 1 year ago

michellemlin commented 1 year ago

Hello,

I am currently working on a research project where we are looking to infer the spatial information for scRNA genes using MERFISH data. Currently, our MERFISH data is analysed using Giotto and thus, stored in a Giotto object. Our scRNA data is currently stored in a Seurat object. I tried working with the tutorial for imputing the spatial information. However, an issue comes up where the code is unable to work with an S4 object . Can you provide some guidance on how I should approach the task of integrating the MERFISH data and scRNA data if they are different types of objects?

Thank you in advance for any assistance provided.

Best, Michelle

Czh3 commented 1 year ago

Hi Michelle,

iSpatial is not used for imputing the spatial information of the cells derived from scRNAseq. It's for imputing the genes (which measured by scRNA-seq but not measured by MERFISH) expression of the cells derived from MERFISH. For your propose, maybe you can try cell2loc( https://github.com/BayraktarLab/cell2location/ ).

You can transform Giotto object to Seurat, then it should be easy to integrate.

Best, Chao

michellemlin commented 1 year ago

Hi Chao, Apologies, I think my description may have been a bit misleading. We are trying to achieve the same thing that you mentioned (imputing the spatial locations of scRNA-seq genes not currently in our MERFISH data). Thank you very much for your response.

Best, Michelle

Czh3 commented 1 year ago

Cool, you can first transform Giotto object to Seurat, and then integrate scRNA and MERFISH to impute.

Chao