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Nanostring-Biostats / SpatialDecon

The SpatialDecon library implements the SpatialDecon algorithm for mixed cell deconvolution in spatial gene expression datasets. (This algorithm also works in bulk expression profiling data.)
MIT License
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Overlay Florets with Spatial Images #48

Open scSeqLiubice opened 1 year ago

scSeqLiubice commented 1 year ago

Hi Nanostring Team,

our working group is currently looking into this package of yours. We are trying to reproduce figures from the nature paper "Advances in mixed cell deconvolution enable quantification of cell types in spatial transcriptomic data" for our own data, where the florets output was overlayed onto the fluoresence images. So far we were not able to reproduce the figues, since we were not able to get any output from the florets function to begin with. We tried to get the coordinate data for the florets function out of a SpatialOverlay object, which roughly reproduced the grouping coordinates, but the positions were off. Is there some function we are simply overlooking?

We appreciate your effort and help.

Kind Regards, Fabian

maddygriz commented 1 year ago

Hi @scSeqLiubice,

Thank you for reaching out. Our customer support team will be able to help you with this. Please email support@nanostring.com with your issue.

Thanks, Maddy