How to plot the aligned image on top of the tissue image?

[quiquevb23]

After I run a pairwise alignment on 2 or more slices and then run pst.stack_slices_pairwise, a new adata object is generated with the aligned coordinate matrix, but this adata object does not contain the aligned "hires" and "lowres" images, as far as I know.

Does PASTE deals with this somehow or should I supply as img_key a tissue image of one of the slices that were aligned? If this is the case, should I edit it with the output of pst.stack_slices_pairwise (such as angles and rotation?)

This is the function I want to run and the error I get
sc.pl.spatial(adata,
img_key="hires",
color=["domain"],
show=False)

ValueError: When .uns['spatial'][library_id] does not exist, spot_size must be provided directly.

[mrland99]

Hi,

Sorry for the late response-- I don't believe PASTE is built to manipulate images in the way you mentioned.

However, since PASTE returns the rotation and translations for each slice, perhaps a workaround would be to do the rotation and translation of the images yourself?