Question on computing niches on spatial data

[abs51295]

Hey,

I just want to use the COVET method to compute niches on spatial data. I have several batches in my data. Should I just use compute_covet function with batch_key to get the COVET_SQRT representation of the spatial data? Can I just compute neighbors and run louvain clustering on that representation to cluster my data? I am assuming adding batch information wouldn't result in separate clusters per batch.

Also, can I use a latent space representation like one from scVI instead of selecting HVGs and compute COVET on the latent representation instead of genes?

Thanks