Computing niches in cosmx data using fov as batch_key

[sarajimenez]

Hi!

Thank you so much for developing ENVI and COVET!

I'm using covet to identify niches in cosmx data. I've two conditions and three replicates per condition; each replicate has several fovs. Then, what I'm doing is, per condition, I'm computing the covet representation for each replicate having the fvo as batch_key. However, after computing the knn and clustering using the covet representation, I'm capturing the technical variability of each fov instead of actual biological niches.

Do you have any suggestion and/or idea?

Any comment would be highly appreciated :)