Hi,
I followed the scanpy tutorial to integrate scRNAseq clusters on spatial RNAseq samples. Now I am trying to measure the colocalization and the distances between these clusters on the spatial samples. I tried to use squidpy interaction_matrix or nhood_enrichment but it does not work, because the ‘leiden’ obs is lost after the integration of scRNAseq clusters using scanpy. Could you help me to fix it please?
Thanks