Clustering spatial data

The clustering workflow accepts both cell suspension datasets and spatial transcriptomics data as input that have been ingested with the qc_spatial workflow and optionally filtered with the spatial_preprocess workflow. The workflow expects a single MuData object with the spatial data saved in mdata.mod["spatial"].

Set spatial: True in the configuration file and customize the spatial modality clustering parameters exactly as you would for a single cell experiment. For more information check the clustering workflow