integration-harmony

Spatial transcriptomics slices can be batch-corrected by aligning PCA embeddings with Harmony. This removes batch effects across multiple gene-expression slices, preserving cell-type interpretation for joint analysis.

Yes, you can transfer cell types from a reference scRNA-seq annotated dataset to spatial slices via KNN label transfer. This requires providing an optional path to the reference h5ad file and enabling the KNN transfer option.

Harmony integration requires at least two spatial slices to merge. You must specify which slices to integrate, and the results are stored back into each slice's adata including harmonized embeddings and provenance.

You can assess batch correction quality by comparing pre- and post-integration UMAPs. Inspecting the harmonized embeddings stored in each slice allows you to evaluate how well batch effects were removed.

Harmony spatial integration aligns PCA embeddings across multiple slices to remove batch effects. The process stores the integrated harmonized embeddings back into each slice's adata for downstream analysis.