Data Merging

Merge all samples into a unified AnnData object.

Layers Created

Layer	Source	Description
raw	Normalization	Normalized, not aligned
aligned	Alignment	Cross-sample aligned
batchcorr	Batch Correction	Batch-corrected

Spatial Graphs

Builds k-NN or radius-based spatial graphs for each sample.

CLI

celltype-refinery preprocess merge \
  --input corrected/ \
  --graph-mode knn \
  --out output/merged.h5ad