Fixed no neighborhood data in h5ad #210

BodenmillerGroup · Dec 13, 2023 · cb0cbd2 · cb0cbd2
1 parent cbc3937
commit cb0cbd2
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/steinbock/export/_cli/data.py b/steinbock/export/_cli/data.py
@@ -275,7 +275,8 @@ def write_anndata(adata, anndata_file, ignore_suffix=False):
             del adata
     if concatenate:
         adata = anndata_concat(
-            adatas, merge="first", label="Image", index_unique=" in "
+            adatas, merge="first", label="Image", index_unique=" in ",
+            pairwise=True
         )
         obs_cols = list(adata.obs.columns)
         obs_cols.insert(0, obs_cols.pop(obs_cols.index("Image")))