adding prior segmenation to data processor in script.py and file_spatial_unlabelled.yaml

Author: heylf

src/api/file_spatial_unlabelled.yaml

@@ -55,6 +55,15 @@ info:
               segmentation prior. This is NOT the ground truth used for
               evaluation (which is held out in spatial_solution); methods may
               freely condition on it.
+    labels:
+      - type: object
+        name: "cell_labels"
+        description: Ground truth cell segmentation labels
+        required: true
+      - type: object
+        name: "nucleus_labels"
+        description: Ground truth nucleus segmentation labels
+        required: false
     tables:
       - type: anndata
         name: "table"

src/data_processors/process_dataset/script.py

@@ -115,6 +115,7 @@ def sc_processing(adata):
 output_spatial = sd.SpatialData(
     images={"morphology_mip": sp_data.images["morphology_mip"]},
     points={"transcripts": clean_transcripts},
+    labels={k: v for k, v in sp_data.labels.items()},
     tables={"table": minimal_table},
 )