Fix regex filter and table parsing on spatialdata I/O

src/segger/export/spatialdata_writer.py

@@ -94,7 +94,7 @@ def __init__(
         shapes_key: str = "cells",
         fragment_shapes_key: str = "fragments",
         include_table: bool = True,
-        table_key: str = "cells_table",  # no duplicate names allowed
+        table_key: str = "cells_table",
         fragment_table_key: str = "fragments_table",
         table_region_key: str = "cell_id",
     ):
@@ -250,7 +250,6 @@ def _create_spatialdata(
         """Create SpatialData object from transcripts and boundaries."""
         import spatialdata
         from spatialdata.models import PointsModel, ShapesModel, TableModel
-        import spatialdata.models._accessor  # for points parsing on pre-release (https://github.com/scverse/spatialdata/issues/1093)
         import dask.dataframe as dd
 
         identity = self._identity_transform()
@@ -291,6 +290,7 @@ def _create_spatialdata(
                 tx_pd[col] = tx_pd[col].astype(float)
 
         # Create Dask DataFrame for points
+        tx_pd[feature_column] = tx_pd[feature_column].astype("category")
         tx_dask = dd.from_pandas(tx_pd)
 
         # Points element
@@ -336,17 +336,17 @@ def _parse_shapes(shapes):
 
         if self.include_boundaries and self.boundary_method != "skip":
             if self.boundary_method == "input":
-                for bd_type in ["cell", "nucleus"]:  # these are segger hard-coded
+                bd_types = {"cell": "cells", "nucleus": "nuclei"}
+                for k, v in bd_types.items():
                     shapes = self._get_input_boundaries(
                         cell_tx_pd,
                         cell_id_column,
                         boundaries,
-                        bd_type)
+                        k)
                     shapes = _ensure_cell_id(shapes)
                     parsed = _parse_shapes(shapes)
                     if parsed is not None:
-                        shapes_elements[f"{bd_type}_boundaries"] = parsed  
-                        # this naming convention is very Xenium-based (ideally one would maintain the input one which is currently lost)
+                        shapes_elements[v] = parsed  
             else:
                 shape_specs = [(self.shapes_key, cell_tx_pd)]
                 if has_fragments and fragment_tx_pd is not None:
@@ -391,6 +391,12 @@ def _parse_shapes(shapes):
                     z_column=z_column,
                 )
 
+        for name, table in tables_elements.items():
+            if 'spatialdata_attrs' not in table.uns.keys():
+                warnings.warn(
+                    f"Table {name} does not contain the `uns['spatialdata_attrs']` field as no shapes element is associated."
+                )
+
         # Create SpatialData (prefer modern constructor methods, keep fallback on single elemnts)
         sdata = self._build_spatialdata(
             spatialdata=spatialdata,
@@ -449,7 +455,7 @@ def _build_table_element(
             obs_index_as_str=True,
         )
         if region is None:
-            return table
+            return TableModel.validate(table)
 
         instance_key = self.table_region_key
         table.obs["region"] = region
@@ -462,7 +468,8 @@ def _build_table_element(
                 region_key="region",
                 instance_key=instance_key or "instance_id",
             )
-        except Exception:
+        except Exception as e:
+            warnings.warn(f"TableModel.parse failed: {e}")
             return table
 
     def _write_spatialdata_zarr(self, sdata, output_path: Path, overwrite: bool) -> None:
@@ -535,6 +542,7 @@ def _get_generated_boundaries(
 
         elif self.boundary_method == "delaunay":
             from segger.export.boundary import generate_boundaries
+            warnings.filterwarnings('ignore', 'GeoSeries.notna', UserWarning)
 
             boundaries_gdf = generate_boundaries(
                 assigned,

src/segger/io/filtering.py

@@ -57,13 +57,13 @@ def platform_feature_filter_patterns(platform: str | None) -> list[str]:
         return list(MerscopeTranscriptFields.filter_substrings)
     return []
 
-
 def glob_patterns_to_regex(patterns: Sequence[str]) -> str:
-    """Convert glob-like patterns (``*``) to a regex union."""
-    return "|".join(
-        f"^{re.escape(pattern).replace(r'\\*', '.*')}$"
-        for pattern in patterns
-    )
+    """Convert glob-like patterns (`*`) to a regex union."""
+    regexes = []
+    for pattern in patterns:
+        regex_pattern = re.escape(pattern).replace(r"\*", ".*")
+        regexes.append(f"^{regex_pattern}$")
+    return "|".join(regexes)
 
 
 def apply_feature_filters(

src/segger/io/spatialdata_loader.py

@@ -314,7 +314,7 @@ def transcripts(
 
         cell_id_col = self._detect_column(
             columns,
-            ["cell_id", "cell", "segger_cell_id", "segmentation_cell_id", "instance_id"],
+            ["cell_id", "cell", "segger_cell_id", "segmentation_cell_id", "instance_id", "cell_ID"],
             optional=True,
         )