add spatial key in obsm

Author: giovp

src/spatialdata_io/readers/mcmicro.py

@@ -56,14 +56,14 @@ def mcmicro(
         raise ValueError("Dataset id is not consistent with sample name.")
 
     images = {}
-    images[dataset_id] = _get_images(
+    images[f"{dataset_id}_image"] = _get_images(
         path,
         dataset_id,
         imread_kwargs,
         image_models_kwargs,
     )
     labels = {}
-    labels[dataset_id] = _get_labels(
+    labels[f"{dataset_id}_cells"] = _get_labels(
         path,
         dataset_id,
         "cell",
@@ -126,5 +126,8 @@ def _get_table(
         obsm={"spatial": table[coords].to_numpy()},
         dtype=np.float_,
     )
+    adata.obs["region"] = f"{sample}_cells"
 
-    return TableModel.parse(adata, region=f"/labels/{sample}", instance_key=McmicroKeys.INSTANCE_KEY.value)
+    return TableModel.parse(
+        adata, region=f"{sample}_cells", region_key="region", instance_key=McmicroKeys.INSTANCE_KEY.value
+    )

src/spatialdata_io/readers/steinbock.py

@@ -61,13 +61,13 @@ def steinbock(
             "They will be ignored."
         )
     for sample in samples:
-        images[sample] = _get_images(
+        images[f"{sample}_image"] = _get_images(
             path,
             sample,
             imread_kwargs,
             image_models_kwargs,
         )
-        labels[sample] = _get_labels(
+        labels[f"{sample}_labels"] = _get_labels(
             path,
             sample,
             labels_kind,
@@ -78,10 +78,11 @@ def steinbock(
     adata = ad.read(path / SteinbockKeys.CELLS_FILE)
     idx = adata.obs.index.str.split(" ").map(lambda x: int(x[1]))
     regions = adata.obs.image.str.replace(".tiff", "", regex=False)
-    regions = regions.apply(lambda x: f"/labels/{x}")
+    regions = regions.apply(lambda x: f"{x}_labels")
     adata.obs["cell_id"] = idx
     adata.obs["region"] = regions
-    if len({f"/labels/{s}" for s in samples}.difference(set(regions.unique()))):
+    adata.obsm["spatial"] = adata.obs[["centroid-0", "centroid-1"]].to_numpy()
+    if len({f"{s}_labels" for s in samples}.difference(set(regions.unique()))):
         raise ValueError("Samples in table and images are inconsistent, please check.")
     table = TableModel.parse(adata, region=regions.unique().tolist(), region_key="region", instance_key="cell_id")
 
@@ -95,7 +96,7 @@ def _get_images(
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
 ) -> Union[SpatialImage, MultiscaleSpatialImage]:
     image = imread(path / SteinbockKeys.IMAGES_DIR / f"{sample}{SteinbockKeys.IMAGE_SUFFIX}", **imread_kwargs)
-    return Image2DModel.parse(image, transformations={sample: Identity()}, **image_models_kwargs)
+    return Image2DModel.parse(data=image, transformations={sample: Identity()}, **image_models_kwargs)
 
 
 def _get_labels(
@@ -106,4 +107,4 @@ def _get_labels(
     image_models_kwargs: Mapping[str, Any] = MappingProxyType({}),
 ) -> Union[SpatialImage, MultiscaleSpatialImage]:
     image = imread(path / labels_kind / f"{sample}{SteinbockKeys.LABEL_SUFFIX}", **imread_kwargs).squeeze()
-    return Labels2DModel.parse(image, transformations={sample: Identity()}, **image_models_kwargs)
+    return Labels2DModel.parse(data=image, transformations={sample: Identity()}, **image_models_kwargs)

src/spatialdata_io/readers/visium.py

@@ -95,6 +95,7 @@ def visium(
 
     adata.obs = pd.merge(adata.obs, coords, how="left", left_index=True, right_index=True)
     coords = adata.obs[[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y]].values
+    adata.obsm["spatial"] = coords
     adata.obs.drop(columns=[VisiumKeys.SPOTS_X, VisiumKeys.SPOTS_Y], inplace=True)
     adata.obs["spot_id"] = np.arange(len(adata))
     adata.var_names_make_unique()

src/spatialdata_io/readers/xenium.py

@@ -182,6 +182,7 @@ def _get_tables_and_circles(
     metadata = pd.read_parquet(path / XeniumKeys.CELL_METADATA_FILE)
     np.testing.assert_array_equal(metadata.cell_id.astype(str).values, adata.obs_names.values)
     circ = metadata[[XeniumKeys.CELL_X, XeniumKeys.CELL_Y]].to_numpy()
+    adata.obsm["spatial"] = circ
     metadata.drop([XeniumKeys.CELL_X, XeniumKeys.CELL_Y], axis=1, inplace=True)
     adata.obs = metadata
     adata.obs["region"] = specs["region"]