diff --git a/src/spatialdata_io/readers/steinbock.py b/src/spatialdata_io/readers/steinbock.py index 8a6223f1..8c8d50a7 100644 --- a/src/spatialdata_io/readers/steinbock.py +++ b/src/spatialdata_io/readers/steinbock.py @@ -77,7 +77,7 @@ def steinbock( image_models_kwargs, ) - adata = ad.read(path / SteinbockKeys.CELLS_FILE) + adata = ad.read_h5ad(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"{x}_labels") @@ -101,7 +101,7 @@ def steinbock( 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") - return SpatialData(images=images, labels=labels, table=table) + return SpatialData(images=images, labels=labels, tables={"table": table}) def _get_images(