changelog

quentinblampey · May 24, 2024 · 94112e1 · 94112e1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning][].
 
 -   (Xenium) support reading multi-polygon selection files from the Xenium Explorer
 -   (ISS) An experimental loader to load elemental ISS data objects, e.g. raw.tif, label.tif and anndata.h5ad
+-   (Stereo-seq) Added reader.
 
 ### Fixed
 

diff --git a/src/spatialdata_io/readers/stereoseq.py b/src/spatialdata_io/readers/stereoseq.py
@@ -196,7 +196,7 @@ def stereoseq(
         adata.obs[column_name] = adata.obs[column_name].astype("category")
 
     images = {
-        f"{name}": Image2DModel.parse(
+        Path(name).stem: Image2DModel.parse(
             imread(path / SK.REGISTER / name, **imread_kwargs), dims=("c", "y", "x"), **image_models_kwargs
         )
         for name in image_filenames
@@ -336,7 +336,7 @@ def stereoseq(
             dims=("c", "y", "x"),
             **image_models_kwargs,
         )
-        images[f"{cell_mask_name}"] = masks
+        images[Path(cell_mask_name).stem] = masks
 
     sdata = SpatialData(images=images, tables=tables, shapes=shapes, points=points)
     return sdata