simplify

src/depiction/tools/ometiff_to_hdf5.py

@@ -1,7 +1,6 @@
+import cyclopts
 from pathlib import Path
 
-import cyclopts
-from depiction.image.multi_channel_image import MultiChannelImage
 from depiction.persistence.image.ome_tiff import OmeTiff
 
 app = cyclopts.App()
@@ -13,12 +12,7 @@ def ometiff_to_hdf5(
     output_hdf5: Path,
 ) -> None:
     """Writes input_ometiff to output_hdf5 using our MultiChannelImage representation."""
-    data = OmeTiff.read(input_ometiff)
-    if "pixel_size" in data.attrs:
-        # TODO this is quite broken and should be fixed in the future, but currently the pixel size cannot
-        # be persisted
-        del data.attrs["pixel_size"]
-    image = MultiChannelImage(data)
+    image = OmeTiff.read_image(input_ometiff, bg_value=0.0)
     image.write_hdf5(output_hdf5)