From 0257c80b59d3e2cffb6eb15629e22a7d975237c7 Mon Sep 17 00:00:00 2001
From: stanbot8 <stanbot8@gmail.com>
Date: Fri, 24 Jul 2026 14:21:45 -0700
Subject: [PATCH] fix: write OME channel labels as strings

---
 src/spatialdata/_io/_utils.py    | 15 ++++++++++-----
 src/spatialdata/_io/io_raster.py |  5 +++++
 tests/io/test_metadata.py        | 19 +++++++++++++++++++
 3 files changed, 34 insertions(+), 5 deletions(-)

diff --git a/src/spatialdata/_io/_utils.py b/src/spatialdata/_io/_utils.py
index fa5af1dd7..ec5a73c24 100644
--- a/src/spatialdata/_io/_utils.py
+++ b/src/spatialdata/_io/_utils.py
@@ -153,15 +153,20 @@ def overwrite_channel_names(group: zarr.Group, element: DataArray | DataTree) ->
     else:
         channel_names = element["scale0"]["image"].coords["c"].data.tolist()
 
-    channel_metadata = [{"label": name} for name in channel_names]
+    attrs = group.attrs.asdict()
+    channel_metadata = [{"label": str(name)} for name in channel_names]
+    spatialdata_attrs = attrs.get("spatialdata_attrs", {})
+    spatialdata_attrs["channel_names"] = channel_names
+    attrs["spatialdata_attrs"] = spatialdata_attrs
     # We don't use the ome-zarr load node API, and ome-zarr-py >= 0.18 emits no `omero` block, so default to empty.
-    omero_meta = group.attrs.get("omero") or group.attrs.get("ome", {}).get("omero") or {}
+    omero_meta = attrs.get("omero") or attrs.get("ome", {}).get("omero") or {}
     omero_meta["channels"] = channel_metadata
-    if ome_meta := group.attrs.get("ome", None):
+    if ome_meta := attrs.get("ome", None):
         ome_meta["omero"] = omero_meta
-        group.attrs["ome"] = ome_meta
+        attrs["ome"] = ome_meta
     else:
-        group.attrs["omero"] = omero_meta
+        attrs["omero"] = omero_meta
+    group.attrs.put(attrs)
 
 
 def _write_metadata(
diff --git a/src/spatialdata/_io/io_raster.py b/src/spatialdata/_io/io_raster.py
index 276f016bd..ab7480224 100644
--- a/src/spatialdata/_io/io_raster.py
+++ b/src/spatialdata/_io/io_raster.py
@@ -168,6 +168,9 @@ def _read_multiscale(
     nodes: list[Node] = []
     image_loc = ZarrLocation(store, fmt=reader_format)
     if exists := image_loc.exists():
+        spatialdata_channels = (
+            zarr.open_group(store=image_loc.store, mode="r").attrs.get(ATTRS_KEY, {}).get("channel_names")
+        )
         image_reader = Reader(image_loc)()
         image_nodes = list(image_reader)
         nodes = _get_multiscale_nodes(image_nodes, nodes)
@@ -213,6 +216,8 @@ def _read_multiscale(
             channels = [d["label"] for d in legacy_channels_metadata["channels"]]
         if omero_metadata is not None:
             channels = [d["label"] for d in omero_metadata["channels"]]
+        if spatialdata_channels is not None:
+            channels = spatialdata_channels
     axes = [i["name"] for i in node.metadata["axes"]]
     if len(datasets) > 1:
         arrays = [node.load(Multiscales).array(resolution=d) for d in datasets]
diff --git a/tests/io/test_metadata.py b/tests/io/test_metadata.py
index c07f026c0..777f4b870 100644
--- a/tests/io/test_metadata.py
+++ b/tests/io/test_metadata.py
@@ -5,6 +5,7 @@
 import tempfile
 
 import pytest
+import zarr
 
 from spatialdata import SpatialData, read_zarr
 from spatialdata._io._utils import _is_element_self_contained
@@ -117,6 +118,24 @@ def test_save_transformations_incremental(element_name, full_sdata, caplog):
 
 
 # test io for channel names
+@pytest.mark.parametrize("expected", [[0, 1, 2], ["0", "1", "2"]], ids=["integers", "numeric-strings"])
+def test_channel_names_store_string_labels_without_changing_coordinates(
+    images: SpatialData, tmp_path, expected: list[int] | list[str]
+) -> None:
+    path = tmp_path / "sdata.zarr"
+    image = images["image2d_xarray"].assign_coords(c=expected)
+    SpatialData(images={"image": image}).write(path)
+    root = zarr.open_group(path, mode="r")
+    attrs = root["images"]["image"].attrs
+    omero = attrs.get("omero") or attrs["ome"]["omero"]
+    labels = [channel["label"] for channel in omero["channels"]]
+    channel_names = attrs["spatialdata_attrs"]["channel_names"]
+    root.store.close()
+    assert labels == [str(value) for value in expected]
+    assert channel_names == expected
+    assert get_channel_names(SpatialData.read(path)["image"]) == expected
+
+
 @pytest.mark.parametrize("write", ["overwrite", "write", "no"])
 def test_save_channel_names_incremental(images: SpatialData, write: str) -> None:
     old_channels2d = get_channel_names(images["image2d"])