Upgrade ome-zarr package

vitessce · Jan 22, 2024 · 983892d · 983892d
1 parent 8934187
commit 983892d
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Showing 2 changed files with 39 additions and 39 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -34,7 +34,7 @@ dependencies = [
   'numpy>=1.21.2',
   'anndata>=0.7.8,<0.9',
   'scanpy>=1.9.3',
-  'ome-zarr==0.2.1',
+  'ome-zarr==0.8.3',
   'tifffile>=2020.10.1',
   'jsonschema>=3.2'
 ]

diff --git a/vitessce/data_utils/ome.py b/vitessce/data_utils/ome.py
@@ -75,30 +75,30 @@ def rgb_img_to_ome_zarr(img_arr, output_path, img_name="Image", chunks=(1, 256,
         image=img_arr,
         group=z_root,
         axes=axes,
-        omero={
-            "name": img_name,
-            "version": "0.3",
-            "rdefs": {},
-            "channels": [
-                {
-                    "label": "R",
-                    "color": "FF0000",
-                    "window": default_window
-                },
-                {
-                    "label": "G",
-                    "color": "00FF00",
-                    "window": default_window
-                },
-                {
-                    "label": "B",
-                    "color": "0000FF",
-                    "window": default_window
-                }
-            ]
-        },
-        chunks=chunks
+        storage_options=dict(chunks=chunks)
     )
+    z_root.attrs["omero"] = {
+        "name": img_name,
+        "version": "0.3",
+        "rdefs": {},
+        "channels": [
+            {
+                "label": "R",
+                "color": "FF0000",
+                "window": default_window
+            },
+            {
+                "label": "G",
+                "color": "00FF00",
+                "window": default_window
+            },
+            {
+                "label": "B",
+                "color": "0000FF",
+                "window": default_window
+            }
+        ]
+    }
 
 
 def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Image", chunks=(1, 256, 256), axes="cyx", channel_colors=None):
@@ -132,19 +132,19 @@ def multiplex_img_to_ome_zarr(img_arr, channel_names, output_path, img_name="Ima
         image=img_arr,
         group=z_root,
         axes=axes,
-        omero={
-            "name": img_name,
-            "version": "0.3",
-            "rdefs": {},
-            "channels": [
-                {
-                    "label": channel_name,
-                    "color": channel_colors[channel_name] if channel_colors is not None else "FFFFFF",
-                    "window": default_window
-                }
-                for channel_name
-                in channel_names
-            ]
-        },
-        chunks=chunks
+        storage_options=dict(chunks=chunks)
     )
+    z_root.attrs["omero"] = {
+        "name": img_name,
+        "version": "0.3",
+        "rdefs": {},
+        "channels": [
+            {
+                "label": channel_name,
+                "color": channel_colors[channel_name] if channel_colors is not None else "FFFFFF",
+                "window": default_window
+            }
+            for channel_name
+            in channel_names
+        ]
+    }