Repository: czbiohub-sf/iohub (language: python)

Issue:
Add far red color code
Currently the `CHANNEL_COLORS` look up table used for OME-Zarr metadata does not contain far red, e.g. Y5 (~700 nm emission).

What will be a good color for those? Currently ~600 nm channels are colored as magenta.

https://github.com/czbiohub-sf/iohub/blob/a4d43a2a8cd8d4abce00e475f9f1699d451eba9f/iohub/display_utils.py#L9-L30


Discussion / hints:
@ieivanov @edyoshikun
There is already Cy5. Will just add Y5 to 'orange'.

Fix patch:
diff --git a/iohub/display_utils.py b/iohub/display_utils.py
index f6bb159f..578c101c 100644
--- a/iohub/display_utils.py
+++ b/iohub/display_utils.py
@@ -26,7 +26,7 @@
     "blue": ["Blue", "DAPI", "BFP", "Hoechst"],
     "red": ["Red"],
     "yellow": ["Yellow", "Cy3"],  # Emission around 540-570 nm
-    "orange": ["Orange", "Cy5"],  # emission around 650-680 nm
+    "orange": ["Orange", "Cy5", "Y5"],  # emission around 650-680 nm
 }
 
 
diff --git a/setup.cfg b/setup.cfg
index b73eb098..3afffeee 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -51,7 +51,7 @@ dev =
     hypothesis>=6.61.0
     requests>=2.22.0
     wget>=3.2
-    ome-zarr>=0.6.1
+    ome-zarr>=0.9.0
 doc =
     matplotlib
     numpydoc>=1.1.0


Test patch:
diff --git a/tests/ngff/test_ngff.py b/tests/ngff/test_ngff.py
index d1aae0ca..a781bc5b 100644
--- a/tests/ngff/test_ngff.py
+++ b/tests/ngff/test_ngff.py
@@ -199,7 +199,7 @@ def test_write_ome_zarr(channels_and_random_5d, arr_name):
         # round-trip test with the offical reader implementation
         ext_reader = Reader(parse_url(dataset.zgroup.store.path))
         node = list(ext_reader())[0]
-        assert node.metadata["name"] == channel_names
+        assert node.metadata["channel_names"] == channel_names
         assert node.specs[0].datasets == [arr_name]
         assert node.data[0].shape == random_5d.shape
         assert node.data[0].dtype == random_5d.dtype