Handle autofluorescence channels and pass through unknown image types (#368)

Co-authored-by: Luca Marconato <m.lucalmer@gmail.com>

Author: MSHelm

.gitignore

@@ -50,5 +50,5 @@ data
 # data folder
 data/
 tests/data
-uv.lock
-.asv/
+.venv
+.uv.lock

src/spatialdata_io/readers/macsima.py

@@ -38,6 +38,7 @@
     "B": "bleach",  # v1
     "AntigenCycle": "stain",  # v0
     "S": "stain",  # v1
+    "AF": "autofluorescence",  # v1
 }
 
 
@@ -499,7 +500,7 @@ def _parse_v0_ome_metadata(ome: OME) -> dict[str, Any]:
 
     # Harmonize imagetype across versions
     if metadata["imagetype"]:
-        metadata["imagetype"] = IMAGETYPE_DICT[metadata["imagetype"]]
+        metadata["imagetype"] = IMAGETYPE_DICT.get(metadata["imagetype"], metadata["imagetype"])
 
     return metadata
 
@@ -579,7 +580,7 @@ def _parse_v1_ome_metadata(ome: OME) -> dict[str, Any]:
 
     # Harmonize imagetype across versions
     if metadata["imagetype"]:
-        metadata["imagetype"] = IMAGETYPE_DICT[metadata["imagetype"]]
+        metadata["imagetype"] = IMAGETYPE_DICT.get(metadata["imagetype"], metadata["imagetype"])
 
     return metadata
 

tests/test_macsima.py

@@ -551,6 +551,26 @@ def test_parse_v0_ome_metadata_bleach_cycle_appends_background() -> None:
     assert md["name"] == "CD4_background"
 
 
+def test_parse_v0_ome_metadata_handles_unknown_imagetypes() -> None:
+    ome = OME(
+        structured_annotations=StructuredAnnotations(
+            map_annotations=[
+                MapAnnotation(
+                    value={
+                        "MICS cycle type": "NOT A VALID TYPE",
+                    }
+                )
+            ]
+        ),
+        screens=[Screen(reagents=[Reagent(name="CD4__RPA-T4")])],
+    )
+
+    md = _parse_v0_ome_metadata(ome)
+
+    # Unknown types should just be passed through
+    assert md["imagetype"] == "NOT A VALID TYPE"
+
+
 def test_parse_v1_ome_metadata_basic_extraction_and_conversions() -> None:
     ome = OME(
         structured_annotations=StructuredAnnotations(
@@ -605,6 +625,26 @@ def test_parse_v1_ome_metadata_invalid_numerics_become_none() -> None:
     assert md["roi"] is None
 
 
+def test_parse_v1_ome_metadata_handles_unknown_imagetypes() -> None:
+    ome = OME(
+        structured_annotations=StructuredAnnotations(
+            map_annotations=[
+                MapAnnotation(
+                    value={
+                        "ScanType": "NOT A VALID TYPE",
+                    }
+                )
+            ]
+        ),
+        screens=[Screen(reagents=[Reagent(name="CD4__RPA-T4")])],
+    )
+
+    md = _parse_v1_ome_metadata(ome)
+
+    # Unknown types should just be passed through
+    assert md["imagetype"] == "NOT A VALID TYPE"
+
+
 def make_ome_with_version(version_value: str, extra_ma: dict[str, Any] | None = None) -> OME:
     base = {"SoftwareVersion": version_value}
     if extra_ma: