From 565a6cdb52e10c66aaae43ce8cf9e41149e2126b Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 17 Jun 2026 14:30:35 +0100
Subject: [PATCH 1/3] scene.coordinateTransformations path optional for input
 and output

---
 schemas/scene.schema | 64 ++++++++++++++++++++++++--------------------
 1 file changed, 35 insertions(+), 29 deletions(-)

diff --git a/schemas/scene.schema b/schemas/scene.schema
index 6c409a85..ee39ed35 100644
--- a/schemas/scene.schema
+++ b/schemas/scene.schema
@@ -16,37 +16,43 @@
             },
             "coordinateTransformations": {
               "$comment": "Merge general coordinate transformations with constraints for scene metadata",
-              "allOf": [
-                {
-                  "$ref": "coordinate_transformations.schema",
-                  "description": "General coordinate transformations defining spatial relationships between coordinate systems"
-                },
-                {
-                  "type": "array",
-                  "items": {
-                    "allOf": [
-                      {
+              "type": "array",
+              "minItems": 1,
+              "items": {
+                "allOf": [
+                  {
+                    "$ref": "coordinate_transformations.schema#/$defs/coordinateTransformation",
+                    "description": "Parameters of any possible transform"
+                  },
+                  {
+                    "type": "object",
+                    "description": "Transformations between two coordinate systems referenced by name in the same metadata document",
+                    "properties": {
+                      "input": {
+                        "type": "object",
                         "properties": {
-                          "input": {
-                            "allOf": [
-                              {"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
-                              {"required": ["name"]}
-                            ]
-                          },
-                          "output": {
-                            "allOf": [
-                              {"$ref": "coordinate_transformations.schema#/$defs/inputOutput"},
-                              {"required": ["name"]}
-                            ]
-                          }
-                        }
+                          "name": {"type": "string"},
+                          "path": {"type": "string"}
+                        },
+                        "required": ["name"],
+                        "additionalProperties": false,
+                        "description": "Must reference a coordinate system defined in the same metadata document (path empty)"
+                      },
+                      "output": {
+                        "type": "object",
+                        "properties": {
+                          "name": {"type": "string"},
+                          "path": {"type": "string"}
+                        },
+                        "required": ["name"],
+                        "additionalProperties": false,
+                        "description": "Must reference a coordinate system defined in the same metadata document (path empty)"
                       }
-                    ]
-                  },
-                  "description": "Constrained input/output for coordinate transformations in scene metadata"
-                }
-              ]
-                
+                    },
+                    "required": ["input", "output"]
+                  }
+                ]
+              } 
             },
             "arrayCoordinateSystem": {
               "type": "object",

From 1fe9135b82410508e6ece8aab729715b710a4cf8 Mon Sep 17 00:00:00 2001
From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>
Date: Wed, 17 Jun 2026 17:12:09 +0200
Subject: [PATCH 2/3] tests: add json to example to CI

---
 tests/attributes/spec/valid/scene/scene.json | 71 ++++++++++++++++++++
 1 file changed, 71 insertions(+)
 create mode 100644 tests/attributes/spec/valid/scene/scene.json

diff --git a/tests/attributes/spec/valid/scene/scene.json b/tests/attributes/spec/valid/scene/scene.json
new file mode 100644
index 00000000..50b1cf44
--- /dev/null
+++ b/tests/attributes/spec/valid/scene/scene.json
@@ -0,0 +1,71 @@
+{
+  "ome": {
+    "version": "0.6.dev3",
+    "scene": {
+      "coordinateTransformations": [
+        {
+          "input": {"path": "4995115_cropped_400_100_400_400_rot10.zarr", "name": "rotated"},
+          "output": {"name": "translated_x50"},
+          "name": "translate_tile_to_stitched_position",
+          "type": "translation",
+          "translation": [
+            0,
+            0,
+            30.608878192215265,
+            11.21775638443053
+          ]
+        },
+        {
+          "input": {"path": "4995115_cropped_700_700_400_400_rot45.zarr", "name": "rotated"},
+          "output": {"name": "translated_x50"},
+          "name": "translate_tile_to_stitched_position",
+          "type": "translation",
+          "translation": [
+            0,
+            0,
+            91.8266345766458,
+            41.8266345766458
+          ]
+        },
+        {
+          "input": {"name": "translated_x50"},
+          "output": {"path": "4995115_full.zarr", "name": "physical"},
+          "name": "translate_tile_to_stitched_position",
+          "type": "translation",
+          "translation": [
+            0,
+            0,
+            0,
+            50
+          ]
+        }
+      ],
+      "coordinateSystems": [
+        {
+          "name": "translated_x50",
+          "axes": [
+            {
+              "name": "c",
+              "type": "channel"
+            },
+            {
+              "name": "z",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "y",
+              "type": "space",
+              "unit": "micrometer"
+            },
+            {
+              "name": "x",
+              "type": "space",
+              "unit": "micrometer"
+            }
+          ]
+        }
+      ]
+    }
+  }
+}
\ No newline at end of file

From 5dfbecdb2e6acbcc0c614bf09325716b0ac77417 Mon Sep 17 00:00:00 2001
From: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>
Date: Wed, 17 Jun 2026 18:51:18 +0200
Subject: [PATCH 3/3] tests: correct version in metadata

---
 tests/attributes/spec/valid/scene/scene.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/attributes/spec/valid/scene/scene.json b/tests/attributes/spec/valid/scene/scene.json
index 50b1cf44..eae5a2de 100644
--- a/tests/attributes/spec/valid/scene/scene.json
+++ b/tests/attributes/spec/valid/scene/scene.json
@@ -1,6 +1,6 @@
 {
   "ome": {
-    "version": "0.6.dev3",
+    "version": "0.6.dev4",
     "scene": {
       "coordinateTransformations": [
         {