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Merged
will-moore merged 8 commits into from
Mar 3, 2026
Merged

Omero metadata optional #2

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2f449c3
Merge remote-tracking branch 'upstream/main' into omero_metadata_schemas
jo-mueller Feb 13, 2026
03568f4
Merge branch 'omero_metadata_optional' of https://github.com/will-moo…
jo-mueller Feb 13, 2026
1ecf820
chore: json example code style
jo-mueller Feb 13, 2026
16eda06
fix: added missing fields to spec text
jo-mueller Feb 13, 2026
b6d5807
chore: semantic line break and text style
jo-mueller Feb 13, 2026
cd4509b
fix: adding missing `coefficient` to schema
jo-mueller Feb 13, 2026
362a988
test: added test cases
jo-mueller Feb 13, 2026
facbf73
Added note to changelog
jo-mueller Feb 13, 2026
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19 changes: 11 additions & 8 deletions index.md
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Original file line number Diff line number Diff line change
Expand Up @@ -1491,12 +1491,13 @@ if not datasets:
### "omero" metadata (transitional)
(omero-md)=

[=Transitional=] information specific to the channels of an image and how to render it can be found under the `omero` key in the group-level metadata:
Information specific to the channels of an image and how to render it
can be found under the `omero` key in the group-level metadata (i.e., under `"ome" > "omero"`):

```json
"id": 1, # ID in OMERO
"name": "example.tif", # Name as shown in the UI
"channels": [ # Array matching the c dimension size
"id": 1, // ID in OMERO
"name": "example.tif", // Name as shown in the UI
"channels": [ // Array matching the c dimension size
{
"active": true,
"coefficient": 1,
Expand All @@ -1513,9 +1514,9 @@ if not datasets:
}
],
"rdefs": {
"defaultT": 0, # First timepoint to show the user
"defaultZ": 118, # First Z section to show the user
"model": "color" # "color" or "greyscale"
"defaultT": 0, // First timepoint to show the user
"defaultZ": 118, // First Z section to show the user
"model": "color" // "color" or "greyscale"
}
```

Expand All @@ -1525,11 +1526,13 @@ for more information.
The `omero` metadata is optional, but if present it MUST contain the field `channels`,
which is an array of objects describing the channels of the image.
The `channels` array length SHOULD correspond to the size of the respective channels axis, if present.
Each object in `channels` MAY contain the following fields:
Each object in `channels` is optional and MAY contain the following fields:

- `color` (string) String of 6 hexadecimal digits specifying the color of the channel in RGB format.
- `label` (string) Channel name.
- `active` (boolean) Indicates whether the channel should be displayed.
- `coefficient`: (float) Value to multiply the pixel values of the channel by when rendering.
- `family`: (string) Used transfer function family for rendering the channel, e.g. "linear", "log", "gamma".
- `window` (dictionary) Values describing the windowing of the channel.
If provided, `start` and `end` values MUST be specified.
All values can be floating-point numbers, but will likely be integers for integer pixel types.
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3 changes: 3 additions & 0 deletions schemas/image.schema
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Expand Up @@ -143,6 +143,9 @@
"label": {
"type": "string"
},
"coefficient": {
"type": "number"
},
"family": {
"type": "string"
},
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56 changes: 56 additions & 0 deletions tests/attributes/spec/invalid/omero/missing_channels.json
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@@ -0,0 +1,56 @@
{
"ome": {
"version": "0.6.dev3",
"multiscales": [
{
"coordinateSystems": [
{
"name": "physical",
"axes": [
{
"name": "z",
"type": "space",
"unit": "micrometer"
},
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
]
}
],
"datasets": [
{
"path": "s0",
"coordinateTransformations": [
{
"scale": [
1,
1,
1
],
"input": "s0",
"output": "physical",
"type": "scale"
}
]
}
]
}
],
"omero": {
}
},
"_conformance": {
"schema": {
"id": "schemas/image.schema"
},
"valid": false
}
}
94 changes: 94 additions & 0 deletions tests/attributes/spec/invalid/omero/missing_start_end.json
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@@ -0,0 +1,94 @@
{
"ome": {
"version": "0.6.dev3",
"multiscales": [
{
"coordinateSystems": [
{
"name": "physical",
"axes": [
{
"name": "z",
"type": "space",
"unit": "micrometer"
},
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
]
}
],
"datasets": [
{
"path": "s0",
"coordinateTransformations": [
{
"scale": [
1,
1,
1
],
"input": "s0",
"output": "physical",
"type": "scale"
}
]
}
]
}
],
"omero": {
"channels": [
{
"label": "Channel:0",
"color": "#ff0000",
"active": true,
"family": "linear",
"coefficient": 1.0,
"inverted": false,
"window": {
"min": 0,
"max": 255
}
},
{
"label": "Channel:1",
"color": "#00ff00",
"active": true,
"family": "log",
"coefficient": 0.5,
"inverted": true,
"window": {
"min": 0,
"max": 255
}
},
{
"label": "Channel:2",
"color": "#0000ff",
"active": true,
"family": "gamma",
"coefficient": 2.0,
"inverted": false,
"window": {
"min": 0,
"max": 255
}
}
]
}
},
"_conformance": {
"schema": {
"id": "schemas/image.schema"
},
"valid": false
}
}
99 changes: 99 additions & 0 deletions tests/attributes/spec/valid/omero/full_omero_metadata.json
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@@ -0,0 +1,99 @@
{
"ome": {
"version": "0.6.dev3",
"multiscales": [
{
"coordinateSystems": [
{
"name": "physical",
"axes": [
{
"name": "z",
"type": "space",
"unit": "micrometer"
},
{
"name": "y",
"type": "space",
"unit": "micrometer"
},
{
"name": "x",
"type": "space",
"unit": "micrometer"
}
]
}
],
"datasets": [
{
"path": "s0",
"coordinateTransformations": [
{
"scale": [
1,
1,
1
],
"input": "s0",
"output": "physical",
"type": "scale"
}
]
}
]
}
],
"omero": {
"channels": [
{
"label": "Channel:0",
"color": "#ff0000",
"active": true,
"family": "linear",
"coefficient": 1.0,
"inverted": false,
"window": {
"min": 0,
"start": 100,
"end": 200,
"max": 255
}
},
{
"label": "Channel:1",
"color": "#00ff00",
"active": true,
"family": "log",
"coefficient": 0.5,
"inverted": true,
"window": {
"min": 0,
"start": 50,
"end": 150,
"max": 255
}
},
{
"label": "Channel:2",
"color": "#0000ff",
"active": true,
"family": "gamma",
"coefficient": 2.0,
"inverted": false,
"window": {
"min": 0,
"start": 25,
"end": 125,
"max": 255
}
}
]
}
},
"_conformance": {
"schema": {
"id": "schemas/image.schema"
}
}
}
1 change: 1 addition & 0 deletions version_history.md
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Expand Up @@ -14,6 +14,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).

- Updated version keys from `0.6.dev2` to `0.6.dev3` everywhere
- style: Homogeneous use of backticks in spec document
- spec: Released requirements for `omero` metadata in the spec document and in schemas.

### Removed

Expand Down