omero fields optional by will-moore · Pull Request #87 · ome/ngff-spec

will-moore · 2026-02-05T10:16:33Z

Fixes ome/ngff#192

ported from ome/ngff#297

github-actions · 2026-02-05T10:16:42Z

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Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

align schema and spec text

…re/ngff-spec into omero_metadata_tests

jo-mueller · 2026-03-03T12:00:35Z

@will-moore small bump here to have a look at will-moore#2 to have this move forward :)

Omero metadata optional

lubianat

I am not super familiar with details, but it looks good as far as I can tell.

jburel · 2026-03-05T09:26:12Z

+          "label": "Channel:2",
+          "color": "#0000ff",
+          "active": true,
+          "family": "gamma",


that does not exist as a mapping family

jburel · 2026-03-05T09:26:55Z

+          "label": "Channel:1",
+          "color": "#00ff00",
+          "active": true,
+          "family": "log",


logarithmic is the term I believe we have for the rendering defi

jburel · 2026-03-05T09:27:17Z

+          "label": "Channel:1",
+          "color": "#00ff00",
+          "active": true,
+          "family": "log",


jburel · 2026-03-05T09:27:24Z

+          "label": "Channel:2",
+          "color": "#0000ff",
+          "active": true,
+          "family": "gamma",


jburel · 2026-03-05T09:28:06Z

+- `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".


this is not correct

we have in the omero rnd: linear, logarithmic, exponential and polynomial.
I believe what you refer as "gamma" will be polynomial.
I would avoid the divergence that we already have at the model level (see comment below)

I think this originates from a PR of mine to this one. I didn't find these terms (i.e., "family" precisely defined anywhere), so I kept it vague. Would be nice to have this clearly mapped out somewhere, i.e., here :)

I think we should remove the "family" and "coefficient" terms from the "omero" examples and docs.
They have never been defined before, and are still not clear, so I don't think they will have ever been used.

jburel · 2026-03-05T09:29:49Z

  - For detailed set of changes see [complete overview](https://ngff.openmicroscopy.org/rfc/5/responses/2/index.html)
 - 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.


We should be more explicit and use the term specification

jburel · 2026-03-05T09:31:17Z

This could also be an opportunity to fix the model value color is not a value used by omero it is rgb

will-moore · 2026-03-05T10:50:25Z

+      "channels": [
+        {
+          "label": "Channel:0",
+          "color": "#ff0000",


All the color values shouldn't include the #.
Definition below is:
(string) String of 6 hexadecimal digits specifying the color of the channel in RGB format.

will-moore · 2026-03-05T10:52:20Z

@jburel We're not changing the color definition here. This PR should not be a breaking change. We're just making some fields optional. The definition for color is:

(string) String of 6 hexadecimal digits specifying the color of the channel in RGB format.

No mention of OMERO.

jburel · 2026-03-09T14:47:37Z

to clarify I am referring to "model": "color" . We are using "omero" metadata but the model in ome-zarr is color and the omero-model is rgb.

jo-mueller · 2026-03-12T10:18:58Z

@jburel @will-moore is there a central place where the fields and possible values of the omero metadata model are documented? There's a link in the spec text but explains some fields, but not all (i.e., family, etc)

joshmoore · 2026-07-02T12:30:39Z

@will-moore @jburel: would you like to get this into one of the upcoming .dev versions? And if so, when would you be thinking?

will-moore · 2026-07-02T12:37:10Z

I actually thought this had made it into v0.6.
So, yes. As soon as possible, thanks.

joshmoore · 2026-07-04T07:18:07Z

@jni is leading dev1 so I'll defer. Otherwise we can get it on a board for dev2 and discuss.

jni · 2026-07-21T10:43:38Z

@will-moore there's a number of unresolved comments here. (log->logarithmic, removing "gamma", removing "#" from the color). Otherwise, I'm happy for this to go into 0.9.dev1 which is due ~end August. Note also that I don't have merge rights in this repo 😅 so someone else will have to do so, presumably after 0.6 is out. (Although, given the backwards compatibility of the change, I would not be opposed if it went into 0.6.rc1/final. CC @jo-mueller)

will-moore · 2026-07-22T11:31:34Z

I think that is all the fixes done.
I was checking https://omero.readthedocs.io/en/stable/developers/Web/WebGateway.html#imgdata for any reference to coefficient and family but it has no info on these and actually has less info than is in these docs themselves so I've removed that link.

I also have therefore also removed the coefficient and family fields from the omero block since these have never been defined and never used AFAIK.

jni · 2026-07-22T15:53:50Z

Great. @will-moore do you want to mark this as ready for review then?

@jo-mueller what do you think about shipping this with 0.6 final?

omero fields optional

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ported from ome/ngff#297

will-moore mentioned this pull request Feb 5, 2026

Omero metadata optional ome/ngff#297

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jo-mueller added this to OME-Zarr 0.6.dev3 Feb 5, 2026

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will-moore and others added 4 commits February 5, 2026 10:33

Apply suggestion from @jo-mueller

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Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

Apply suggestion from @jo-mueller

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Co-authored-by: Johannes Soltwedel <38459088+jo-mueller@users.noreply.github.com>

dictionaries renamed to objects

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Merge branch 'main' into omero_metadata_optional

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lubianat approved these changes Feb 5, 2026

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jo-mueller added 3 commits February 10, 2026 16:48

Merge branch 'main' into omero_metadata_optional

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Update index.md

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align schema and spec text

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jo-mueller mentioned this pull request Feb 12, 2026

align schema and spec text will-moore/ngff-spec#1

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will-moore and others added 9 commits February 12, 2026 16:58

Merge pull request #1 from jo-mueller/omero_metadata_optional

87b04ae

align schema and spec text

Merge branch 'main' into omero_metadata_optional

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Merge remote-tracking branch 'upstream/main' into omero_metadata_schemas

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Merge branch 'omero_metadata_optional' of https://github.com/will-moo…

03568f4

…re/ngff-spec into omero_metadata_tests

chore: json example code style

1ecf820

fix: added missing fields to spec text

16eda06

chore: semantic line break and text style

b6d5807

fix: adding missing coefficient to schema

cd4509b

test: added test cases

362a988

jo-mueller mentioned this pull request Feb 13, 2026

Omero metadata optional will-moore/ngff-spec#2

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Added note to changelog

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lubianat mentioned this pull request Feb 23, 2026

NGFF PR Review (2026-03-03) German-BioImaging/incubator#54

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Merge pull request #2 from jo-mueller/omero_metadata_optional

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Omero metadata optional

jo-mueller approved these changes Mar 3, 2026

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Merge branch 'main' into omero_metadata_optional

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jo-mueller requested a review from joshmoore March 4, 2026 23:13

jburel requested changes Mar 5, 2026

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will-moore commented Mar 5, 2026

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lubianat self-requested a review March 10, 2026 13:07

lubianat mentioned this pull request Mar 10, 2026

NGFF PR Review (2026-03-13) German-BioImaging/incubator#55

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Merge branch 'main' into omero_metadata_optional

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lubianat mentioned this pull request Mar 30, 2026

NGFF PR Review (2026-04-01) German-BioImaging/incubator#60

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lubianat mentioned this pull request Jun 12, 2026

EPIC: rendering settings ome/ngff#537

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joshmoore marked this pull request as draft July 2, 2026 12:30

jni moved this to Backlog in OME-Zarr 0.9.dev1 Jul 21, 2026

jni added this to OME-Zarr 0.9.dev1 Jul 21, 2026

will-moore added 5 commits July 22, 2026 11:54

Merge remote-tracking branch 'origin/main' into omero_metadata_optional

9446d58

Remove 'family' and 'coefficient' from 'omero' schema, docs and samples

8d19fd3

Remove # from color strings

ec207e4

Update full_omero_metadata.json to 0.6rc0

71caad2

Remove link to omero docs WebGateway.html since this has no extra info

e69e118

will-moore marked this pull request as ready for review July 22, 2026 16:27

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will-moore commented Feb 5, 2026 •

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