Transformations0.6 by AlexSurtees · Pull Request #80 · BioNGFF/vizarr

AlexSurtees · 2026-05-15T07:34:46Z

Description

Implements scene specification and 0.6 multiscales coordinateSystems.

Adds test images including scene. URL can be found at fixtures/scene.yaml e.g.

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/test-data/v0.6.dev3/idr0050/4995115_scene.zarr

NOTE

Due to image metadata mis-specification, the image WILL NOT align correctly while conforming to the specification rules. However, if the additional 'rotated' transformations are included the image DOES align correctly (i.e. the rotation transformation logic is correctly implemented). This is because the scene-level transformations specified here

https://will-moore.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/test-data/v0.6.dev3/idr0050/4995115_scene.zarr

for each image have input coordinate system 'physical', meaning we should only apply the coordinate transformations with coordinate system 'physical' from these images.

codecov · 2026-06-01T16:18:24Z

Codecov Report

❌ Patch coverage is 90.96386% with 15 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
viewer/src/coordinate-transformations.ts	86.79%	7 Missing ⚠️
viewer/src/io.ts	57.14%	5 Missing and 1 partial ⚠️
viewer/src/ome.ts	97.33%	2 Missing ⚠️

📢 Thoughts on this report? Let us know!

will-moore · 2026-06-03T11:06:34Z

It would be good to test this with @jo-mueller's test samples listed at https://forum.image.sc/t/ngff-weekly-dev-update-thread/110810/98.
I tried running locally with e.g. http://localhost:5173/?source=https://s3.zih.tu-dresden.de/johamuel:rfc5-transform-sanity-checks/logan_shepp_rotation_30_degree_anticlockwise_around_center.ome.zarr/
but it seems this fails due to no validParsers being found for this data.

const parser = validParsers[validParsers.length - 1];

  return {
->    data: parser.schema.parse(data),

TypeError: Cannot read properties of undefined (reading 'schema')
    at parse (parse.ts:34:18)
    at createSourceData (io.ts:81:24)
    at async VizarrViewer.tsx:68:30

AlexSurtees · 2026-06-18T08:28:43Z

German-BioImaging/incubator#72

Sample images to test against

jo-mueller · 2026-06-18T12:50:15Z

German-BioImaging/incubator#72

Sample images to test against

I will mirror these in the image.sc dev thread

davehorsfall

This is good. Left some comments for discussion.

davehorsfall · 2026-06-29T09:22:18Z

+    const parsedData = parse(node.attrs);
+    if (parsedData.version === "v06") {
+      if (parsedData.type === "SceneSchema") {
+        //Temporary assertion until parsing layer implemented


If it doesn't already exist, can we create an Issue in the Backlog to follow up on this. Thanks.

Added note/sub-issue to existing issue #64

davehorsfall · 2026-06-29T09:25:17Z

+    coordinateSystems?: CoordinateSystem[];
+  }
+
+  //Once parsing and transforming is set up, it should be possible to significantly simplify these types


Please also point here from the Issue that is setup to track full implementation of the transformations from the ZOD schema parsing.

Added TODO and added sub-issue to #64

davehorsfall · 2026-06-29T09:47:37Z

+  const parser = validParsers[validParsers.length - 1];
+
+  return {
+    data: parser.schema.parse(data),


What happens when the schema can't parse the data? How is this handled?

Schema parsing uses the safeParse method which prevents errors from being raised if the metadata does not match the given schema.

davehorsfall · 2026-06-29T09:58:33Z

+        );
+        console.log("Applying scene transformations to image: ", config.source);
+        const sceneModelMatrix = coordinateTransformationsToMatrix(transformations, [
+          { type: "channel", name: "c" },


This appears to be passing a hard-coded 4-element [c, z, y, x] axes array to coordinateTransformationsToMatrix regardless of the scene's actual coordinate systems. Is that intended, and long term?

coordinateTransformationsToMatrix also seems to throw and error if the shape of the axes and the transformations don't match.

Changed to dynamically select the first coordinate system axes in the scene metadata.
Left a TODO for future work to allow the user to change between coordinate systems.
Linked TODO to sub-issue in existing issue #69

davehorsfall · 2026-06-29T10:00:05Z

  const labels = await resolveOmeLabelsFromMultiscales(grp);
+  const modelMatrix = coordinateTransformationsToMatrix(
+    getOrderedTransformations(attrs.multiscales, selectedCoordinateSystem),
+    coordinateSystems[0].axes,


Should this perhaps be selectedCoordinateSystem.axes, or what is the selectedCoordinateSystem intended to be used for?

TL;DR

It is the coordinateSystem name that is important for this function, not the axes. I have removed the nested function calls for clarity.

Explanation

The scene metadata defines which output coordinate systems should be used for each multiscale image in the scene (we can imagine that each multiscale image may have multiple coordinate systems and multiple transformations associated with each coordinate system). So, to create the multiscale image, the loadScene function takes the name of the selectedCoordinateSystem from the scene metadata. This is then used to filter which transformations are actually applied to the image.

This may be more clear from the example data:

Scene:

https://ome.github.io/ome-ngff-validator/?source=https%3A%2F%2Fuk1s3.embassy.ebi.ac.uk%2Fidr%2Fzarr%2Ftest-data%2Fv0.6.dev3%2Fidr0050%2F4995115_scene.zarr&roi=0&viewState=%7B%22target%22%3A%5B73.80140630789678%2C78.72150006175659%5D%2C%22zoom%22%3A2.508669115245146%7D

Scene.coordinateTransformations[0].input defines:

input: { "path": "4995115_full.zarr" , "name": "physical" } ,

i.e. the path to the image and the coordinate system of the image to use.

Multiscale image

https://ome.github.io/ome-ngff-validator/?source=https%3A%2F%2Fuk1s3.embassy.ebi.ac.uk%2Fidr%2Fzarr%2Ftest-data%2Fv0.6.dev3%2Fidr0050%2F4995115_scene.zarr&roi=0&viewState=%7B%22target%22%3A%5B73.80140630789678%2C78.72150006175659%5D%2C%22zoom%22%3A2.508669115245146%7D/4995115_full.zarr

Defines:

coordinateSystems: [ { "name": "physical" , axes: [ { ... } , // 2 items { ... } , // 3 items { ... } , // 3 items { ... } // 3 items ] } ]

and transformation:

transformations: [ { ... } , // 2 items { ... } // 2 items ] , "input": "s0" , "output": "physical" } ]

davehorsfall · 2026-06-29T10:00:59Z

+      mat = coordinateTransformationsToMatrix(transform.transformations, axes, mat);
+    }
+    if (transform.type === "affine") {
+      console.log("Affine transformation detected");


Perhaps also add an Issue to track support for this as it develops, and as test datasets start to be generated/shared.

Uncommented this as it actually works - it doesn't have any impact on the test image because the affine transformation defined is the identity. I think this was commented out while debugging at some point.

davehorsfall · 2026-06-29T10:39:45Z

+  //No type information for SceneSchema
+  scene: Ome.Scene,
+): Promise<SourceData[]> {
+  console.log("Loading scene: ", config.source);


Currently there are lots of informational logs printed to the console (even in production?)

It would be good to start wrapping this into the app level logger (and error handler) we've been discussing, so it is easier to control what is printed, and where.

Agreed to add these once logging PR has been merged #95

AlexSurtees · 2026-07-02T08:32:22Z

@davehorsfall addressed comments and workflows passing.

will-moore · 2026-07-02T09:22:58Z

https://ome.github.io/ome-ngff-validator/?source=https://livingobjects.ebi.ac.uk/idr/zarr/test-data/v0.6.dev4/idr0050/4995115_output_to_ms.zarr is a more up-to-date scene example, although slightly more complex than the v0.6.dev3 one above. The dev3 one is failing validation because it's using latest schemas which have been updated for dev4.

Alex Surtees added 11 commits April 13, 2026 11:24

WIP schema

f7b05ef

WIP

543123d

Scene transformations

d16629c

Re-enable affine transformation

42d5d15

Re-enable labels init

fc377ec

Read coordinate systems from labels

92b2423

Re-enable tests

c20db5b

Cleanup

7d19316

Clean up types and linting

119a697

Merge dev and tests passing

63d7b0d

Linting

82010de

davehorsfall added this to the RFC-5: Transformations and Coordinate systems milestone Jun 10, 2026

This was referenced Jun 10, 2026

[Feature] Implement multiscale coordinateTransformations from v0.4 specification #73

Open

[Feature] Implement 'scenes' functionality from ome ngff 0.6 specification #68

Open

davehorsfall added 2 commits June 29, 2026 09:22

Merge branch 'transformations0.5' into transformations0.6

583d1da

Complete dev merge

0372ac1

davehorsfall requested changes Jun 29, 2026

View reviewed changes

feat: Remove hardcoded axes in scene, plus cleanup

da9bb57

AlexSurtees requested a review from davehorsfall July 2, 2026 08:32

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AlexSurtees commented May 15, 2026

Description

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will-moore commented Jun 3, 2026

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AlexSurtees commented Jun 18, 2026

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jo-mueller commented Jun 18, 2026

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TL;DR

Explanation

Scene:

Multiscale image

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AlexSurtees commented Jul 2, 2026

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