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Merged
joshmoore merged 3 commits into from
Apr 17, 2026
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livingobjects #497

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310eaf5
livingobjects
pwalczysko Apr 10, 2026
a311888
Update 2 places inside neuroglancer link cf. Kola's comment
pwalczysko Apr 13, 2026
3532509
bia-integrator-data -> bioimaging-integrator-data
pwalczysko Apr 13, 2026
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2 changes: 1 addition & 1 deletion resources/data/index.md
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Expand Up @@ -12,7 +12,7 @@ Data Resources
| [JAX](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory | 17000 | 192 TB |
| [Glencoe](https://glencoesoftware.com/ngff) | Glencoe Software, Inc. | 8 | 165 GB |
| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | EBI | 88 | 3 TB |
| [IDR Studies](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/idr_ngff_data.html) | EBI | 1644 | 47 TB |
| [IDR Studies](https://livingobjects.ebi.ac.uk/bia-integrator-data/pages/idr_ngff_data.html) | EBI | 1644 | 47 TB |
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@will-moore will-moore Apr 13, 2026

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Again, this hasn't been migrated yet (not idr bucket) but it will be migrated by the BIA team, so we'll want to update this url at some point.

So, we could leave this PR open till it's done or create a separate list of urls to check and update in the not-too-distant future (not sure of the timescale)

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@kbab kbab Apr 13, 2026

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In this case, the new url is https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html.

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@kbab kbab Apr 13, 2026

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The bia-integrator-data bucket on Embassy is now bioimaging-integrator-data on LivingObjects. I will create a ticket on our side to update the urls of the ome.zarrs in the idr_ngff_data.html page.

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@pwalczysko pwalczysko Apr 13, 2026

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fixed in 3532509

| [MoBIE](https://mobie.github.io/specs/ngff.html) | EMBL-HD | 21 | 2 TB |
| [Neural Dynamics](https://registry.opendata.aws/allen-nd-open-data/) | AWS Open Data Program | 90 | 200 TB |
| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) | AWS Open Data Program | 624 | 372 GB |
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2 changes: 1 addition & 1 deletion rfc/6/index.md
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Expand Up @@ -87,7 +87,7 @@ This RFC proposes to change the `multiscales` array into a single `multiscale` o

The current spec of OME-Zarr (version 0.5) defines that the metadata for a multiscale is stored in a `multiscales` array.

However, there seem to be only very few OME-Zarr images with mutltiple multiscales in the wild. There is one example from IDR: [4995115.zarr](https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0050A/4995115.zarr)
However, there seem to be only very few OME-Zarr images with mutltiple multiscales in the wild. There is one example from IDR: [4995115.zarr](https://ome.github.io/ome-ngff-validator/?source=https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0050A/4995115.zarr)

Additionally, most visualization and processing tools today simply process the first multiscale object in the `multiscales` array, ignoring any subsequent entries. Here is a selection of tools that only load the first multiscale object:

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2 changes: 1 addition & 1 deletion rfc/9/reviews/2/index.md
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Expand Up @@ -38,7 +38,7 @@ However, no explicit guidance is given on size limitations associated with the s

6. Is the example dataset at [https://static.webknossos.org/misc/6001240.ozx](https://static.webknossos.org/misc/6001240.ozx) supposed to be accessible by viewers? I can download, but I cannot access with bioNGFF using [https://biongff.github.io/biongff-viewer/?source=https://static.webknossos.org/misc/6001240.ozx](https://biongff.github.io/biongff-viewer/?source=https://static.webknossos.org/misc/6001240.ozx). I get: Access to fetch at 'https://static.webknossos.org/misc/6001240.ozx/zarr.json' from origin 'https://biongff.github.io' has been blocked by CORS policy: No 'Access-Control-Allow-Origin' header is present on the requested resource.

7. [Neuroglancer link](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22y%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22z%22:%5B5.002025531914894e-7%2C%22m%22%5D%7D%2C%22position%22:%5B135%2C137%2C118%5D%2C%22crossSectionScale%22:1%2C%22projectionScale%22:512%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22https://static.webknossos.org/misc/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B0%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B7%2C927%5D%2C%22window%22:%5B0%2C1159%5D%7D%2C%22color%22:%22#ff0000%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c-0.5%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22https://static.webknossos.org/misc/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B1%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B25%2C824%5D%2C%22window%22:%5B0%2C1025%5D%7D%2C%22color%22:%22#00ff00%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c0.5%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%226001240.ozx%20c-0.5%22%7D%2C%22layout%22:%224panel-alt%22%2C%22settingsPanel%22:%7B%22row%22:3%7D%2C%22toolPalettes%22:%7B%22Shader%20controls%22:%7B%22side%22:%22left%22%2C%22row%22:2%2C%22query%22:%22type:shaderControl%22%7D%7D%7D) does not seem to work (on 26/01/2026 @ 16:04GMT) Changing the url to be served from [EBI S3 Embassy](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22y%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22z%22:%5B5.002025531914894e-7%2C%22m%22%5D%7D%2C%22position%22:%5B135%2C137%2C118%5D%2C%22crossSectionScale%22:1%2C%22projectionScale%22:512%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22https://uk1s3.embassy.ebi.ac.uk/testbucket-bia/test-ozx/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B0%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B7%2C927%5D%2C%22window%22:%5B0%2C1159%5D%7D%2C%22color%22:%22#ff0000%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c-0.5%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22https://uk1s3.embassy.ebi.ac.uk/testbucket-bia/test-ozx/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B1%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B25%2C824%5D%2C%22window%22:%5B0%2C1025%5D%7D%2C%22color%22:%22#00ff00%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c0.5%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%226001240.ozx%20c-0.5%22%7D%2C%22layout%22:%224panel-alt%22%2C%22settingsPanel%22:%7B%22row%22:3%7D%2C%22layerListPanel%22:%7B%22visible%22:true%7D%2C%22toolPalettes%22:%7B%22Shader%20controls%22:%7B%22side%22:%22left%22%2C%22row%22:2%2C%22query%22:%22type:shaderControl%22%7D%7D%7D) with acl to public and CORS to allow all origins works.
7. [Neuroglancer link](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22y%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22z%22:%5B5.002025531914894e-7%2C%22m%22%5D%7D%2C%22position%22:%5B135%2C137%2C118%5D%2C%22crossSectionScale%22:1%2C%22projectionScale%22:512%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22https://static.webknossos.org/misc/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B0%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B7%2C927%5D%2C%22window%22:%5B0%2C1159%5D%7D%2C%22color%22:%22#ff0000%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c-0.5%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22https://static.webknossos.org/misc/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B1%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B25%2C824%5D%2C%22window%22:%5B0%2C1025%5D%7D%2C%22color%22:%22#00ff00%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c0.5%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%226001240.ozx%20c-0.5%22%7D%2C%22layout%22:%224panel-alt%22%2C%22settingsPanel%22:%7B%22row%22:3%7D%2C%22toolPalettes%22:%7B%22Shader%20controls%22:%7B%22side%22:%22left%22%2C%22row%22:2%2C%22query%22:%22type:shaderControl%22%7D%7D%7D) does not seem to work (on 26/01/2026 @ 16:04GMT) Changing the url to be served from [EBI S3 Embassy](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22y%22:%5B3.6039815346402084e-7%2C%22m%22%5D%2C%22z%22:%5B5.002025531914894e-7%2C%22m%22%5D%7D%2C%22position%22:%5B135%2C137%2C118%5D%2C%22crossSectionScale%22:1%2C%22projectionScale%22:512%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22https://livingobjects.ebi.ac.uk/testbucket-bia/test-ozx/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B0%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B7%2C927%5D%2C%22window%22:%5B0%2C1159%5D%7D%2C%22color%22:%22#ff0000%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c-0.5%22%7D%2C%7B%22type%22:%22image%22%2C%22source%22:%22https://livingobjects.ebi.ac.uk/testbucket-bia/test-ozx/6001240.ozx%7Czip:%7Czarr3:%22%2C%22localDimensions%22:%7B%22c%27%22:%5B1%2C%22%22%5D%7D%2C%22localPosition%22:%5B1%5D%2C%22tab%22:%22source%22%2C%22opacity%22:1%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20contrast%5Cn#uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%20%20float%20contrast_value%20=%20contrast%28%29%3B%5Cn%20%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%20%20%20%20emitRGBA%28vec4%28color%20%2A%20contrast_value%2C%20contrast_value%29%29%3B%5Cn%20%20%7D%5Cn%20%20else%20%7B%5Cn%20%20%20%20emitRGB%28color%20%2A%20contrast_value%29%3B%5Cn%20%20%7D%5Cn%7D%5Cn%22%2C%22shaderControls%22:%7B%22contrast%22:%7B%22range%22:%5B25%2C824%5D%2C%22window%22:%5B0%2C1025%5D%7D%2C%22color%22:%22#00ff00%22%7D%2C%22volumeRenderingDepthSamples%22:256%2C%22name%22:%226001240.ozx%20c0.5%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%226001240.ozx%20c-0.5%22%7D%2C%22layout%22:%224panel-alt%22%2C%22settingsPanel%22:%7B%22row%22:3%7D%2C%22layerListPanel%22:%7B%22visible%22:true%7D%2C%22toolPalettes%22:%7B%22Shader%20controls%22:%7B%22side%22:%22left%22%2C%22row%22:2%2C%22query%22:%22type:shaderControl%22%7D%7D%7D) with acl to public and CORS to allow all origins works.
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@will-moore will-moore Apr 13, 2026

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The data at https://uk1s3.embassy.ebi.ac.uk/testbucket-bia/test-ozx/6001240.ozx hasn't been migrated to "livingobjects" store yet. That's not even in the idr bucket so that's not our data.
We can leave that to the BIA team: cc @kbab

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@kbab kbab Apr 13, 2026

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Hi @will-moore / @pwalczysko . Thanks for updating the link. We have migrated the data, however, the prefix in the new location changed. Please can the uris be updated to https://livingobjects.ebi.ac.uk/bioimaging-sandbox/testbucket-bia/test-ozx/6001240.ozx

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@kbab kbab Apr 13, 2026

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testbucket-bia on Embassy moved to bioimaging-sandbox/testbucket-bia on LivingObjects

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@pwalczysko pwalczysko Apr 13, 2026

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Thank you @kbab . Fixed in a311888


8. Tutorials and Examples -> I see an example dataset and a Neuroglancer link (see above comments). A short worked example of how to write/construct .ozx would be valuable. The comment at [https://github.com/ome/ngff/pull/316#issuecomment-3302456557](https://github.com/ome/ngff/pull/316#issuecomment-3302456557) contains useful information, perhaps this could be turned into a gist and linked from the RFC?

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