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IDR / ome-ngff-samples

A catalog of all public OME-NGFF representative samples derived from IDR data
https://idr.github.io/ome-ngff-samples
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Itk vtk viewer #14

Closed will-moore closed 1 year ago

will-moore commented 1 year ago

We can view OME-NGFF directly in itk-vtk-viewer via a URL like: https://kitware.github.io/itk-vtk-viewer/app/?rotate=false&fileToLoad=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr as shown in https://github.com/InsightSoftwareConsortium/itkwidgets/issues/548#issuecomment-1278244841

However, the viewer doesn't do so well with pre v0.4 images that don't have the scale coordinateTransformations metadata (see same comment).

This PR adds a itk-vtk-viewer link to all v0.4 (and future) images (not for OME-NGFF Plate samples).

I also added the instructions I used to deploy locally, so that I don't lose them and might be useful to others.

joshmoore commented 1 year ago

cc: @thewtex 🤩

will-moore commented 1 year ago

@joshmoore This PR look OK? - I can't seem to request reviewers?

joshmoore commented 1 year ago

No, only folks in the org can be added (sadly).

Let's go ahead and go with it, and we'll see what the response is. It might be that we need to re-address the N-viewers issue, e.g. after the OME2022 meeting.