ome-ngff-tools
The following versions of each viewer were used in testing:
- napari 0.5.6 with plugin napari-ome-zarr 0.6.1 and ome-zarr 0.10.3.
- Open via command line:
napari https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr - Use napari console to open additional image:
viewer.open("https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")
- Open via command line:
- vizarr using current viewer April 2025. Open via URL - see example.
- Vol-E
- BigDataViewer comes with Fiji. Jar versions include bigdataviewer_fiji-6.4.1.jar, bigdataviewer-core-10.6.4, bigdataviewer-image-loaders-0.9.0, bigdataviewer-n5-1.0.2.jar.
- Open with:
Plugins > BigDataViewer > HDF5/N5/Zarr/OME-NGFF Viewer. In the dialog, enter the URL and clickOK. - To include labels, enter the image URL in the dialog, then click
Detect datasets. Expand the tree and select a labels image underlabelsAND use Cmd-click to also select the top-level parent image. With both selected, clickOK.
- Open with:
- MoBIE plugin for ImageJ/Fiji (mobie-viewer-fiji v6.3.1, mobie-io v4.0.3).
- See MoBIE guide for installation instructions. Hint: Press
pto bring the rendering settings controls. - To open images:
Plugins > MoBIE > Open > Open OME ZARRthen enter imageURL.zarr. If you want to include labels, also fill the labels field withURL.zarr/labels/<name>(Open the image in ome-ngff-validator first (OME icon in table below) and browse to labels to get the correct URL). - To open Plates:
Plugins > MoBIE > Open > Open HCS Dataset.
- See MoBIE guide for installation instructions. Hint: Press
- itkwidgets. Use in a python notebook, or open via URL: See example.
- neuroglancer.
- webKnossos version 24.03.0.
- OMERO with BioFormats ZarrReader 0.2.0.
NB: the N5-viewer, a Fiji plugin based on BigDataViewer, will also support OME-NGFF soon.
Key
| Feature supported | |
| Not supported (no effect) | |
| Image doesn't open correctly | |
| Not tested / not confirmed |
| feature | sample data | avivator | vizarr | Vol-E | vtk-itk-viewer | neuroglancer | webknossos | napari | BigDataViewer | MoBIE | OMERO |
|---|---|---|---|---|---|---|---|---|---|---|---|
web viewer
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Z downsample
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9836832.zarr
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omero info
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6001240.zarr
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multiscales downsampling not=2
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9846318.zarr/0
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axes (v0.3)
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9836998.zarr
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axes (v0.4)
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6001240.zarr
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labels
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5514375.zarr
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HCS plate
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idr0001
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bioformats2raw.layout
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sample_files.zarr
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multiple 'multiscales'
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4995115.zarr
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scale within coordinateTransformations on datasets (v0.4)
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6001240.zarr
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translation within coordinateTransformations on datasets (v0.4)
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13457537.zarr
translate onto 13457227.zarr
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scale within coordinateTransformations on multiscales (v0.4)
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13457539.zarr
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translation within coordinateTransformations on multiscales (v0.4)
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13457539.zarr
translate onto 13457227.zarr
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overlay multiple images
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multiple Channels
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13457227.zarr
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multiple Time-points
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13457227.zarr
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