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://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr
  • Use napari console to open additional image: viewer.open("https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457537.zarr", plugin="napari-ome-zarr")
• 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 click OK.
  • To include labels, enter the image URL in the dialog, then click Detect datasets. Expand the tree and select an image under labels AND use Cmd-click to also select the top-level parent image. With both selected, click OK.
• MoBIE plugin for ImageJ/Fiji (mobie-viewer-fiji v6.3.1, mobie-io v4.0.3).
  • See MoBIE guide for installation instructions. Hint: Press p to bring the rendering settings controls.
  • To open images: Plugins > MoBIE > Open > Open OME ZARR then enter image URL.zarr. If you want to include labels, also fill the labels field with URL.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.
• itkwidgets. Use in a python notebook, or open via URL: See example.
• neuroglancer.
• webKnossos version 24.11.0.
• OMERO with BioFormats ZarrReader 0.2.0.
• Microscopy Nodes plugin to load microscopy data in Blender. Tested with Blender 4.4.1 and Microscopy Nodes 2.2.0.

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

Scroll right for more viewers ->

feature	sample data	avivator	vizarr	Vol-E	vtk-itk-viewer	neuroglancer	WEBKNOSSOS	napari	BigDataViewer	MoBIE	OMERO	Microscopy Nodes
Z downsample	9836832.zarr
omero info	6001240.zarr
multiscales downsampling not=2	9846318.zarr/0
axes (v0.3)	9836998.zarr
axes (v0.4)	6001240.zarr
labels	5514375.zarr
HCS plate	idr0001
bioformats2raw.layout	sample_files.zarr
multiple 'multiscales'	4995115.zarr
scale within coordinateTransformations on datasets (v0.4)	6001240.zarr
translation within coordinateTransformations on datasets (v0.4)	13457537.zarr translate onto 13457227.zarr
scale within coordinateTransformations on multiscales (v0.4)	13457539.zarr
translation within coordinateTransformations on multiscales (v0.4)	13457539.zarr translate onto 13457227.zarr
overlay multiple images
multiple Channels	13457227.zarr
multiple Time-points	13457227.zarr

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