BIOMERO OME-Zarr Viewer¶
Explore OME-Zarr images, segmentation labels, Z stacks, time series and plates from OMERO.web. The viewer works with standalone OMERO and BIOMERO. Use Neuroglancer for streamed 3D images and physical label surfaces, or Viv for intensity volumes; both support Volume, Slice, Orthogonal and clipping views.
Stable release: 0.8.1, based on the validated 0.8.1b14 candidate. See installation for the package and Docker deployment options.
Start viewing¶
Select a registered OME-Zarr Image, Plate or Well and choose Open With ? OME-Zarr Viewer. Standard ExternalInfo/OMERO CLI Zarr registrations do not require a BIOMERO annotation. With the optional HTTP-Zarr provider, ordinary OMERO TIFF/SVS images can also be opened without exporting a complete physical Zarr store first.
Read the viewer guide, also available from the viewer's Help button, for channels, labels, Fit and 1:1 zoom, navigation, 3D controls and sharing. See movie playback and export for temporal data and large volumes and memory for streaming, memory budgets, sharded 2D tile reads and bounded high-resolution loading.
Administration¶
- Installation and configuration
- Standalone Docker and optional HTTP-Zarr
- NL-BIOMERO deployment
- OMERO deployment kit
- Supported data and OMERO registration
The viewer remains read-only and uses OMERO permissions. Physical OME-Zarr 0.4/0.5 stores must be registered and mounted for authenticated access. The optional HTTP provider serves conventional OMERO pixels on demand; it is not required for physical OME-Zarr or BIOMERO sources. The viewer does not import images or edit segmentations.