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Viewer guide

Open supported data

Sign in through the NL-BIOMERO Nginx endpoint, select an eligible Image, Plate, or Well, and choose Open With → OME-Zarr Viewer. The entry becomes available from the registration metadata stored in OMERO. Full filesystem and NGFF validation happens when the viewer opens.

Supported data includes:

  • OME-Zarr images with multiscale intensity data;
  • OME-Zarr HCS plates, wells, acquisitions, and fields;
  • integer segmentation labels declared through NGFF label metadata;
  • BIOMERO shallow results whose intensity pixels remain in a canonical store;
  • Z, T, and multichannel image dimensions.

Image controls

Each intensity channel has visibility, color, display-range, histogram, and automatic fitting controls. The viewer starts at the middle Z plane and supports slice, maximum, mean, and minimum projections. A bounded 3D intensity view is available for compatible Z stacks and WebGL 2 browsers.

The navigator, physical scale bar, fullscreen control, and URL state help users inspect and share the same view. URL state can retain the selected field, planes, viewport, channels, labels, and focused object without exposing a filesystem path or signed storage context.

Labels

Label layers can be shown independently, reordered, and rendered as a fill or outline. Each layer can keep its built-in multicolor instance palette or use cyan, magenta, yellow, red, green, or blue. Monochrome choices are useful when comparing two segmentation methods over the same intensity image.

Hovering the image reports the instance ID from every visible label layer under the pointer, including overlapping labels. Outline width can be adjusted up to 20 screen pixels.

Well and Plate overview thumbnails display intensity data. Open a Field to inspect its label overlays and controls.

Canonical and shallow stores

For a complete OME-Zarr store, all metadata and chunks resolve below that store. For a BIOMERO shallow result, the viewer validates the shallow manifest, reads intensity pixels and plate metadata from the canonical source, and routes retained label paths to the shallow result. This keeps split labels aligned with their original pixels without copying the intensity pyramid.

Managed locators are resolved through the trusted BIOMERO group mapping. Both canonical and shallow paths must remain below the configured read-only mount. Missing, ambiguous, or unsafe routes are rejected.

Current limits

  • The viewer is read-only and does not edit labels or OMERO annotations.
  • Three-dimensional rendering displays intensity channels; labels remain in the two-dimensional field view.
  • Well and Plate overviews use intensity thumbnails; label inspection begins after opening a Field.
  • Volume loading is bounded by browser and GPU limits and is not an out-of-core renderer.
  • An outline segment can be absent where an instance boundary falls exactly on a label tile seam because a tile shader cannot sample its neighboring tile.

Troubleshooting

If Open With remains disabled, confirm that the selected object is readable and carries one unambiguous BIOMERO registration. If the viewer opens but shows Failed to fetch, confirm that the browser uses the Nginx endpoint and that OMERO.web and Nginx mount the same store with the same relative directory tree.

Administrators can continue with the NL-BIOMERO deployment and verification guide.