OMERO-Vitessce compatibility spike¶
The production viewer does not depend on Vitessce. The spike is retained as a deployment validation checklist because it requires the target OMERO session, mounted BIOMERO stores, and representative institutional data.
Static findings¶
- Viv 0.22 exposes modern
loadOmeZarr/loadOmeZarrFromStoreloaders and uses Zarrita-compatible readable stores. - Vitessce's bitmask implementation confirms nearest-neighbour integer mask rendering on top of Viv layers, but its explicit per-object color textures grow with label cardinality.
- This viewer instead uses a Viv shader extension with an integer hash, so normal rendering has constant client memory relative to the number of IDs.
- Viv's volume layer provides field-level intensity ray casting. The viewer limits its raw volume payload to 256 MiB, checks the WebGL 3D-texture limit, and defaults to the coarsest safe multiscale level.
- The viewer accepts OME-Zarr 0.4/Zarr v2 and OME-Zarr 0.5/Zarr v3 through distinct backend metadata adapters and shared normalized frontend state.
Local OMERO.web integration check¶
On 2026-07-22 the wheel was installed into the local NL-BIOMERO OMERO.web
container and Nginx was placed in front of Gunicorn. The authenticated host
route loaded the production React bundle and the packaged Open With entry was
verified against Image 539. BIOMERO had removed the .ome.zarr suffix from
the OMERO Image name and recorded the source in a biomero.import annotation;
the provenance fallback resolved it as OME-Zarr 0.4/Zarr v2 and the
asynchronous menu check enabled the entry. The menu check now uses a dedicated
registration-only endpoint, leaving filesystem and NGFF inspection to the
viewer capability request. Nginx served image and label chunks
successfully through authenticated /data/images/539/... requests, and a
direct request to the internal storage location returned 404. A Viv 0.22
shader incompatibility exposed by the first successful chunk load was fixed by
using screen-space derivatives for label outlines instead of referencing Viv's
private channel sampler declaration.
Required live matrix before release¶
Run each row first in OMERO-Vitessce as a reference and then in this viewer:
| Store | Image | 3D intensity | Labels | Plate navigation | Result |
|---|---|---|---|---|---|
| 0.4 / Zarr v2 | multiscale C/Z/T | field at selected T | multiple integer labels in 2D | n/a | pending deployment |
| 0.4 / Zarr v2 | HCS field | selected field and T | field labels in 2D | sparse wells/FOVs | verified locally: complete, canonical, and shallow Plates; Well entry |
| 0.5 / Zarr v3 | multiscale C/Z/T | field at selected T | multiple integer labels in 2D | n/a | pending deployment |
| 0.5 / Zarr v3 | HCS field | selected field and T | field labels in 2D | sparse wells/FOVs | pending deployment |
For each row verify authenticated metadata/chunk requests, default channel rendering, zero-background transparency, hover/click IDs, outline mode, 2D/3D deep links, anisotropic voxel scaling, camera reset, safe quality choices, time/field reload cancellation, and session-context refresh. Also test a single-Z field, disabled WebGL 2, and a volume above the 256 MiB limit to confirm that each remains safely in 2D. Record fixture identifiers and screenshots in the deployment's validation report; do not commit patient or unpublished data to this repository.