BIOMERO OME-Zarr Viewer

Explore OME-Zarr images and segmentation results directly from OMERO.web. BIOMERO ZarrViewer is a read-only viewer for multichannel images, Z stacks, time series and high-content screening plates. It works with standalone OMERO and with BIOMERO deployments.

Open your data

In OMERO.web, select a registered OME-Zarr Image, Plate or Well, then choose Open With ? OME-Zarr Viewer. Your existing OMERO permissions apply. Physical OME-Zarr 0.4/0.5 stores can be registered with standard omero zarr import / ExternalInfo, without extra BIOMERO annotations. With the optional omero-web-zarr integration enabled, ordinary OMERO images such as TIFFs can also be opened as virtual OME-Zarr 0.4, without a full export.

Installation options

Install the stable package in your OMERO.web Python environment:

python -m pip install biomero-zarr-viewer==0.8.1

Configure the shared storage and authenticated Nginx route using the deployment instructions below. The wheel includes the browser assets; Node.js is not needed in the running OMERO.web environment.

Standalone OMERO

BIOMERO, Slurm and OMERO.Analysis are not required. The standalone Docker recipe uses an official OMERO.web image pinned by digest and tested runtime constraints. The default build installs the viewer for physical OME-Zarr 0.4/0.5, with the shared data mount and authenticated Nginx route described in the build and installation instructions. See OMERO source registration for linking the physical store to its OMERO Image.

Optional omero-web-zarr

Build with ENABLE_HTTP_ZARR=true to also install and enable the optional provider from the NL-BioImaging performance fork. The recipe pins a fork commit and verifies its archive checksum. Ordinary OMERO images are then served on demand as virtual OME-Zarr 0.4, using the existing OMERO permissions. Virtual sources support Neuroglancer and Viv for 3D viewing. See the HTTP Zarr guide.

The provider is disabled by default and is not a required viewer dependency. Physical OME-Zarr and BIOMERO continue working when it is absent.

Virtual HTTP images use OME-Zarr 0.4 by default. Viewer 0.8.1 can also select optional unsharded OME-Zarr 0.5 with omero.web.zarr_viewer.http_ngff_version=0.5; see the format selection guide.

Existing BIOMERO deployments

Existing imports, HCS plates and shallow segmentation results remain supported. Their physical-store registrations keep precedence over the optional HTTP provider. Follow the NL-BIOMERO deployment guide for integrated installation.

To add the optional pinned HTTP provider to an existing combined web image, use the BIOMERO Docker recipe. It preserves the installed BIOMERO/Analysis components and existing storage configuration.

Explore the image

• 2D: pan, zoom, navigate Z and time, and compare maximum, mean or minimum projections.
• Channels: toggle individual channels or the whole group, choose colors, adjust contrast, and inspect intensity histograms.
• Labels: compare segmentation layers with colors, opacity, fills and outlines; inspect object IDs in 2D.
• 3D: use Neuroglancer (default) for physical OME-Zarr and virtual HTTP-Zarr 0.4/0.5 images, including ordinary TIFF stacks. Physical stores also support label surfaces. Viv remains available for intensity volumes. Select resolution quality, display blending, and intensity brightness while keeping physical XYZ proportions. Volume, Slice and Orthogonal layouts are available in both engines. In Volume view, expand Clipping planes to trim X/Y/Z visually in either engine, with a reset icon per axis. Right-drag pans in both engines.
• Navigation: explore fields, wells and plates; use the 2D navigator, calibrated scale bars, Fit, native-pixel 1:1 zoom, fullscreen and the 3D reset control. Image cursors show zoom, pan, rotation or slice/depth movement as controls change.
• Share and export: copy the viewer URL, save focused ROI images, or export 2D sequences or rendered 3D views as MP4 movies in a supported browser.

Click Help in the top toolbar for the searchable viewer guide. The help window can be moved and resized while you inspect the image.

See large-volume loading and memory for engine-specific quality estimates, cache behavior and above-budget Neuroglancer levels.

Documentation

Part of BIOMERO. The published documentation tracks the main branch. The guide links above are pinned to version 0.8.1.

License and source

Copyright (C) 2026 NL-BioImaging contributors. Licensed under AGPL-3.0-or-later. See NOTICE, third-party notices and source provenance.