Metadata-Version: 2.4
Name: biomero-zarr-viewer
Version: 0.8.1
Summary: Authenticated OME-Zarr viewer for BIOMERO and OMERO.web
Author: NL-BioImaging
License-Expression: AGPL-3.0-or-later
Project-URL: Repository, https://github.com/NL-BioImaging/BIOMERO.ZarrViewer
Project-URL: Documentation, https://nl-bioimaging.github.io/BIOMERO.ZarrViewer/
Classifier: Development Status :: 4 - Beta
Classifier: Framework :: Django
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
License-File: NOTICE
License-File: THIRD_PARTY_NOTICES.md
License-File: docs/open-source-provenance.md
Requires-Dist: omero-web>=5.6.0
Requires-Dist: numpy<3,>=1.24
Requires-Dist: Pillow<13,>=10
Requires-Dist: zarr<4,>=2.18
Requires-Dist: scikit-image<1,>=0.25
Requires-Dist: scipy<2,>=1.11.4
Provides-Extra: test
Requires-Dist: Django<6,>=3.2; extra == "test"
Requires-Dist: pytest>=8; extra == "test"
Requires-Dist: pytest-django>=4.8; extra == "test"
Requires-Dist: build>=1.2; extra == "test"
Dynamic: license-file

# BIOMERO OME-Zarr Viewer

<img src="https://raw.githubusercontent.com/NL-BioImaging/BIOMERO.ZarrViewer/main/docs/assets/biomero-logo.svg" alt="BIOMERO" height="28">

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:

```bash
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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docker/Dockerfile.standalone)
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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/http-zarr.md#reproduce-the-standalone-docker-installation).
See [OMERO source registration](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/data-and-registration.md#standard-omero-cli-zarr-imports)
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](https://github.com/NL-BioImaging/omero-web-zarr).
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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/http-zarr.md).

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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/http-zarr.md#optional-virtual-ome-zarr-05-without-sharding).

### 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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/deployment-nl-biomero.md)
for integrated installation.

To add the optional pinned HTTP provider to an existing combined web image,
use the [BIOMERO Docker recipe](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/deployment-nl-biomero.md#optional-pinned-http-zarr-provider-in-an-existing-biomero-stack).
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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/large-volumes.md) for engine-specific
quality estimates, cache behavior and above-budget Neuroglancer levels.

## Documentation

| For | Guide |
| --- | --- |
| Viewer users | [Viewer guide](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/viewer-guide.md) · [Movies](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/movies.md) |
| Administrators | [Installation](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/installation.md) · [Configuration and cache](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/configuration.md) |
| Deployment | [NL-BIOMERO](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/deployment-nl-biomero.md) · [OMERO deployment kit](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/deployment-omero-deployment-kit.md) |
| Data providers | [Supported data and OMERO registration](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/data-and-registration.md) |
| Developers | [Development](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/development.md) · [API and integrations](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/api.md) · [Compatibility checks](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/compatibility-spike.md) |

Part of [BIOMERO](https://nl-bioimaging.github.io/NL-BIOMERO/).
The [published documentation](https://nl-bioimaging.github.io/BIOMERO.ZarrViewer/)
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](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/LICENSE). See [NOTICE](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/NOTICE),
[third-party notices](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/THIRD_PARTY_NOTICES.md) and
[source provenance](https://github.com/NL-BioImaging/BIOMERO.ZarrViewer/blob/v0.8.1/docs/open-source-provenance.md).
