sources.md

Official Sources and Version Snapshot

Research date: 2026-07-23

This file records the authoritative basis for skill version 1.2. The snapshot must not replace checking the target server's own version and discovery endpoints.

Current Versions

• OMERO.server 5.6.18 — May 2026 bug-fix release.
• OMERO.py / omero-py 5.22.1 — released 2026-03-25.
• OMERO.web 5.31.0 — the version tested with OMERO.server 5.6.18.
• Bio-Formats 8.5.0 — bundled by OMERO.server 5.6.18.
• ZeroC IcePy 3.6.5 — exact client binding version in current official installation examples and OMERO-linked wheel matrix.

The OMERO.server history explicitly says 5.6.18 was tested with OMERO.py 5.22.1 and OMERO.web 5.31.0. That tested pairing is stronger evidence than assuming compatibility from package version numbers.

Release and Package Metadata

• OMERO version history https://omero.readthedocs.io/en/stable/users/history.html Basis for server 5.6.18, tested client/web pairing, and Bio-Formats 8.5.0.

• omero-py on PyPI https://pypi.org/project/omero-py/ Basis for 5.22.1, 2026-03-25 release date, Python >=3.10, IcePy 3.6, NumPy/Pillow requirements, OMERODIR notes, and GPL-2.0-or-later package license.

• Official OME omero-py repository and changelog https://github.com/ome/omero-py https://github.com/ome/omero-py/blob/v5.22.1/CHANGELOG.md Basis for recent Python/NumPy compatibility and historical deprecations.

• Official OME OMERO.server component releases https://github.com/ome/omero-server/releases Cross-check for current server component releases.

Installation and Compatibility

• OMERO Python language bindings https://omero.readthedocs.io/en/stable/developers/Python.html Basis for the current omero-py==5.22.1 examples, IcePy 3.6.5 ordering, BlitzGateway patterns, objects, annotations, tables, ROIs, pixels, and rendering.

• OMERO version requirements https://omero.readthedocs.io/en/stable/sysadmins/version-requirements.html Basis for Python 3.10/3.11 support, Python 3.12 recommendation, Python 3.13/3.14 “upcoming” status, Ice 3.6 recommendation, Ice 3.7 unsupported status, and server platform/runtime matrix.

• OMERO-linked Glencoe Ice binary matrix https://www.glencoesoftware.com/blog/2023/12/08/ice-binaries-for-omero.html Basis for exact prebuilt IcePy 3.6.5 wheel coverage through Python 3.12. Glencoe is identified in OME's Python installation page as its commercial partner. Select the exact wheel from the linked release repositories.

• OMERO CLI installation https://omero.readthedocs.io/en/stable/users/cli/installation.html Basis for client installation and import/admin prerequisites.

Connection and Security

• BlitzGateway documentation https://omero.readthedocs.io/en/stable/developers/PythonBlitzGateway.html Basis for context-manager closure, wrappers/lazy loading, stateless versus stateful service reuse, and stale stateful proxies after reconnection.

• Server security and firewalls https://omero.readthedocs.io/en/stable/sysadmins/server-security.html Basis for login encryption, optional full transport encryption, session-ID exposure on insecure post-login traffic, and default router ports 4063/4064.

• Client/server SSL verification https://omero.readthedocs.io/en/stable/sysadmins/client-server-ssl.html Basis for the warning that standard clients do not automatically verify the host and for the documented IceSSL verification properties.

• CLI session management https://omero.readthedocs.io/en/stable/users/cli/sessions.html Basis for prompted login, session files, omero sessions, group switching, -k session reuse, and logout.

Data, Metadata, ROIs, and Tables

• OMERO Python examples https://omero.readthedocs.io/en/stable/developers/Python.html Primary current examples for bounded getObjects, annotations, pixels, rendering, tables, and ROI model operations.

• OMERO.tables https://omero.readthedocs.io/en/stable/developers/Tables.html Basis for current column signatures, reads, queries, paging, global locking, and HDF implementation details.

• Structured annotations https://omero.readthedocs.io/en/stable/developers/Model/StructuredAnnotations.html Basis for annotation type hierarchy, namespaces, and link semantics.

• OME ROI model 5.6.3 https://docs.openmicroscopy.org/ome-model/5.6.3/developers/roi.html Basis for the eight shape types, optional TheZ/TheT/TheC, RGBA fields, and union-of-2D-shapes representation. The page itself was last updated in 2018 but documents the June 2016 schema still used by OMERO 5.6.

• Current generated IRoi API https://docs.openmicroscopy.org/omero-blitz/5.8.5/slice2html/omero/api/IRoi.html Basis for the explicit IRoi deprecation warning.

• OMERO application services https://omero.readthedocs.io/en/stable/developers/Modules/Api.html Basis for service categories and current IRoi/IShare deprecation status.

CLI Import, Export, and Download

• Import images https://omero.readthedocs.io/en/stable/users/cli/import.html Basis for omero import, -f serverless scanning, target syntax, depth/output options, experimental parallelism warning, and diagnostic upload disclosure.

• Import targets https://omero.readthedocs.io/en/stable/users/cli/import-target.html Basis for current-group target behavior and target syntax.

• Export images https://omero.readthedocs.io/en/stable/users/cli/export.html Basis for OME-TIFF/XML-only export and experimental Dataset iteration.

• Current omero-py==5.22.1 CLI help (omero download -h) Verified in an isolated environment on 2026-07-23. Basis for explicit OriginalFile, FileAnnotation, Image, and Fileset download forms. This was cross-checked against the official ome/omero-py package.

OMERO.web and Public Data

• OMERO.web framework https://omero.readthedocs.io/en/stable/developers/Web.html Basis for treating only api and webgateway as stable public APIs and treating other app URLs as internal.

• OMERO JSON API https://omero.readthedocs.io/en/stable/developers/json-api.html Basis for version discovery, API version headers, CSRF/login behavior, pagination/maxLimit, ROI endpoints, and limited create/update object types.

• Publishing data using OMERO.web https://omero.readthedocs.io/en/stable/sysadmins/public.html Basis for dedicated read-only public groups/users, GET-only default, URL filters, and publication URL examples.

• OMERO configuration properties https://omero.readthedocs.io/en/stable/sysadmins/config.html Basis for public-user defaults (enabled=false, get_only=true, and a URL filter that allows nothing until configured).

Research Method

The refresh used focused parallel-cli search queries restricted primarily to:

• omero.readthedocs.io
• docs.openmicroscopy.org
• ome-model.readthedocs.io
• openmicroscopy.org
• pypi.org
• official github.com/ome/* repositories

Canonical pages above were then fetched with parallel-cli extract using objectives specific to versions, Python/Ice compatibility, connection security, BlitzGateway APIs, CLI behavior, tables, ROIs/annotations, rendering, and OMERO.web/public APIs.

No Parallel JSON research artifacts were written into the repository.

Known Documentation Tensions

• PyPI declares Python >=3.10 without an upper bound, while the OMERO support matrix currently supports through 3.12 and marks 3.13/3.14 upcoming. Installation is also constrained by matching IcePy wheels. This skill uses Python 3.12 as the reproducible recommendation.
• Current Python docs still demonstrate IRoi while the generated API marks the interface deprecated. The skill documents and isolates this dependency rather than pretending a replacement is official.
• OMERO.web documents webclient publication links, while separately stating that webclient is not a stable public API. Durable publication links should use administrator-managed redirects/DOIs.
• secure=True encrypts traffic but standard clients do not automatically provide full hostname verification. High-assurance deployments need the administrator-provided IceSSL trust/name configuration.