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sources.md

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1# Official Sources and Version Snapshot
2
3Research date: **2026-09-30**
4
5This file records the authoritative basis for skill version 1.6. The snapshot
6must not replace checking the target server's own version and discovery
7endpoints.
8

Official Sources and Version Snapshot

Research date: 2026-09-30

This file records the authoritative basis for skill version 1.6. The snapshot must not replace checking the target server's own version and discovery endpoints.

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9## Versions and Tested Pairing
11- **OMERO.server 5.6.18** — May 2026 bug-fix release.
12- **OMERO.py / `omero-py` 5.23.0** — latest PyPI release, 2026-07-30.
13 The server history still records testing with **5.22.1** (2026-03-25).
14- **OMERO.web 5.33.2** — latest PyPI release. **5.31.0** remains the version
15 recorded as tested with OMERO.server 5.6.18.
16- **Bio-Formats 8.5.0** — bundled by OMERO.server 5.6.18.
17- **ZeroC IcePy 3.6.5** — exact client binding version in current official
18 installation examples and OMERO-linked wheel matrix.
20The OMERO.server history explicitly says 5.6.18 was tested with OMERO.py
215.22.1 and OMERO.web 5.31.0. That tested pairing is stronger evidence than
22assuming compatibility from package version numbers.

Versions and Tested Pairing

  • OMERO.server 5.6.18 — May 2026 bug-fix release.
  • **OMERO.py / omero-py 5.23.0 — latest PyPI release, 2026-07-30. The server history still records testing with 5.22.1** (2026-03-25).
  • OMERO.web 5.33.2 — latest PyPI release. 5.31.0 remains the version recorded as 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.

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24## Release and Package Metadata
26- OMERO version history
27 https://omero.readthedocs.io/en/stable/users/history.html
28 Basis for server 5.6.18, tested client/web pairing, and Bio-Formats 8.5.0.
30- `omero-py` on PyPI
31 https://pypi.org/project/omero-py/
32 Basis for latest 5.23.0, its 2026-07-30 release, Python `>=3.10`, IcePy 3.6,
33 NumPy/Pillow requirements, OMERODIR notes, and GPL-2.0-or-later package
34 license.
36- Official OME `omero-py` repository and changelog
37 https://github.com/ome/omero-py
38 https://github.com/ome/omero-py/releases/tag/v5.23.0
39 https://github.com/ome/omero-py/blob/v5.23.0/src/omero/gateway/__init__.py
40 Source check for gateway signatures, session lifecycle, context forwarding,
41 annotation materialization, channel inversion, and ROI/model handling.
42 The 5.23.0 release adds default-group CLI support and shape externalInfo
43 loading; it does not announce IRoi removal.
45- Current OMERO.web package and API implementation
46 https://pypi.org/project/omero-web/
47 https://github.com/ome/omero-web/blob/v5.33.2/omeroweb/api/urls.py
48 https://github.com/ome/omero-web/blob/v5.33.2/omeroweb/api/views.py
49 https://github.com/ome/omero-web/blob/v5.33.2/omeroweb/webgateway/views.py
50 Cross-check for discovery, ROI routes, list defaults, login body/cookies,
51 version 0.2 and Project/Dataset/Screen save support.
53- Official OME OMERO.server component releases
54 https://github.com/ome/omero-server/releases
55 Cross-check for current server component releases.

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 latest 5.23.0, its 2026-07-30 release, 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/releases/tag/v5.23.0 https://github.com/ome/omero-py/blob/v5.23.0/src/omero/gateway/__init__.py Source check for gateway signatures, session lifecycle, context forwarding, annotation materialization, channel inversion, and ROI/model handling. The 5.23.0 release adds default-group CLI support and shape externalInfo loading; it does not announce IRoi removal.
  • Current OMERO.web package and API implementation https://pypi.org/project/omero-web/ https://github.com/ome/omero-web/blob/v5.33.2/omeroweb/api/urls.py https://github.com/ome/omero-web/blob/v5.33.2/omeroweb/api/views.py https://github.com/ome/omero-web/blob/v5.33.2/omeroweb/webgateway/views.py Cross-check for discovery, ROI routes, list defaults, login body/cookies, version 0.2 and Project/Dataset/Screen save support.
  • Official OME OMERO.server component releases https://github.com/ome/omero-server/releases Cross-check for current server component releases.
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57## Installation and Compatibility
59- OMERO Python language bindings
60 https://omero.readthedocs.io/en/stable/developers/Python.html
61 Basis for the current `omero-py==5.22.1` examples, IcePy 3.6.5 ordering,
62 BlitzGateway patterns, objects, annotations, tables, ROIs, pixels, and
63 rendering.
65- OMERO version requirements
66 https://omero.readthedocs.io/en/stable/sysadmins/version-requirements.html
67 Basis for Python 3.10/3.11 support, Python 3.12 recommendation,
68 Python 3.13/3.14 “upcoming” status, Ice 3.6 recommendation, Ice 3.7
69 unsupported status, and server platform/runtime matrix.
71- OMERO-linked Glencoe Ice binary matrix
72 https://www.glencoesoftware.com/blog/2023/12/08/ice-binaries-for-omero.html
73 Basis for exact prebuilt IcePy 3.6.5 wheel coverage through Python 3.12.
74 Glencoe is identified in OME's Python installation page as its commercial
75 partner. Select the exact wheel from the linked release repositories.
77- OMERO CLI installation
78 https://omero.readthedocs.io/en/stable/users/cli/installation.html
79 Basis for client installation and import/admin prerequisites.

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.
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81## Connection and Security
83- BlitzGateway documentation
84 https://omero.readthedocs.io/en/stable/developers/PythonBlitzGateway.html
85 Basis for context-manager closure, wrappers/lazy loading, stateless versus
86 stateful service reuse, and stale stateful proxies after reconnection.
88- Server security and firewalls
89 https://omero.readthedocs.io/en/stable/sysadmins/server-security.html
90 Basis for login encryption, optional full transport encryption, session-ID
91 exposure on insecure post-login traffic, and default router ports 4063/4064.
93- Client/server SSL verification
94 https://omero.readthedocs.io/en/stable/sysadmins/client-server-ssl.html
95 Basis for the warning that standard clients do not automatically verify the
96 host and for the documented IceSSL verification properties.
98- CLI session management
99 https://omero.readthedocs.io/en/stable/users/cli/sessions.html
100 Basis for prompted login, session files, `omero sessions`, group switching,
101 `-k` session reuse, and logout.

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.
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103## Data, Metadata, ROIs, and Tables
105- OMERO Python examples
106 https://omero.readthedocs.io/en/stable/developers/Python.html
107 Primary current examples for bounded `getObjects`, annotations, pixels,
108 rendering, tables, and ROI model operations.
110- OMERO.tables
111 https://omero.readthedocs.io/en/stable/developers/Tables.html
112 Basis for current column signatures, reads, queries, paging, global locking,
113 and HDF implementation details.
115- Structured annotations
116 https://omero.readthedocs.io/en/stable/developers/Model/StructuredAnnotations.html
117 Basis for annotation type hierarchy, namespaces, and link semantics.
119- OME ROI model 5.6.3
120 https://docs.openmicroscopy.org/ome-model/5.6.3/developers/roi.html
121 Basis for the eight shape types, optional TheZ/TheT/TheC, RGBA fields, and
122 union-of-2D-shapes representation. The page itself was last updated in 2018
123 but documents the June 2016 schema still used by OMERO 5.6.
125- Current generated `IRoi` API
126 https://docs.openmicroscopy.org/omero-blitz/5.8.5/slice2html/omero/api/IRoi.html
127 Basis for the explicit `IRoi` deprecation warning.
129- OMERO application services
130 https://omero.readthedocs.io/en/stable/developers/Modules/Api.html
131 Basis for service categories and current `IRoi`/`IShare` deprecation status.

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.
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133## CLI Import, Export, and Download
135- Import images
136 https://omero.readthedocs.io/en/stable/users/cli/import.html
137 Basis for `omero import`, `-f` serverless scanning, target syntax,
138 depth/output options, experimental parallelism warning, and diagnostic
139 upload disclosure.
141- Import targets
142 https://omero.readthedocs.io/en/stable/users/cli/import-target.html
143 Basis for current-group target behavior and target syntax.
145- Export images
146 https://omero.readthedocs.io/en/stable/users/cli/export.html
147 Basis for OME-TIFF/XML-only export and experimental Dataset iteration.
149- Current `omero-py==5.23.0` CLI help (`omero download -h`)
150 Verified in an isolated environment on 2026-09-30. Basis for explicit
151 OriginalFile, FileAnnotation, Image, and Fileset download forms. This was
152 cross-checked against the official `ome/omero-py` package.

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==5.23.0 CLI help (omero download -h) Verified in an isolated environment on 2026-09-30. Basis for explicit OriginalFile, FileAnnotation, Image, and Fileset download forms. This was cross-checked against the official ome/omero-py package.
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154## OMERO.web and Public Data
156- OMERO.web framework
157 https://omero.readthedocs.io/en/stable/developers/Web.html
158 Basis for treating only `api` and `webgateway` as stable public APIs and
159 treating other app URLs as internal.
161- OMERO JSON API
162 https://omero.readthedocs.io/en/stable/developers/json-api.html
163 Basis for version discovery, API version headers, CSRF/login behavior,
164 pagination/maxLimit, ROI endpoints, and limited create/update object types.
166- Publishing data using OMERO.web
167 https://omero.readthedocs.io/en/stable/sysadmins/public.html
168 Basis for dedicated read-only public groups/users, GET-only default, URL
169 filters, and publication URL examples.
171- OMERO configuration properties
172 https://omero.readthedocs.io/en/stable/sysadmins/config.html
173 Basis for public-user defaults (`enabled=false`, `get_only=true`, and a
174 URL filter that allows nothing until configured).

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).
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176## Review Evidence and Endpoint Coverage
178The 2026-09-30 review read all bundled scripts and references, the stable OME
179release/JSON API pages, current PyPI metadata, and official source at
180`ome/omero-py` v5.23.0 and `ome/omero-web` v5.33.2. Direct extraction of
181Read the Docs pages returned HTTP 403, so the corresponding source files in
182[OME's documentation repository](https://github.com/ome/omero-documentation)
183were used alongside browser-readable pages. The generated IRoi definition and
184OME ROI model were fetched directly.
186| Surface used by this skill | Verified contract |
187| --- | --- |
188| `GET /api/`, `GET /api/v0/` | `data` versions, `url:base` and discovered starting links; current API header is 0.2, independent of server release. |
189| `GET /api/v0/servers/`, `GET /api/v0/token/` | Server IDs and CSRF value in `data`; the latter is not a bearer credential endpoint. |
190| `POST /api/v0/login/` | Form parameters `server`, `username`, `password`; session cookies and CSRF; current 5.33.2 source also accepts JSON. Response includes sensitive `eventContext` and `success`. |
191| `GET /api/v0/m/rois/` | `image`, `group`, `owner`, `limit`, `offset`, `normalize`; `data` includes shapes, `meta` reports pagination. Also `/api/v0/m/images/{image_id}/rois/`. |
192| JSON object writes (capability description only) | `POST`/`PUT` through discovered `url:save`; model support remains Project/Dataset/Screen, with explicit group and schema `@type`. No generic Image write endpoint implied. |
193| BlitzGateway / Ice services | Not HTTP endpoints. Checked gateway, IQuery/IUpdate, IRoi, RawFileStore, pixel/rendering, SharedResources/Table and model signatures against source/generated API. Direct proxy calls need the selected group context. |
194| CLI | Session, group, download, import target/scan/depth, export and script upload/launch syntax checked against current source/help; import additionally needs the server Java distribution. |
195| Public webclient links | Navigation examples, not a supported API contract or proof of public access. |
197Local checks installed OMERO.py 5.22.1 and 5.23.0 with the OMERO-linked
198macOS universal IcePy 3.6.5 wheel on Python 3.12. Real annotation/shape model regression tests
199and CLI help ran without a server. All Python documentation blocks were
200syntax-checked. Pure local planners and mocked group/session tests ran in the
201repository suite. No login, remote read/write, import, export, rendering,
202server script, table service, or deployed HTTP API was executed. These examples
203remain illustrative until validated against the selected installation.

Review Evidence and Endpoint Coverage

The 2026-09-30 review read all bundled scripts and references, the stable OME release/JSON API pages, current PyPI metadata, and official source at ome/omero-py v5.23.0 and ome/omero-web v5.33.2. Direct extraction of Read the Docs pages returned HTTP 403, so the corresponding source files in OME's documentation repository were used alongside browser-readable pages. The generated IRoi definition and OME ROI model were fetched directly.

Surface used by this skillVerified contract
GET /api/, GET /api/v0/data versions, url:base and discovered starting links; current API header is 0.2, independent of server release.
GET /api/v0/servers/, GET /api/v0/token/Server IDs and CSRF value in data; the latter is not a bearer credential endpoint.
POST /api/v0/login/Form parameters server, username, password; session cookies and CSRF; current 5.33.2 source also accepts JSON. Response includes sensitive eventContext and success.
GET /api/v0/m/rois/image, group, owner, limit, offset, normalize; data includes shapes, meta reports pagination. Also /api/v0/m/images/{image_id}/rois/.
JSON object writes (capability description only)POST/PUT through discovered url:save; model support remains Project/Dataset/Screen, with explicit group and schema @type. No generic Image write endpoint implied.
BlitzGateway / Ice servicesNot HTTP endpoints. Checked gateway, IQuery/IUpdate, IRoi, RawFileStore, pixel/rendering, SharedResources/Table and model signatures against source/generated API. Direct proxy calls need the selected group context.
CLISession, group, download, import target/scan/depth, export and script upload/launch syntax checked against current source/help; import additionally needs the server Java distribution.
Public webclient linksNavigation examples, not a supported API contract or proof of public access.

Local checks installed OMERO.py 5.22.1 and 5.23.0 with the OMERO-linked macOS universal IcePy 3.6.5 wheel on Python 3.12. Real annotation/shape model regression tests and CLI help ran without a server. All Python documentation blocks were syntax-checked. Pure local planners and mocked group/session tests ran in the repository suite. No login, remote read/write, import, export, rendering, server script, table service, or deployed HTTP API was executed. These examples remain illustrative until validated against the selected installation.

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

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.
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