Mmcp.market

omero-integration skill

by K-Dense-AI·K-Dense-AI/scientific-agent-skills·47k stars·MIT

Securely inspect and automate microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and documented OMERO.web APIs. Use for scoped OMERO inventory, metadata export, import/export planning, or reviewed write workflows.

A100/100content scan

Is the omero-integration skill safe?

Clean: nothing in its files matched our rules. We read 15 files in the folder on 2026-09-28.

No findings.

Install the omero-integration skill

A skill is a folder. Copy it into your agent's skills folder and the agent loads it when the task matches its description. 

git clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/scientific-agent-skills
mkdir -p ~/.claude/skills
cp -r /tmp/scientific-agent-skills/skills/omero-integration ~/.claude/skills/omero-integration
available in every project

In the Claude apps, zip the folder and upload it from the Skills settings. The folder on GitHub

The instructions your agent would load

SKILL.md as published, without the frontmatter. Read it on GitHub

OMERO Integration

Use current OME documentation and the smallest explicit data scope. OMERO data may contain unpublished images, identifiers, annotations, original files, and derived measurements.

Verified Baseline

This skill was refreshed on 2026-07-23:

OMERO.web 5.31.0.

  • OMERO.server 5.6.18 (May 2026) is the current documented stable server.
  • It was tested by OME with OMERO.py/omero-py 5.22.1 and

supports 3.10 and 3.11, recommends 3.12, and still labels 3.13/3.14 “upcoming.”

  • omero-py==5.22.1 requires Python 3.10 or newer. The OMERO support matrix

for Python versions through 3.12.

  • OMERO 5.6 uses IcePy 3.6, with 3.6.5 prebuilt client wheels documented

The pin above is a reproducible skill snapshot, not a promise that every OMERO.server release accepts that client. For another server version, consult its release entry and use the OMERO.py version tested with it. See references/sources.md.

Operating Contract

selected the host, group, object type, IDs, and result limit.

  1. Start with local validation or a dry run. Do not connect until the user has

Never search parent directories or load .env files.

  1. Read credentials only from the named OMERO_* variables in the frontmatter.

output JSON, logs, tracebacks, or chat. A session key is a bearer credential.

  1. Never place a password or session key in command arguments, source code,

data and the session ID may otherwise travel unencrypted. secure=True does not by itself guarantee certificate hostname verification.

  1. Default to secure=True. OMERO encrypts login by default, but post-login

local file scan. Do not turn an object request into a group-wide or cross-group export without explicit approval.

  1. Bound every list, page, ROI, shape, annotation, table row, pixel plane, and

saves, image creation, imports, script uploads, table writes, ownership or group changes, and deletion require an exact reviewed target.

  1. Treat all writes separately: annotation/link creation, rendering-default

engines, script clients, and other stateful services in finally blocks or documented context-manager patterns.

  1. Close BlitzGateway, table handles, raw stores, thumbnail stores, rendering
  1. Never connect to a real server merely to “test” examples.

Choose the Interface

pixels, annotations, ROIs, rendering, and services.

  • BlitzGateway (omero-py): primary Python client for object traversal,

scripts, and administrative plugins. Most client commands are remote; import also needs the matching server-side Java libraries through OMERODIR.

  • OMERO CLI: sessions, import scanning/import, OME-TIFF or XML export,

documentation calls stable public APIs. The documented JSON API is version-discovered and has limited object coverage; it is not evidence that every webclient URL is a supported REST endpoint.

  • OMERO.web api and webgateway: the only OMERO.web apps that official

They are different from the bundled local client helpers in scripts/.

  • OMERO.server scripts: uploaded plugins executed by server infrastructure.

Install a Reproducible Client

Create a Python 3.12 environment:

uv venv --python 3.12 .venv
source .venv/bin/activate

Install the exact IcePy 3.6.5 wheel matching the interpreter, OS, architecture, and wheel tags, then OMERO.py:

# Download the matching 3.6.5 wheel from the official OMERO-linked matrix.
uv pip install "/absolute/path/to/zeroc_ice-3.6.5-<matching-tags>.whl"
uv pip install "omero-py==5.22.1"

Do not substitute Ice 3.7: the OMERO 5.6 support matrix marks Ice 3.6 as recommended and 3.7 as unsupported. A plain install may attempt to compile IcePy from source; prefer a reviewed matching wheel. The upstream package is GPL-2.0-or-later; this skill’s own files are MIT.

For import/admin commands only, OMERODIR must point to a compatible extracted OMERO.server directory. A normal remote BlitzGateway client does not require that server tree. Read references/connection.md before installation or authentication work.

Credentials and Connection

Set named variables in the calling environment or secret manager. Do not put the password on an omero CLI command:

export OMERO_HOST="omero.example.org"
export OMERO_PORT="4064"
export OMERO_USER="researcher"
export OMERO_SECURE="true"
# Supply OMERO_PASSWORD through the environment/secret manager, or use
# OMERO_SESSION_KEY as an alternative. Do not echo either value.

A password-authenticated, exception-safe read pattern is:

import os
from omero.gateway import BlitzGateway

conn = None
try:
    conn = BlitzGateway(
        os.environ["OMERO_USER"],
        os.environ["OMERO_PASSWORD"],
        host=os.environ["OMERO_HOST"],
        port=int(os.environ.get("OMERO_PORT", "4064")),
        secure=True,
    )
    if not conn.connect():
        raise RuntimeError("OMERO connection failed")

    images = conn.getObjects(
        "Image",
        opts={"limit": 25, "offset": 0, "order_by": "obj.id"},
    )
    for image in images:
        print(image.getId())  # Do not print names unless requested.
finally:
    if conn is not None:
        conn.close()

For existing-session and CLI prompt patterns, certificate verification, group context, and cleanup details, read references/connection.md.

Bundled Safe Helpers

All helpers use argparse; --help works without OMERO installed. Remote helpers are dry-run by default and require --execute.

python -B scripts/validate_config.py --help
python -B scripts/inventory.py --help
python -B scripts/export_image_metadata.py --help
python -B scripts/plan_transfer.py --help

optional DNS resolution still does not contact OMERO.

  • validate_config.py: validates only named endpoint/auth variables locally;

redaction defaults and per-category limits; it never downloads file bytes or pixels.

  • inventory.py: bounded, read-only object inventory with paged JSON output.
  • exportimagemetadata.py: explicit-image annotation/ROI JSON export with

invokes OMERO and never emits credential flags.

  • plan_transfer.py: local-only import scan or per-image export plan; it never

Read references/scripts.md before using them.

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