Omero Integration

What it does

When your agent uses it

• Scoped OMERO inventory
• Metadata export
• Import/export planning
• Reviewed write workflows

Example prompts

• “Use the omero-integration skill to inspect and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI…”
• “/omero-integration”

Requirements

• Python 3
• A credential in OMERO_SESSION_KEY
• Compatibility (from SKILL.md): Requires network access to a user-selected OMERO.server for remote operations. The server-tested snapshot uses OMERO.py 5.22.1 with ZeroC IcePy 3.6.5; OMERO supports Python 3.10-3.12 (3.12 recommended) while 3.13-3.14 remain upcoming in its support matrix. Bundled local planners require Python 3.10+ and read only named OMERO_* variables; they never load .env files.

Workflow steps

8 steps, taken from the first numbered list in SKILL.md.

1. 1Start with local validation or a dry run. Do not connect until the user has
2. 2Read credentials only from the named OMERO_* variables in the frontmatter.
3. 3Never place a password or session key in command arguments, source code,
4. 4Default to secure=True. OMERO encrypts login by default, but post-login
5. 5Bound every list, page, ROI, shape, annotation, table row, pixel plane, and
6. 6Treat all writes separately: annotation/link creation, rendering-default
7. 7Close BlitzGateway, table handles, raw stores, thumbnail stores, rendering
8. 8Never connect to a real server merely to “test” examples.

What it can do on your machine

Read from SKILL.md and the folder at commit 92ace75. It shows what the files ask for, not the result of running them.

• Tool permissions

  Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

  From allowed-tools in the SKILL.md frontmatter.

• Runs code

  Ships 5 files in scripts/ (Python), which the agent can run.

  Shell commands in SKILL.md call:

  • python
  • uv

  From the folder's file list and the shell code blocks in SKILL.md.

• Network

  Links to these hosts (documentation or services it may open):

  • arxiv.org
  • omero.readthedocs.io
  • doi.org
  • export.arxiv.org

  From URLs in SKILL.md, links to its own repository left out.

• Credentials

  Names these keys or tokens, usually read from environment variables:

  • OMERO_PASSWORD
  • OMERO_SESSION_KEY

  From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

• Compatibility

  Requires network access to a user-selected OMERO.server for remote operations. The server-tested snapshot uses OMERO.py 5.22.1 with ZeroC IcePy 3.6.5; OMERO supports Python 3.10-3.12 (3.12 recommended) while 3.13-3.14 remain upcoming in its support matrix. Bundled local planners require Python 3.10+ and read only named OMERO_* variables; they never load .env files.

  From compatibility in the SKILL.md frontmatter.

Context cost

Omero Integration loads about 2.8k tokens when it runs, and up to ~25k if it reads all its reference files. Until then it costs about 77 tokens; SKILL.md has 1,033 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it

~77

When it runs · the whole SKILL.md, loaded when a task matches

~2.8k

With references · SKILL.md plus every file in references/, read only if the agent opens them

~25k

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

• NoteMentions a .env fileSKILL.md:10

  named OMERO_* variables; they never load .env files.

• NoteMentions a .env fileSKILL.md:73

  Never search parent directories or load `.env` files.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from K-Dense-AI/scientific-agent-skills at commit 92ace75, republished under its MIT licence (© K-Dense-AI). 1,033 words, ~2,783 tokens.

name

omero-integration

description

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

compatibility

Requires network access to a user-selected OMERO.server for remote operations. The server-tested snapshot uses OMERO.py 5.22.1 with ZeroC IcePy 3.6.5; OMERO supports Python 3.10-3.12 (3.12 recommended) while 3.13-3.14 remain upcoming in its support matrix. Bundled local planners require Python 3.10+ and read only named OMERO_* variables; they never load .env files.

license

MIT

metadata.version

1.6

metadata.last-reviewed

2026-09-30

metadata.skill-author

K-Dense Inc.

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

# 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"

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.

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()

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

© K-Dense-AI, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 14 other files (scripts, references) in skills/omero-integration of K-Dense-AI/scientific-agent-skills.

• SKILL.md
• references/advanced.md
• references/connection.md
• references/data_access.md
• references/image_processing.md
• references/metadata.md
• references/rois.md
• references/scripts.md
• references/sources.md
• references/tables.md
• scripts/export_image_metadata.py
• scripts/inventory.py
• scripts/omero_common.py
• scripts/plan_transfer.py
• scripts/validate_config.py

Open the folder on GitHubat commit 92ace75

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in K-Dense-AI/scientific-agent-skills, which our catalogue first saw on October 7, 2026.

• lingxling/awesome-skills-cnclaude-scientific-skills/skills/omero-integration