Scientific Agent Skills is a collection of reusable procedures that give AI agents capabilities for scientific research across areas such as biology, chemistry, medicine, and drug discovery. It is used by researchers and by people building AI scientist workflows with compatible coding agents. The catalogue contains many of the project's skills and supporting instructions.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add K-Dense-AI/scientific-agent-skills --skill omero-integrationgit clone --depth 1 https://github.com/K-Dense-AI/scientific-agent-skillsWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/omero-integration)<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/omero-integration"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/omero-integration/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/k-dense-ai/scientific-agent-skills/omero-integration"><img src="https://agentmods.dev/badge/skills/k-dense-ai/scientific-agent-skills/omero-integration.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- Socket pass
- Snyk warn
- NVIDIA SkillSpector warn
SkillSpector: 1 finding, up to high
These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →
- high Privilege Escalation · line 10 Code accesses credential files (SSH keys, AWS credentials, etc.). This could indicate credential theft attempts.Fix: Remove references to credential paths. Use environment variables or secrets managers. For docs, use placeholder paths (e.g., /path/to/config). Never load .env or token files in production code paths.
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00065 | $0.02465 |
| Opus 5 | $0.00032 | $0.01233 |
| Sonnet 5 | $0.00013 | $0.00493 |
| Haiku 4.5 | $0.00006 | $0.00247 |
Grade A, and why
omero-integration scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 240 lines — stays where its author put it; the contents beside it link to each section 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.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 OMERO.web 5.31.0.
omero-py==5.22.1requires Python 3.10 or newer. The OMERO support matrix supports 3.10 and 3.11, recommends 3.12, and still labels 3.13/3.14 “upcoming.”- OMERO 5.6 uses IcePy 3.6, with 3.6.5 prebuilt client wheels documented for Python versions through 3.12.
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
- Start with local validation or a dry run. Do not connect until the user has selected the host, group, object type, IDs, and result limit.
- Read credentials only from the named
OMERO_*variables in the frontmatter. Never search parent directories or load.envfiles. - Never place a password or session key in command arguments, source code, output JSON, logs, tracebacks, or chat. A session key is a bearer credential.
- Default to
secure=True. OMERO encrypts login by default, but post-login data and the session ID may otherwise travel unencrypted.secure=Truedoes not by itself guarantee certificate hostname verification. - Bound every list, page, ROI, shape, annotation, table row, pixel plane, and local file scan. Do not turn an object request into a group-wide or cross-group export without explicit approval.
- Treat all writes separately: annotation/link creation, rendering-default saves, image creation, imports, script uploads, table writes, ownership or group changes, and deletion require an exact reviewed target.
- Close
BlitzGateway, table handles, raw stores, thumbnail stores, rendering engines, script clients, and other stateful services infinallyblocks or documented context-manager patterns. - Never connect to a real server merely to “test” examples.
What ships with it
14 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
- references/advanced.md 9.4 KB
- references/connection.md 9.7 KB
- references/data_access.md 9.3 KB
- references/image_processing.md 7.7 KB
- references/metadata.md 8.8 KB
- references/rois.md 8.2 KB
- references/scripts.md 8.2 KB
- references/sources.md 8.1 KB
- references/tables.md 8.3 KB
- scripts/export_image_metadata.py 16 KB runs code
- scripts/inventory.py 8.2 KB runs code
- scripts/omero_common.py 14 KB runs code
- scripts/plan_transfer.py 12 KB runs code
- scripts/validate_config.py 4.0 KB runs code
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 240 lines · 65 tokens per session scan A 242ba431ebc6
omero-integration is a skill published in the GitHub repository K-Dense-AI/scientific-agent-skills (44,469 stars, last pushed yesterday), licensed MIT. It adds 65 tokens to every session and 2,465 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
Other skills, from other repositories
discovery-toolbox
A routed repertoire of 90 scientific thinking operators for biological research agents - visual reasoning, detectability and information budgets, search reframing, causal identification, competing explanations, observation and selection processes, pipeline artifact diagnosis, effort allocation, and confirmation…
discovery-director
Operate as a research director making original discoveries from a given biological question and dataset. Use when the task is open-ended scientific research, exploring omics or experimental data for findings, hypothesis generation and testing, screening a large candidate space of genes, variants, features or…
bio-interdomain-hgt
Detect and polarize interdomain horizontal gene transfer with homology, context, and phylogenetic checks. Use when studying lateral gene transfer, virus-host gene exchange, endogenous viral elements, or donor direction.
polars-dovmed
Search PMC Open Access and bioRxiv corpora with polars-dovmed. Use when structured, reproducible literature queries should run through the hosted API or local parquet indexes.
csag-extraction
Extract a Conditional Scientific Argumentation Graph and grounded Q&A from a manuscript. Use when representing assertions, contexts, evidence links, and inference steps in machine-readable form.
exploratory-data-analysis
Inspect scientific data and generate a Markdown structure-and-quality report. Use when triaging tabular, array, sequence, HDF5, JSON, or raster files before downstream analysis.