registry / contribute

Publish a skill to the index

Submissions enter a review queue where a maintainer checks the manifest, runs the fixture invocation, and confirms the safety note before the entry is listed. Provide the source repository and the metadata below.

A valid SKILL.md at the repository root

Frontmatter with name, technique, category and license; a scope section that states the limits of the skill.

A runnable MCP server or reference implementation

Typed tool definitions and a sample invocation that completes against the bundled fixture data.

An instrument safety note

Anything that moves a stage, changes beam conditions, or mills material must declare it in plain language.

Reproducible outputs

Pinned dependencies and a deterministic mode so a reviewer can reproduce your reported numbers.

Submit your skill

Indexing is not certification. Listed skills are references to read and adapt — verify every procedure against your own instrument and sample before running it unattended.

SKILL.md template & folder layout

The registry repository is emskills-mcp/em-skills. Add one folder per skill under skills/<slug>/ and open a pull request. On merge, the importer validates every manifest and drops it into the moderation queue — the folder name must equal the slug in front matter.

repository layout

em-skills/
├── README.md
└── skills/
    ├── cryo2d-classify/
    │   ├── SKILL.md          # required — manifest + instructions
    │   ├── skill.json        # optional — overrides/extends front matter
    │   ├── examples/
    │   │   └── invoke.json   # sample tool call + expected output
    │   └── fixtures/
    │       └── sample.mrc    # small deterministic test input
    └── edax-phase-map/
        └── SKILL.md

skills/<slug>/SKILL.md

---
name: Cryo-EM 2D class triage
slug: cryo2d-classify
technique: cryo-EM
category: Segmentation
kind: MCP server
summary: Ranks 2D class averages and flags junk classes before 3D refinement
description: >
  Scores RELION/cryoSPARC 2D class averages on resolution, particle count and
  radial symmetry, then returns a keep/discard recommendation per class.
org: Example Structural Biology Lab
repo: emskills-mcp/em-skills
version: 0.1.0
license: MIT
runtime: python 3.11
tool_call: cryo2d_classify
mcp_endpoint: https://mcp.example.org/cryo2d
tags:
  - cryo-em
  - 2d-classification
  - qc
---

# Cryo-EM 2D class triage

## Scope
What this skill does, the data it expects (format, pixel size, box size), and
what it explicitly does not do. State the limits an agent must not exceed.

## Safety
Declare any action that touches hardware: stage movement, beam or dose changes,
aperture or valve control, milling. Read-only analysis skills state
"Read-only — no instrument control".

## Usage
```json
{
  "tool": "cryo2d_classify",
  "arguments": {
    "job_dir": "/data/relion/Class2D/job012",
    "min_particles": 500
  }
}
```

Expected output shape, units, and a deterministic example result produced from
the bundled fixture.

## Reproducibility
Pinned dependencies, seed/deterministic mode, and the command a reviewer runs
to reproduce the reported numbers.

skills/<slug>/skill.json (optional)

{
  "slug": "cryo2d-classify",
  "technique": "cryo-EM",
  "category": "Segmentation",
  "tool_call": "cryo2d_classify",
  "tags": ["cryo-em", "qc"]
}

required front matter

name: Human-readable skill name, e.g. “Cryo-EM 2D class triage”.
slug: Lowercase kebab-case id; must match the folder name.
technique: One of the registry techniques, one of SEM, TEM, STEM, EDS, EELS, cryo-EM, FIB.
category: One of the registry categories, e.g. Segmentation, Image acquisition, Calibration.
kind: “MCP server” or “SKILL.md”.
summary: One sentence, 20–200 characters, no trailing period needed.
license: SPDX id such as MIT, Apache-2.0, BSD-3-Clause.
version: Semantic version such as 0.1.0.
runtime: Execution environment, e.g. “python 3.11” or “node 20”.
tool_call: Canonical tool name agents invoke, snake_case.

optional front matter

org: Publishing lab, group or company. Defaults to the repo owner.
repo: Upstream source repository if it differs from this registry.
mcp_endpoint: HTTPS endpoint for a hosted MCP server.
tags: Up to 12 short tags, YAML list or [a, b, c].
description: Longer prose; falls back to the first body paragraph.

required body sections

## Scope — what the skill does and the instruments/data it assumes.
## Safety — beam dose, stage motion, or sample-damage limits an agent must respect.
## Usage — the exact tool call, arguments, and expected output.

Validation rejects unknown techniques or categories, non-semver versions, summaries outside 20–200 characters, and missing sections — each error names the file, the field, and how to fix it.