slicer-cli

Slicer CLI

Unofficial agent-first CLI for 3D Slicer's in-process HTTP WebServer (default 127.0.0.1:2016), so AI coding agents and humans can drive Slicer from outside the application.

The CLI speaks JSON envelopes with stable error codes (E_*), refuses empty MRML selectors, gates destructive operations behind --confirm, and ships an Agent Skills Spec– compliant skill so any compatible AI agent can learn the surface on first contact.

slicer-cli --json status            # is Slicer up?
slicer-cli --json volume list       # what's loaded?
slicer-cli --json render slice \
  --orientation axial --offset 12 \
  --out /tmp/ax.png                 # render an axial slice

Features

• Agent-first JSON output — one envelope per call; branch on stable error.code strings, never on message text.
• Safe by default — scene clear, system shutdown, node delete "", and exec are all gated by explicit flags or refused outright.
• Reusable typed Python client — slicer_cli.client.SlicerClient is importable on its own; the CLI is just one consumer.
• Bundled AI agent skill — drop-in skill at .agents/skills/slicer-cli/ for any Agent Skills– compatible agent (Claude Code, Codex, Cursor, Goose, OpenHands, …).

Prerequisites

• 3D Slicer 5.x, with the Web Server module started (Slicer → Welcome → search "Web Server" → Start server).
• Python 3.11+ and uv.

Installation

The project is not on PyPI; install directly from GitHub.

Recommended: uv tool install from a GitHub Release

Once a release exists, install the wheel asset directly:

uv tool install \
  https://github.com/Lightbridge-KS/slicer-cli/releases/download/vX.X.X/slicer_cli-0.1.0-py3-none-any.whl

Or install straight from a tagged commit (works without a release artifact):

uv tool install git+https://github.com/Lightbridge-KS/slicer-cli.git@vX.X.X

For a one-shot run without a persistent install:

uvx --from git+https://github.com/Lightbridge-KS/slicer-cli.git slicer-cli status

After install, two console scripts are on PATH: slicer-cli and the short alias slcli. Verify against your running Slicer:

slicer-cli status
# ✓ Slicer is up at http://127.0.0.1:2016
#   applicationName     Slicer
#   applicationVersion  5.11.0-...

To upgrade later:

uv tool upgrade slicer-cli

Alternative: clone and install from source (development)

git clone https://github.com/Lightbridge-KS/slicer-cli.git
cd slicer-cli
uv sync
uv run slicer-cli status

Use this path if you want to hack on the CLI itself or run the unit test suite (uv run pytest -m "not integration").

Basic CLI usage

# Liveness probe + version.
slicer-cli status

# Capability matrix (render, dicomweb, power-tool-endpoint, ...).
slicer-cli doctor

# What's loaded?
slicer-cli volume list
slicer-cli scene nodes --class vtkMRMLScalarVolumeNode

# Render a sagittal slice 12 mm anterior of origin from the green viewer.
slicer-cli render slice \
  --view green --orientation sagittal --offset 12 --size 512 \
  --out /tmp/sag.png

# Export a volume to NRRD on disk.
slicer-cli volume export vtkMRMLScalarVolumeNode1 --out /tmp/mr.nrrd

# Discover the underlying HTTP surface, offline.
slicer-cli api routes --json | jq '.routes[] | select(.note != null)'

Pass --json for one-line JSON envelopes (the agent default); leave it off for human-friendly tables on a TTY. The full surface and every flag lives in docs/Slicer-CLI-UserManual.md.

AI agent skill

This repo bundles an Agent Skills Spec– compliant skill at:

.agents/skills/slicer-cli/
├── SKILL.md
└── references/
    ├── commands.md         # full command surface
    ├── errors.md           # E_* codes ↔ exit codes
    ├── safety.md           # destructive ops, exec gating, audit log
    ├── dicomweb.md         # Orthanc → Slicer pull → QIDO/WADO
    └── troubleshooting.md  # symptom → cause → fix

The skill is agent-agnostic — it is plain Markdown with YAML frontmatter per the spec, so any compatible agent can load it.

Use with Claude Code

A symlink at .claude/skills/slicer-cli → ../../.agents/skills/slicer-cli is already wired in this repo, so opening this directory in Claude Code picks the skill up automatically. To enable it in other repos on the same machine, symlink it into your user skills directory once:

ln -s "$(pwd)/.agents/skills/slicer-cli" ~/.claude/skills/slicer-cli

Use with other agents

Point your agent's skills directory at .agents/skills/slicer-cli/. The Agent Skills client list covers the loading mechanism for each one (Claude, Codex, Cursor, Gemini CLI, Goose, OpenHands, OpenCode, GitHub Copilot, Roo, Kiro, and many more).

Try the skill

Once the skill is wired into your agent of choice, prompt it with something like:

"Load MRHead in Slicer and render an axial slice at offset 12 mm."

A compatible agent should auto-activate the skill, run slicer-cli --json status first, find the volume by name, and write a PNG to disk — branching on error.code if anything fails.

Documentation

Status

Alpha — Phases 0–3 shipped (core read/write + render + DICOMweb + markup

• formal exec + GUI layout + audit log). Phase 4 (this skill) is the current iteration. See docs/TODOS.md for the live phase tracker.

License

MIT