slicer

name	slicer
description	Search and reason over 3D Slicer source code, extensions, and community discussions. Use for questions about medical imaging, MRML scene graphs, VTK/ITK pipelines, Slicer Python scripting, C++ module development, extension development, Qt-based module UI, segmentation, volume rendering, DICOM workflows, and the Slicer build system.
version	1.1
setup	./setup.sh
requires	["git","perl","bash"]

Slicer Skill

This repository contains the information and helper scripts needed by an AI coding agent ("skill") that is designed to answer questions about the 3D Slicer application and its extension ecosystem. It is intentionally generic so that it can be consumed by any tool that understands the SKILLS.md convention (e.g. Claude Code, OpenAI agents, etc.).

Setup Modes

The setup script (./setup.sh) has two orthogonal axes:

1. mode — what gets cloned (full / lightweight / web)
2. indexes — what ranked-search indexes get built (none / bm25 / hybrid)

On first run, setup.sh prompts for both. Subsequent runs reuse the previous choices, recorded in .setup-stamp.json as the "mode" and "indexes" fields. You can override interactively or via flags.

Mode (which clones)

Mode	Disk	Setup time	What's local
full	~15 GB	~20 min	Source, deps, all 200+ extensions, discourse archive
lightweight	~1 GB	~2 min	Source + ExtensionsIndex metadata (JSON only)
web	minimal	instant	Nothing cloned — all access via web APIs

Override: ./setup.sh --mode full|lightweight|web

Indexes (which ranked-search backends)

Indexes	Disk	Setup time	What it gives you
none	0	instant	No ranked search; the agent uses grep/find/web APIs.
bm25	~65 MB	~15 s (foreground)	Lexical search (BM25) over slicer-source + slicer-discourse. Best for exact identifiers, symbols, paths.
hybrid	~300 MB	~15 s up front, ~20 min in the background	bm25 PLUS dense embeddings (sentence-transformers/all-MiniLM-L6-v2). Adds semantic / paraphrase search. Lexical search is ready as soon as setup.sh exits; vector/hybrid search becomes available when the background build finishes.

Override: ./setup.sh --indexes none|bm25|hybrid

Background build progress for the hybrid level:

• tail -f .vector-build.log from the workspace root, or
• call the MCP index_status tool — it reports "building": true with the process PID and the last log lines while the embed job is running.

web mode forces indexes=none (there are no local clones to index).

Determining the active state: Read .setup-stamp.json in the skill workspace and look at "mode" and "indexes". If the file does not exist, run ./setup.sh.

Goal

Depending on the active mode, the skill provides access to these resources either locally (via cloned repositories) or remotely (via web APIs):

1. The Slicer source code – the official C++/Python repositories that make up the application. (Local in full and lightweight modes.)
2. The Extensions Index – a machine‑readable list of third‑party extensions and their repositories. The skill should iterate through the index files and clone each listed repository so that extension code is available for searching.
3. The Discourse archive – a mirror of the Slicer Discourse forum content (see https://github.com/pieper/slicer-discourse-archive) to allow question‑answering based on past community discussions.
4. The NA-MIC Project Week repository – a collection of tutorials, presentations, and code from NA-MIC Project Weeks (https://github.com/NA-MIC/ProjectWeek), providing additional examples and educational materials for Slicer programming. The scripts/extract_pw_stats.py utility can be used to extract statistics about project weeks, including participant lists and project counts. This is useful for finding papers, collaborations, or expertise by searching for people who have attended NA-MIC Project Weeks.
5. Build dependencies (VTK, ITK, CTK, etc.) – cloned from SuperBuild references. (Local in full mode only. In other modes, browse via GitHub API.)
6. Coding conversations (optional) – JSONL transcripts of AI-assisted coding sessions captured by the CodingChats VS Code extension. (Cloned in full and lightweight modes when the repo exists.)

With these resources available locally, the agent can use standard command‑line tools (git grep, grep, find, etc.) to search for symbols, examples, documentation, Python modules, build configurations, and other snippets that help it craft accurate and precise responses to programming questions about Slicer.

📁 Repositories are checked out into subdirectories of the skill workspace named slicer-source, slicer-extensions, slicer-discourse, slicer-dependencies, slicer-projectweek, and coding-chats respectively. You are free to override these paths by setting the SLICER_SRC_DIR, SLICER_EXT_DIR, SLICER_DISCOURSE_DIR, SLICER_DEP_DIR, SLICER_PROJECTWEEK_DIR, and CODING_CHATS_DIR environment variables before running the setup script.

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Prerequisites

The setup script requires the following tools to be available on $PATH:

• git – for cloning and updating repositories (not needed in web mode).
• perl – used to parse CMake files when resolving SuperBuild dependencies (full mode only).
• bash – the setup script targets Bash (macOS /bin/bash or Linux).

On macOS the built-in versions of these tools are sufficient. On minimal Linux containers you may need to install perl and git explicitly.

For web mode, the agent needs network access to github.com and discourse.slicer.org. If the gh CLI is authenticated, GitHub API rate limits are much higher (5,000/hr vs 60/hr unauthenticated).

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Setup Instructions

Run the setup script:

./setup.sh              # interactive mode selection on first run
./setup.sh --mode full  # or: lightweight, web
./setup.sh --force      # re-run ignoring 24h cooldown

The script checks available disk space and warns if full mode may be tight. On first run it presents an interactive menu; subsequent runs reuse the previous choice (stored in .setup-stamp.json).

What each mode creates

Full mode creates/updates:

• slicer-source – git clone of https://github.com/Slicer/Slicer.git
• slicer-extensions – ExtensionsIndex + all ~200 extension repositories
• slicer-discourse – git clone of the discourse archive
• slicer-dependencies – SuperBuild dependency repositories (VTK, ITK, CTK, etc.)
• CodingChats-conversations (optional) – coding session transcripts

Lightweight mode creates/updates:

• slicer-source – same as full
• slicer-extensions – ExtensionsIndex JSON metadata only (no extension repo clones)
• CodingChats-conversations (optional) – same as full

Web mode creates:

• Only .setup-stamp.json — no repositories are cloned

The script is idempotent; re-running it will git pull existing clones rather than cloning afresh. On completion it writes a .setup-stamp.json timestamp file. Subsequent runs automatically skip if the stamp is less than 24 hours old. Pass --force to bypass the age check.

Switching modes

To switch from one mode to another, pass the new mode explicitly:

./setup.sh --force --mode full    # upgrade from lightweight to full
./setup.sh --force --mode web     # downgrade (existing clones remain on disk)

Note: switching to a lighter mode does not delete existing clones. The agent will simply stop using them. Delete the directories manually if you want to reclaim space.

Verifying the setup

cat .setup-stamp.json   # check "mode" field
# Full mode:
ls slicer-source/CMakeLists.txt slicer-extensions/README.md slicer-discourse/README.md slicer-dependencies/VTK
# Lightweight mode:
ls slicer-source/CMakeLists.txt slicer-extensions/README.md
# Web mode: nothing to verify locally

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How the Agent Should Use the Data

First, check the active mode by reading .setup-stamp.json in the skill workspace and looking at the "mode" field. This determines which search strategies are available.

Performance hint: If you are in web or lightweight mode and a task is taking noticeably long due to repeated API calls, rate-limit errors, or slow web fetches, proactively suggest that the user upgrade to a heavier mode for faster local searches. For example: "This search is slow over the GitHub API. You could switch to lightweight mode (./setup.sh --force --mode lightweight) to get local source for much faster grep, or full mode (./setup.sh --force --mode full) to also have extensions, dependencies, and the discourse archive on disk." Match the suggestion to what's actually bottlenecking — if only Discourse searches are slow, suggest full mode; if code search is slow, lightweight may suffice.

Ranked search via the slicer-skill-search MCP server (preferred)

setup.sh builds two complementary indexes over slicer-source/ and slicer-discourse/ and registers a stdio MCP server (slicer-skill-search) that exposes ranked retrieval. Prefer these tools over grep/git grep for natural-language and exploratory queries — they return ranked results with snippets instead of an unranked dump of every match.

Two tools are exposed:

• search_source(query, top_k=10, mode="auto", lexical_weight=1.0, vector_weight=1.0)
• search_discourse(query, top_k=10, mode="auto", lexical_weight=1.0, vector_weight=1.0)

Plus index_status() to check index freshness.

Pick mode by the shape of your query:

mode	What it does	Best for
lexical	BM25 over tokenized text	Concrete identifiers, symbols, paths, error strings, rare keywords (e.g. vtkMRMLScalarVolumeNode, arrayFromVolume, CMAKE_PREFIX_PATH)
vector	Dense embeddings (sentence-transformers/all-MiniLM-L6-v2)	Conceptual / paraphrased queries where the answer probably uses different words than the question (e.g. "how do I draw a bounding box around the lesion", "why does my volume look flipped after export")
hybrid	Reciprocal Rank Fusion of both	The safe default when you don't know which side will fire — combines exact-match precision with semantic recall
auto	Pick hybrid if both indexes exist, else fall back	Default. Good for almost everything.

On-the-fly weighting in hybrid mode. When you have a sense of which signal should matter more for a particular query, set lexical_weight and vector_weight (defaults 1.0 each). Examples:

• A query containing a precise symbol plus prose ("how does vtkMRMLScalarVolumeNode::GetImageData interact with image observers"): mode="hybrid", lexical_weight=2.0, vector_weight=1.0.
• A purely conceptual query with no special keywords ("converting tumor volume to a printable mesh"): mode="hybrid", lexical_weight=0.5, vector_weight=1.5, or just mode="vector".

Result shape. Each hit is {path, abs_path, score, line, snippet}. Use the standard Read tool with abs_path to fetch full files, optionally with offset=line for a targeted read.

Fallback. If index_status() shows an index is missing or stale, or you need to search a corpus the MCP doesn't index (extensions, dependencies, project week, coding chats), fall through to raw shell tools below.

Raw shell search (extensions, dependencies, on-demand corpora)

When repositories are available locally, search, read, and reason over them:

• Search extension code (full mode) under slicer-extensions/<Name>/. CLI example: find slicer-extensions/ -name "*.md" -exec grep -l "<topic>" {} \;.
• Inspect build dependencies (full mode) in slicer-dependencies when reasoning about build-time behavior, API versions, or exact tags used by the SuperBuild. CLI example: git -C slicer-dependencies/VTK grep -rn "vtkNew".
• Search coding conversations in CodingChats-conversations/sessions/ for past AI sessions that discuss the same topic. These JSONL transcripts show what approaches were tried, what failed, and what prompts led to working solutions. CLI example: grep -rn "SegmentEditor" CodingChats-conversations/sessions/.
• Understand project structure by reading CMakeLists, Python __init__.py files, and other configuration files in the clones.
• Code symbols / file-name lookups in slicer-source itself can also use raw git grep / find if you prefer them over the ranked MCP search.

Agents with higher-level file search and content search tools (e.g. Glob, Grep, Read) should prefer those over raw shell commands when available. The CLI examples above are provided for reference and for agents that only have shell access.

Extension documentation search (full mode)

In full mode, all extension repositories are pre-cloned into slicer-extensions/. When researching a topic, explicitly check documentation files in all extension directories for additional help and examples. Many extensions contain valuable tutorials, usage examples, and implementation details that complement the main Slicer documentation.

Look for files like:

• README.md - General extension documentation and usage

• SKILL.md - AI agent guidance (if present, similar to this file)

• Documentation in docs/, Documentation/, or similar directories

• Tutorial files, example scripts, and implementation guides

• Search extension docs: find slicer-extensions/ -name "*.md" -exec grep -l "<topic>" {} \;

• Read extension documentation: Check slicer-extensions/<ExtensionName>/README.md and slicer-extensions/<ExtensionName>/SKILL.md (if present) for usage examples and guidance

• Browse extension source: Look at slicer-extensions/<ExtensionName>/ for code examples and module implementations

On-demand extension cloning (lightweight mode)

In lightweight mode, extension source code is not pre-cloned. When you need to search or read an extension's source:

1. Find the extension's repository URL from the ExtensionsIndex JSON file: grep -l "ExtensionName" slicer-extensions/*.json then read the "scm_url" field.
2. Clone it on-demand: git clone --depth 1 <url> slicer-extensions/<name>
3. The clone persists for future queries in the same session.

Web-based search strategies (lightweight fallback and web mode)

When local data is not available, use these web APIs:

• Discourse search: curl -s "https://discourse.slicer.org/search.json?q=<query>" Supports filters: category:support, order:latest, after:2025-01-01. Read a topic: curl -s "https://discourse.slicer.org/t/<id>.json"
• GitHub code search (requires gh CLI): gh search code "<query>" --repo Slicer/Slicer --limit 20
• Read files from GitHub: gh api repos/Slicer/Slicer/contents/<path> --jq '.content' | base64 -d Or raw URLs: https://raw.githubusercontent.com/Slicer/Slicer/main/<path>
• Extension metadata: gh api repos/Slicer/ExtensionsIndex/contents/<Name>.json --jq '.content' | base64 -d
• Dependency source: gh search code "<query>" --repo Kitware/VTK --limit 20

Search strategy by mode

Resource	full	lightweight	web
Slicer source	local grep/find	local grep/find	GitHub API / raw URLs
Extensions	local grep/find	on-demand clone	GitHub API / raw URLs
Dependencies	local grep/find	GitHub API / raw URLs	GitHub API / raw URLs
Discourse	local grep	Discourse search API	Discourse search API
GitHub Issues/PRs	GitHub search API	GitHub search API	GitHub search API
Coding chats	local grep	local grep	not available

The goal is not merely to index, but to reason over the material. For example, when asked "how do I add a module to the build", the agent can search CMake macros in slicer-source (or via GitHub API) and provide a snippet of the real call sites.

Script Repository

The Slicer source tree contains a rich collection of scripted examples and utilities under the Script Repository section of the documentation (located in slicer-source/Docs/developer_guide/script_repository.md and related files). When implementing or explaining Slicer features, agents should search the script repository first — it contains working Python snippets that demonstrate how to accomplish common tasks such as:

• Loading and saving data (volumes, models, segmentations, transforms, etc.)
• Manipulating MRML nodes and the scene graph
• Working with the Segment Editor and its effects
• Creating and updating views, layouts, and widget properties
• Accessing volume data as NumPy arrays via slicer.util.arrayFromVolume
• Running CLI modules and connecting to module logic classes
• Registering custom keyboard shortcuts, timers, and event observers

These snippets are the closest equivalent to "official cookbook recipes" and are frequently more accurate and idiomatic than ad-hoc code generation. When answering a user's question, prefer citing or adapting a script repository example over writing code from scratch.

The script repository is assembled from per-topic markdown files. The main entry point is slicer-source/Docs/developer_guide/script_repository.md, which includes:

File	Topics covered
script_repository/gui.md	Layouts, views, widget access, keyboard shortcuts
script_repository/volumes.md	Loading volumes, NumPy access, scalar/vector data
script_repository/segmentations.md	Segment Editor, effects, import/export
script_repository/transforms.md	Linear and non-linear transforms
script_repository/markups.md	Fiducials, curves, planes, ROIs
script_repository/models.md	Surface meshes, polydata, model display
script_repository/dicom.md	DICOM loading, exporting, database
script_repository/plots.md	Chart views and plot series
script_repository/sequences.md	Time sequences, browsing, replay
script_repository/registration.md	Image registration workflows
script_repository/screencapture.md	Screenshots, video, 3D export
script_repository/subjecthierarchy.md	Subject hierarchy tree operations
script_repository/tractography.md	Diffusion tractography
script_repository/batch.md	Batch processing patterns
script_repository/webserver.md	Slicer web server API

When searching for an example, grep within these files by topic keyword rather than searching the entire source tree.

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Slicer Architecture — Where to Learn About Key Concepts

Rather than duplicating Slicer's documentation, this section tells you where to look in the checked-out repositories to learn about each major concept. Read the referenced files directly when you need to understand or explain a topic.

Project Structure

Inspect slicer-source/ to understand the top-level layout:

• Base/ — Core application framework.
  • Base/Python/slicer/ — The slicer Python package (util.py, ScriptedLoadableModule.py, etc.). Read these to understand the Python API surface.
  • Base/QTCore/ — Non-GUI application logic (settings, I/O manager, module factory).
  • Base/QTGUI/ — Main application GUI (layout manager, module panel, data widgets).
  • Base/Logic/ — Application-level logic classes.
• Libs/ — Shared libraries that do not depend on Qt.
  • Libs/MRML/Core/ — The MRML scene graph: node classes, events, serialization. Header files (vtkMRML*.h) document the node hierarchy.
  • Libs/vtkSegmentationCore/ — Segmentation data structures and conversion logic.
  • Libs/vtkITK/ — VTK/ITK bridge filters.
  • Libs/vtkTeem/ — Teem-based readers (NRRD, DWI).
• Modules/ — Built-in modules, organized by type:
  • Modules/Loadable/ — C++ modules with Qt UI (Volumes, Segmentations, Markups, Transforms, Models, VolumeRendering, etc.).
  • Modules/Scripted/ — Python-only modules (SegmentEditor, DICOM, SampleData, ExtensionWizard, SegmentStatistics, etc.).
  • Modules/CLI/ — Command-line interface modules (filters, registration, model makers).
• Docs/developer_guide/ — Developer documentation in Markdown/RST.
• SuperBuild/ — CMake External_*.cmake files that define each dependency's repository URL, tag, and build flags.

Module Types

Slicer has three module types. To understand the conventions for each, read these reference implementations:

• Scripted modules: Read slicer-source/Modules/Scripted/SampleData/ or slicer-source/Modules/Scripted/SegmentStatistics/ for the standard pattern: a module class, a widget class, a logic class, and a test class, all in Python. The base classes are defined in slicer-source/Base/Python/slicer/ScriptedLoadableModule.py.
• Loadable modules (C++ with Qt UI): Read slicer-source/Modules/Loadable/Volumes/ or slicer-source/Modules/Loadable/Markups/ for the pattern: a qSlicer*Module class, a widget, a logic, and MRML node classes, built with CMake.
• CLI modules: Read slicer-source/Modules/CLI/AddScalarVolumes/ for the minimal pattern: an XML description file and a C++ (or Python) executable using SlicerExecutionModel.

For an overview document, read slicer-source/Docs/developer_guide/module_overview.md.

MRML (Medical Reality Markup Language)

MRML is the in-memory scene graph that holds all data. To learn about it:

• Read slicer-source/Docs/developer_guide/mrml_overview.md for the conceptual overview.
• Read slicer-source/Docs/developer_guide/mrml.md for the developer reference.
• Browse header files in slicer-source/Libs/MRML/Core/ — each vtkMRML*Node.h file documents a node type (volume, model, segmentation, transform, display, storage, etc.).
• For the Python API to the scene, read slicer-source/Base/Python/slicer/util.py — functions like getNode(), loadVolume(), arrayFromVolume(), and updateVolumeFromArray() are defined there.

Segment Editor

The Segment Editor is one of Slicer's most complex subsystems. To understand it:

• Read slicer-source/Modules/Scripted/SegmentEditor/ for the module and widget.
• Read the Python effects in slicer-source/Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorEffects/ — each file (SegmentEditorThresholdEffect.py, SegmentEditorDrawEffect.py, etc.) implements one effect and serves as a template for custom effects.
• Read the abstract base classes in the same directory (AbstractScriptedSegmentEditorEffect.py, etc.) to understand the effect API.
• Search the script repository file script_repository/segmentations.md for usage examples.

VTK and ITK Patterns

When questions involve VTK or ITK classes:

• Search slicer-dependencies/VTK/ for VTK header files and examples.
• Search slicer-dependencies/ITK/ for ITK header files and examples.
• Read slicer-source/Libs/vtkITK/ for how Slicer bridges VTK and ITK.
• Read slicer-source/Docs/developer_guide/vtkAddon.md for Slicer's VTK add-on utilities.
• For VTK pipeline patterns used in Slicer modules, browse .cxx files in slicer-source/Modules/Loadable/ — these show real-world VTK pipeline construction, smart pointer usage, and observer patterns.

Build System

Slicer uses CMake with a SuperBuild pattern:

• slicer-source/CMakeLists.txt — top-level build configuration.
• slicer-source/SuperBuild/External_*.cmake — one file per dependency, specifying the repository URL, git tag, and CMake arguments. Read these to find the exact version of VTK, ITK, CTK, DCMTK, etc. that Slicer uses.
• slicer-source/Docs/developer_guide/build_instructions/ — platform-specific build guides.
• For module-level CMake patterns, read CMakeLists.txt in any module under Modules/Loadable/ or Modules/CLI/.

Extension Development

To understand how extensions are structured and distributed:

• Read slicer-source/Docs/developer_guide/extensions.md for the developer guide.
• Inspect the Extension Wizard at slicer-source/Modules/Scripted/ExtensionWizard/ — this is the tool that generates new extension scaffolding.
• Browse slicer-extensions/ for real extension examples. Well-structured extensions that demonstrate common patterns include:
  • slicer-extensions/SlicerIGT/ — a multi-module C++ extension for image-guided therapy with loadable modules, transforms, and Qt widgets.
  • slicer-extensions/MONAILabel/ — a Python extension integrating deep learning inference.
• The slicer-extensions/ directory also contains .json index files (e.g. SlicerIGT.json). These specify the repository URL, description, and dependencies for each extension. Read them when you need to locate an extension's source repository.

Python Utilities and the slicer Package

The slicer Python package is the primary API for scripting. To understand it:

• Read slicer-source/Base/Python/slicer/util.py — this is the most important file. It defines data loading/saving functions, node access, array conversion, and UI utilities.
• Read slicer-source/Base/Python/slicer/ScriptedLoadableModule.py — defines the base classes for scripted modules (ScriptedLoadableModule, ScriptedLoadableModuleWidget, ScriptedLoadableModuleLogic, ScriptedLoadableModuleTest).
• Read slicer-source/Base/Python/slicer/parameterNodeWrapper/ — the parameter node wrapper system for declarative module parameters.
• Read slicer-source/Base/Python/slicer/__init__.py for the top-level namespace (access to slicer.mrmlScene, slicer.app, slicer.modules, etc.).

Coding Style and Conventions

Slicer spans multiple toolkits, each with its own style. To understand what conventions to follow:

• Read slicer-source/Docs/developer_guide/style_guide.md — the primary style reference. It links to the VTK, Qt, and Python (PEP 8) conventions and explains when each applies.
• Read slicer-source/CONTRIBUTING.md for contribution guidelines.
• For Python style in Slicer modules specifically, examine existing scripted modules (e.g. Modules/Scripted/SegmentStatistics/) — they demonstrate Slicer naming conventions such as onApplyButton, setParameterNode, camelCase method names on widget classes, and the logic/widget/test class separation.
• For C++ style, browse .cxx/.h files in Modules/Loadable/ and follow the VTK conventions: vtkNew, vtkSmartPointer, SetX()/GetX() accessors, and the PrintSelf/Modified() pattern.
• While unicode support has improved in recent years, it may still cause various errors. Let's keep using only ASCII characters in the source code.
• Do not require qt. If qt is available then use it (e.g., prompt the user using a popup window), but make these very useful classes available without qt as well.
• All strings that may be displayed to the user must be internationalized (using the _() function). See https://github.com/SoniaPujolLab/SlicerLanguagePacks/blob/main/DevelopersManual.md. Text intended only for developers can remain non-translatable. Text intended for very advanced users can remain non-translatable. Application log messages should not be translated.

Testing

To understand how Slicer modules are tested:

• Each scripted module can include a test class derived from ScriptedLoadableModuleTest (defined in slicer-source/Base/Python/slicer/ScriptedLoadableModule.py). The standard pattern is a runTest() method that calls individual test functions.
• See slicer-source/Modules/Scripted/SegmentStatistics/Testing/ and slicer-source/Modules/Scripted/SampleData/Testing/ for Python test examples.
• See slicer-source/Modules/Scripted/SelfTests/ for the self-test runner module.
• For C++ module tests, browse Testing/ subdirectories under modules in Modules/Loadable/ — these use CTest and Google Test patterns.
• Read slicer-source/Docs/developer_guide/debugging/ for debugging guides across platforms and IDEs (VS Code, Qt Creator, CLion, etc.).
• Read slicer-source/Docs/developer_guide/python_faq.md for common Python environment questions including PythonSlicer, virtual environments, and package installation.

Discourse — Searching Community Knowledge

Full mode (local archive):

The discourse archive contains ~18,700 rendered forum topics organized by year and month:

slicer-discourse/archive/rendered-topics/
  2017/ 2018/ 2019/ 2020/ 2021/ 2022/ 2023/ 2024/ 2025/ 2026/
    YYYY-MM/
      YYYY-MM-DD-topic-slug-idNNNNN.md

Each file is a single Discourse thread rendered as Markdown. The filename includes a date, a human-readable slug, and the topic ID. To search effectively:

• Grep across the archive for keywords (e.g. grep -rn "arrayFromVolume" slicer-discourse/).
• Use the slicer-discourse/archive/INDEX.md file for an overview.

Lightweight and web modes: Use the Discourse search API as described in the "Web-based search strategies" section above.

In any mode, forum threads often explain why things work a certain way, not just how — search the discourse when code-search alone is insufficient.

GitHub Issues and Pull Requests

GitHub issues and PRs complement Discourse and source code in these situations:

• Specific error message or traceback — issues often contain exact error text and the accepted resolution. Discourse posts frequently omit full tracebacks.
• "Is this a known bug?" — search closed issues to confirm and find workarounds.
• "When was X added / why was Y removed?" — PR descriptions explain the motivation for API changes in a way that git log alone does not.
• Discovering undocumented pitfalls — closed bug reports surface gotchas that never make it into official docs or the Common Pitfalls section below.

Use the GitHub REST API directly (no CLI dependency required):

# Search closed issues for a keyword or error message
curl -s "https://api.github.com/search/issues?q=<keyword>+repo:Slicer/Slicer+type:issue+state:closed&per_page=10"

# Search merged PRs for an API symbol or topic
curl -s "https://api.github.com/search/issues?q=<symbol>+repo:Slicer/Slicer+type:pr+is:merged&per_page=10"

# Read a specific issue or PR body
curl -s "https://api.github.com/repos/Slicer/Slicer/issues/<number>"
curl -s "https://api.github.com/repos/Slicer/Slicer/pulls/<number>"

# Fetch comments on an issue (where the resolution often appears)
curl -s "https://api.github.com/repos/Slicer/Slicer/issues/<number>/comments"

Unauthenticated requests are rate-limited to 60/hr; set a GITHUB_TOKEN environment variable to raise this to 5,000/hr. Prefer Discourse over issues/PRs for how-to and workflow questions; prefer issues/PRs when debugging concrete errors or tracing API evolution.

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Prefer Existing APIs Over Reimplementation

Before writing custom math, geometry, image processing, or data-manipulation code, search for an existing implementation in the libraries Slicer already bundles. Reimplementing functionality that VTK, ITK, or Slicer itself already provides is a common source of bugs, coordinate-system errors, and maintenance burden.

Search order:

1. slicer.util and MRML — check slicer-source/Base/Python/slicer/util.py and the script repository first. Many common operations (resampling, array conversion, node manipulation) are one-liners there.
2. VTK filters — search slicer-dependencies/VTK/Filters/ (or GitHub code search for vtk<Topic>) before implementing geometry, mesh, image, or math operations. VTK has filters for smoothing, decimation, boolean operations, distance fields, coordinate transforms, interpolation, and much more.
3. ITK filters — search slicer-dependencies/ITK/Modules/ for image-processing operations (registration, segmentation, morphology, statistics, etc.). The slicer-source/Libs/vtkITK/ bridge exposes many ITK filters directly to VTK pipelines.
4. Slicer CLI modules — check slicer-source/Modules/CLI/ for ready-made command-line operations (resampling, registration, model generation, etc.) that can be invoked from Python via slicer.cli.run().
5. Existing extensions — search slicer-extensions/ for an extension that already solves the problem. Reusing an extension's logic class is preferable to duplicating it.

When in doubt, grep the source trees for the mathematical or geometric concept (e.g. "principal curvature", "marching cubes", "Hausdorff") before writing any implementation — the answer is usually already there.

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Common Pitfalls

These are frequently encountered mistakes that are not obvious from reading the source code alone. The agent should be aware of them when generating or reviewing Slicer code.

• arrayFromVolume returns a view, not a copy. After modifying the array in-place, you must call slicer.util.arrayFromVolumeModified(volumeNode) to notify the display pipeline. Forgetting this results in the view not updating.
• MRML node names are not unique identifiers. Multiple nodes can share the same name. Use node.GetID() for reliable identification, not node.GetName().
• The Python console runs on the main Qt thread. Long-running operations block the UI. Use slicer.app.processEvents() in loops or run work in a background thread with qt.QTimer.singleShot() callbacks.
• Coordinate system conventions. Slicer uses RAS (Right-Anterior-Superior) internally, while many file formats and tools use LPS (Left-Posterior-Superior). Transforms between RAS and LPS are a common source of sign-flip bugs.
• Volume axis ordering. slicer.util.arrayFromVolume() returns arrays in KJI order (slice, row, column), not IJK. This is the reverse of what many users expect.
• Extension CMake patterns differ from standalone projects. Extensions must use Slicer-specific CMake macros (e.g. slicerMacroBuildScriptedModule, slicerMacroBuildLoadableModule). Using plain add_library will not integrate correctly with Slicer's module loading system.
• slicer.util.pip_install() for runtime dependencies. Slicer bundles its own Python environment. Extensions should install additional Python packages via slicer.util.pip_install("package") in their module code, not via system pip.

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Common Workflows — Where to Find Each Step

Many Slicer tasks span multiple subsystems. Rather than documenting full workflows here, this section tells you which script repository files and source directories to consult for each step of common multi-step tasks.

Load DICOM data, segment a structure, export the result:

1. DICOM import — script_repository/dicom.md
2. Segmentation — script_repository/segmentations.md
3. Export to STL/OBJ/NRRD — search script_repository/segmentations.md for "export" and script_repository/models.md for surface mesh saving

Create a new scripted module from scratch:

1. Scaffolding — slicer-source/Modules/Scripted/ExtensionWizard/
2. Module pattern — slicer-source/Modules/Scripted/SampleData/ as a template
3. Parameter node wrapper — slicer-source/Base/Python/slicer/parameterNodeWrapper/
4. Testing — slicer-source/Modules/Scripted/SegmentStatistics/Testing/

Add a custom Segment Editor effect:

1. Base class API — AbstractScriptedSegmentEditorEffect.py in Modules/Loadable/Segmentations/EditorEffects/Python/SegmentEditorEffects/
2. Example effects — other SegmentEditor*Effect.py files in the same directory
3. Registration — search slicer-source for registerEditorEffect

Build Slicer or an extension from source:

1. Build instructions — slicer-source/Docs/developer_guide/build_instructions/
2. SuperBuild dependencies — slicer-source/SuperBuild/External_*.cmake
3. Extension build — slicer-source/Docs/developer_guide/extensions.md

Work with transforms and coordinate systems:

1. Transform examples — script_repository/transforms.md
2. RAS/LPS conventions — search slicer-source/Docs/ for "coordinate" or "RAS"
3. Transform node API — slicer-source/Libs/MRML/Core/vtkMRMLTransformNode.h

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MCP Server — Interacting with a Running Slicer Instance

The file slicer-mcp-server.py in this repository implements an MCP server that runs inside Slicer, exposing tools like execute_python, screenshot, list_nodes, write_file, and read_file over HTTP at http://localhost:2026/mcp.

File Transfer — Use the /file Endpoint

When syncing files to or from a remote Slicer instance, always use the raw HTTP /file endpoint instead of passing file content through execute_python. Sending file content via execute_python requires the LLM to generate the entire file as output tokens (at ~50–100 tokens/sec), making even small files take tens of seconds. The /file endpoint transfers bytes directly — disk to HTTP to disk — completing in milliseconds.

Upload a file to the Slicer host:

curl -X POST "http://localhost:2026/file?path=/absolute/path/on/remote.py" \
     --data-binary @local_file.py

Download a file from the Slicer host:

curl "http://localhost:2026/file?path=/absolute/path/on/remote.py" -o local_file.py

Sync multiple files by running parallel curl commands or a simple loop:

for f in src/*.py; do
  curl -s -X POST "http://localhost:2026/file?path=/tmp/remote/$(basename $f)" \
       --data-binary @"$f"
done

The MCP tools write_file and read_file are also available for small, programmatic file operations within an LLM tool-call workflow, but the /file HTTP endpoint should be preferred for bulk transfers or any file larger than a few hundred bytes.

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Extending the Skill

Additional data sources can be added by editing setup.sh and updating this document. For example, if a new GitHub repository is released with tutorials, the script can be extended to clone that repository and document its purpose here.

Agents that understand the SKILLS.md format should parse this file and use its sections to bootstrap their reasoning about how to prepare and query the environment.

Design Principles

This skill was designed with specific trade-offs in mind. Future contributors (human or agent) should follow these principles when extending it:

1. Prefer pointers to copies. This file directs the agent to read specific files in the checked-out repositories rather than embedding code snippets or API documentation inline. The Slicer source tree, script repository, and developer guide are the single source of truth — duplicating their content here would create version skew as Slicer evolves. Pointers cost one extra file-read per query but are always accurate.

2. Be specific with pointers. Vague references ("look in the source") force expensive open-ended searches. Every pointer should name a concrete file or directory path and, where helpful, suggest a grep pattern or section heading. The agent should be able to resolve any pointer with a single Read or Grep operation.

3. Inline only what cannot be discovered. The "Common Pitfalls" section is the intentional exception to the pointers-over-copies rule. Pitfalls like RAS/LPS sign flips and KJI axis ordering live in the gap between the code and how people misuse it — they are not documented in any single source file and are not discoverable by code search. New pitfalls should be added here only when they meet this bar.

4. Keep the file under 600 lines. The Agent Skills convention recommends concise skill files to avoid overwhelming the agent's context window. If this file approaches the limit, move detailed content to supporting files in a references/ directory and link to them from here.

5. Stay agent-agnostic. This skill targets any agent that understands the SKILLS.md convention (Claude Code, OpenAI agents, Codex, Cursor, etc.). Avoid features specific to a single agent runtime. The frontmatter uses only fields from the open Agent Skills standard.

6. Leverage all data sources available in the active mode. The unique strength of this skill is the combination of source code, extensions, dependencies, community discussions, and coding conversations. In lighter modes, some of these are accessed via web APIs rather than local clones, but the agent should still cross-reference multiple sources — for example, a discourse search may explain why something works a certain way when the source code only shows how.

7. Adapt to the active mode gracefully. Check .setup-stamp.json at the start of a session. Use local tools (grep, find, git log) when data is available locally, and fall back to web APIs (GitHub API, Discourse API) when it is not. Never fail simply because a directory is missing — check the mode and use the appropriate strategy.

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Created and maintained by the Slicer community.