---

name: simpleitk description: "Use SimpleITK for medical-image IO, image metadata, NumPy conversion, filtering, segmentation, registration, transforms, and source-build troubleshooting." disable-model-invocation: true metadata: disco-role: operating license: Apache 2.0

SimpleITK Repo Skill

Use this repo skill when a task names SimpleITK, simpleitk, import SimpleITK as sitk, medical-image IO, DICOM series, image spacing/origin/direction, NumPy image conversion, SimpleITK filters, segmentation, registration, transforms, resampling, or SimpleITK source builds and wrapping.

Start Here

• Read references/repo-provenance.md before deciding whether this skill is current for a SimpleITK checkout or whether refresh-repo-skill is needed.
• Read references/source-evidence-map.md to see which source, docs, examples, tests, scripts, and existing skills informed this self-contained skill.
• Read references/troubleshooting.md for cross-cutting install/import/version, optional feature, ImageIO, and workflow routing failures.
• Run scripts/check_simpleitk_env.py to inspect a local SimpleITK install, NumPy bridge, ImageIO discovery, registration availability, and optional elastix wrappers without needing source data.

Installation and Import

For ordinary Python usage, prefer a binary install before attempting source builds:

python -m pip install --upgrade pip
python -m pip install simpleitk
python - <<'PY'
import SimpleITK as sitk
print(sitk.Version())
PY

Use conda-forge consistently when the project is conda-based:

conda create --name sitk python=3.11 simpleitk --channel conda-forge --override-channels
conda activate sitk

Import the Python package with import SimpleITK as sitk; the distribution name is simpleitk.

Route by Task

User task	Read this sub-skill
Construct sitk.Image, preserve spacing/origin/direction, inspect pixel IDs, convert to or from NumPy, debug shape reversal	image-core
Read/write MHA, NRRD, NIfTI, PNG, DICOM series, metadata tags, transforms, or ImageIO backends	io-and-data
Apply filters, smooth/threshold images, run morphology, connected components, segmentation, N4, or label statistics	filtering-segmentation
Configure transforms, resampling, registration metrics/optimizers, callbacks, reproducibility, or optional elastix/transformix workflows	registration-transforms
Install/build SimpleITK, choose PyPI vs conda vs source/SuperBuild, inspect CMake WRAP_*, enable optional wrappers, or run maintainer checks	builds-and-wrapping

Core Rules

• Treat a SimpleITK image as a physical object: preserve GetOrigin(), GetSpacing(), and GetDirection() when replacing pixels or moving through NumPy.
• Remember axis order: SimpleITK indexes are (x, y, z, ...); NumPy arrays from SimpleITK are reversed spatially, such as (z, y, x) for a 3D scalar image.
• Use sitk.ImageFileReader().GetRegisteredImageIOs() and sitk.ImageFileWriter().GetRegisteredImageIOs() for registered ImageIO discovery in Python examples.
• Use .mha or .nrrd for deterministic smoke tests; avoid lossy formats such as JPEG when pixel equality matters.
• Cast registration inputs deliberately to sitk.sitkFloat32 or sitk.sitkFloat64 when a metric or optimizer requires floating-point images.
• For label images, use nearest-neighbor interpolation during resampling; use linear interpolation for intensities unless a workflow says otherwise.
• Treat ElastixImageFilter and TransformixImageFilter as optional build-dependent APIs; absence in a binary install is an installation/build feature issue, not necessarily a typo.

Source Build Guardrails

Do not start a source build for ordinary SimpleITK API usage. Source builds use native C++/CMake/SWIG tooling and can fetch/build ITK or other dependencies. Route source-build, SuperBuild, wrapping, and optional elastix requests to builds-and-wrapping, and ask before running expensive or mutating commands.

Self-Containment

This skill distills repository docs, examples, tests, source code, and an installed-package inspection into bundled references and scripts. Runtime instructions here do not require access to the original SimpleITK checkout.