alterlab-pydicom

# Pydicom ## Overview Pydicom is a pure Python package for working with DICOM files, the standard format for medical imaging data. This skill provides guidance on reading, writing, and manipulating DICOM files, including working with pixel data, metadata, and various compression formats. ## When to Use This Skill Use this skill when working with: - Medical imaging files (CT, MRI, X-ray, ultrasound, PET, etc.) - DICOM datasets requiring metadata extraction or modification - Pixel data extraction and image processing from medical scans - DICOM anonymization for research or data sharing - Converting DICOM files to standard image formats - Compressed DICOM data requiring decompression - DICOM sequences and structured reports - Multi-slice volume reconstruction - PACS (Picture Archiving and Communication System) integration ## Installation Targets **pydicom 3.x** (3.0 reorganized the pixel APIs — see the version note below). Install pydicom and common dependencies: ```bash uv pip install "pydicom>=3.0" uv pip install pillow # For image format conversion uv pip install numpy # For pixel array manipulation uv pip install matplotlib # For visualization ``` For handling compressed DICOM files, additional packages may be needed: ```bash uv pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg # JPEG / JPEG 2000 uv pip install python-gdcm # Alternative compression handler uv pip install pyjpegls # JPEG-LS encode/decode (replaces older JPEG-LS handlers) ``` ### p...