Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
Python library for working with DICOM (Digital Imaging and Communications in Medicine) files. Use this skill when reading, writing, or modifying medical imaging data in DICOM format, extracting pixel data from medical images (CT, MRI, X-ray, ultrasound), anonymizing DICOM files, working with DICOM metadata and tags, converting DICOM images to other formats, handling compressed DICOM data, or processing medical imaging datasets. Applies to tasks involving medical image analysis, PACS systems, radiology workflows, and healthcare imaging applications.
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
Install pydicom and common dependencies:
uv pip install pydicom
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:
import pydicom
import numpy as np
from pathlib import Path
# Read all DICOM files in a directory
dicom_dir = Path('dicom_series/')
slices = []
for file_path in dicom_dir.glob('*.dcm'):
ds = pydicom.dcmread(file_path)
slices.append(ds)
# Sort by slice location or instance number
slices.sort(key=lambda x: float(x.ImagePositionPatient[2]))
# Or: slices.sort(key=lambda x: int(x.InstanceNumber))# Create 3D volume
volume = np.stack([s.pixel_array for s in slices])
print(f"Volume shape: {volume.shape}") # (num_slices, rows, columns)# Get spacing information for proper scaling
pixel_spacing = slices[0].PixelSpacing # [row_spacing, col_spacing]
slice_thickness = slices[0].SliceThickness
print(f"Voxel size: {pixel_spacing[0]}x{pixel_spacing[1]}x{slice_thickness} mm")
Helper Scripts
This skill includes utility scripts in the scripts/ directory:
anonymize_dicom.py
Anonymize DICOM files by removing or replacing Protected Health Information (PHI).
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