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.
Use this skill when working with:
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:
uv pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg # JPEG compression
uv pip install python-gdcm # Alternative compression handler
Read a DICOM file using pydicom.dcmread():
import pydicom
# Read a DICOM file
ds = pydicom.dcmread('path/to/file.dcm')
# Access metadata
print(f"Patient Name: {ds.PatientName}")
print(f"Study Date: {ds.StudyDate}")
print(f"Modality: {ds.Modality}")
# Display all elements
print(ds)
Key points:
dcmread() returns a Dataset objectds.PatientName) or tag notation (e.g., ds[0x0010, 0x0010])ds.file_meta to access file metadata like Transfer Syntax UIDgetattr(ds, 'AttributeName', default_value) or hasattr(ds, 'AttributeName')Extract and manipulate image data from DICOM files:
import pydicom
import numpy as np
import matplotlib.pyplot as plt
# Read DICOM file
ds = pydicom.dcmread('image.dcm')
# Get pixel array (requires numpy)
pixel_array = ds.pixel_array
# Image information
print(f"Shape: {pixel_array.shape}")
print(f"Data type: {pixel_array.dtype}")
print(f"Rows: {ds.Rows}, Columns: {ds.Columns}")
# Apply windowing for display (CT/MRI)
if hasattr(ds, 'WindowCenter') and hasattr(ds, 'WindowWidth'):
from pydicom.pixel_data_handlers.util import apply_voi_lut
windowed_image = apply_voi_lut(pixel_array, ds)