Pydicom Medical Imaging

Pydicom Medical Imaging

Overview

Pydicom is a pure Python library for reading, writing, and modifying DICOM (Digital Imaging and Communications in Medicine) files. It provides access to DICOM metadata tags and pixel data as NumPy arrays, supporting CT, MRI, X-ray, ultrasound, and other medical imaging modalities. The library handles compressed and uncompressed transfer syntaxes with optional codec plugins.

When to Use

• Reading DICOM files and extracting metadata (patient info, study parameters, imaging settings)
• Extracting pixel data from DICOM images for analysis or visualization
• Converting DICOM images to standard formats (PNG, JPEG, TIFF)
• Anonymizing DICOM files by removing Protected Health Information (PHI)
• Modifying DICOM metadata tags for relabeling or correction
• Creating DICOM files from scratch (e.g., wrapping NumPy arrays as DICOM)
• Processing CT/MRI series into 3D volumetric arrays for reconstruction
• Extracting frames from multi-frame DICOM (cine/video)
• For whole-slide pathology images (SVS, NDPI), use histolab-wsi-processing instead
• For NIfTI neuroimaging volumes (.nii/.nii.gz), use nibabel instead

Prerequisites

• Python packages: pydicom, numpy, pillow
• Optional codecs: pylibjpeg + pylibjpeg-libjpeg (JPEG), pylibjpeg-openjpeg (JPEG 2000), python-gdcm (most formats)
• Data format: DICOM files (.dcm, .ima, or extensionless) per NEMA PS3.10

pip install pydicom numpy pillow

# Optional: compression codec handlers (install as needed)
pip install pylibjpeg pylibjpeg-libjpeg   # JPEG Baseline/Lossless
pip install pylibjpeg-openjpeg             # JPEG 2000
pip install python-gdcm                    # Comprehensive codec support

Quick Start

import pydicom
import numpy as np