gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/pydicom/references/transfer_syntaxes.md

DICOM Transfer Syntaxes Reference

This document provides a comprehensive reference for DICOM transfer syntaxes and compression formats. Transfer syntaxes define how DICOM data is encoded, including byte ordering, compression method, and other encoding rules.

Overview

A Transfer Syntax UID specifies:

1. Byte ordering: Little Endian or Big Endian
2. Value Representation (VR): Implicit or Explicit
3. Compression: None, or specific compression algorithm

Uncompressed Transfer Syntaxes

Implicit VR Little Endian (1.2.840.10008.1.2)

• Default transfer syntax
• Value Representations are implicit (not explicitly encoded)
• Little Endian byte ordering
• Pydicom constant: pydicom.uid.ImplicitVRLittleEndian

Usage:

import pydicom
ds.file_meta.TransferSyntaxUID = pydicom.uid.ImplicitVRLittleEndian

Explicit VR Little Endian (1.2.840.10008.1.2.1)

• Most common transfer syntax
• Value Representations are explicit
• Little Endian byte ordering
• Pydicom constant: pydicom.uid.ExplicitVRLittleEndian

Usage:

ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian

Explicit VR Big Endian (1.2.840.10008.1.2.2) - RETIRED

• Value Representations are explicit
• Big Endian byte ordering
• Deprecated - not recommended for new implementations
• Pydicom constant: pydicom.uid.ExplicitVRBigEndian

JPEG Compression

JPEG Baseline (Process 1) (1.2.840.10008.1.2.4.50)

• Lossy compression
• 8-bit samples only
• Most widely supported JPEG format
• Pydicom constant: pydicom.uid.JPEGBaseline8Bit

Dependencies: Requires pylibjpeg or pillow

Usage:

# Compress
ds.compress(pydicom.uid.JPEGBaseline8Bit)

# Decompress
ds.decompress()

JPEG Extended (Process 2 & 4) (1.2.840.10008.1.2.4.51)

• Lossy compression
• 8-bit and 12-bit samples
• Pydicom constant: pydicom.uid.JPEGExtended12Bit

JPEG Lossless, Non-Hierarchical (Process 14) (1.2.840.10008.1.2.4.57)

• Lossless compression
• First-Order Prediction
• Pydicom constant: pydicom.uid.JPEGLossless

Dependencies: Requires pylibjpeg-libjpeg or gdcm

JPEG Lossless, Non-Hierarchical, First-Order Prediction (1.2.840.10008.1.2.4.70)

• Lossless compression
• Uses Process 14 Selection Value 1
• Pydicom constant: pydicom.uid.JPEGLosslessSV1

Usage:

# Compress to JPEG Lossless
ds.compress(pydicom.uid.JPEGLossless)

JPEG-LS Lossless (1.2.840.10008.1.2.4.80)

• Lossless compression
• Low complexity, good compression
• Pydicom constant: pydicom.uid.JPEGLSLossless

Dependencies: Requires pylibjpeg-libjpeg or gdcm

JPEG-LS Lossy (Near-Lossless) (1.2.840.10008.1.2.4.81)

• Near-lossless compression
• Allows controlled loss of precision
• Pydicom constant: pydicom.uid.JPEGLSNearLossless

JPEG 2000 Compression

JPEG 2000 Lossless Only (1.2.840.10008.1.2.4.90)

• Lossless compression
• Wavelet-based compression
• Better compression than JPEG Lossless
• Pydicom constant: pydicom.uid.JPEG2000Lossless

Dependencies: Requires pylibjpeg-openjpeg, gdcm, or pillow

Usage:

# Compress to JPEG 2000 Lossless
ds.compress(pydicom.uid.JPEG2000Lossless)

JPEG 2000 (1.2.840.10008.1.2.4.91)

• Lossy or lossless compression
• Wavelet-based compression
• High quality at low bit rates
• Pydicom constant: pydicom.uid.JPEG2000

Dependencies: Requires pylibjpeg-openjpeg, gdcm, or pillow

JPEG 2000 Part 2 Multi-component Lossless (1.2.840.10008.1.2.4.92)

• Lossless compression
• Supports multi-component images
• Pydicom constant: pydicom.uid.JPEG2000MCLossless

JPEG 2000 Part 2 Multi-component (1.2.840.10008.1.2.4.93)

• Lossy or lossless compression
• Supports multi-component images
• Pydicom constant: pydicom.uid.JPEG2000MC

RLE Compression

RLE Lossless (1.2.840.10008.1.2.5)

• Lossless compression
• Run-Length Encoding
• Simple, fast algorithm
• Good for images with repeated values
• Pydicom constant: pydicom.uid.RLELossless

Dependencies: Built into pydicom (no additional packages needed)

Usage:

# Compress with RLE
ds.compress(pydicom.uid.RLELossless)

# Decompress
ds.decompress()

Deflated Transfer Syntaxes

Deflated Explicit VR Little Endian (1.2.840.10008.1.2.1.99)

• Uses ZLIB compression on entire dataset
• Not commonly used
• Pydicom constant: pydicom.uid.DeflatedExplicitVRLittleEndian

MPEG Compression

MPEG2 Main Profile @ Main Level (1.2.840.10008.1.2.4.100)

• Lossy video compression
• For multi-frame images/videos
• Pydicom constant: pydicom.uid.MPEG2MPML

MPEG2 Main Profile @ High Level (1.2.840.10008.1.2.4.101)

• Lossy video compression
• Higher resolution than MPML
• Pydicom constant: pydicom.uid.MPEG2MPHL

MPEG-4 AVC/H.264 High Profile (1.2.840.10008.1.2.4.102-106)

• Lossy video compression
• Various levels (BD, 2D, 3D, Stereo)
• Modern video codec

Checking Transfer Syntax

Identify Current Transfer Syntax

import pydicom

ds = pydicom.dcmread('image.dcm')

# Get transfer syntax UID
ts_uid = ds.file_meta.TransferSyntaxUID
print(f"Transfer Syntax UID: {ts_uid}")

# Get human-readable name
print(f"Transfer Syntax Name: {ts_uid.name}")

# Check if compressed
print(f"Is compressed: {ts_uid.is_compressed}")

Common Checks

# Check if little endian
if ts_uid.is_little_endian:
    print("Little Endian")

# Check if implicit VR
if ts_uid.is_implicit_VR:
    print("Implicit VR")

# Check compression type
if 'JPEG' in ts_uid.name:
    print("JPEG compressed")
elif 'JPEG2000' in ts_uid.name:
    print("JPEG 2000 compressed")
elif 'RLE' in ts_uid.name:
    print("RLE compressed")

Decompression

Automatic Decompression

Pydicom can automatically decompress pixel data when accessing pixel_array:

import pydicom

# Read compressed DICOM
ds = pydicom.dcmread('compressed.dcm')

# Pixel data is automatically decompressed
pixel_array = ds.pixel_array  # Decompresses if needed

Manual Decompression

import pydicom

ds = pydicom.dcmread('compressed.dcm')

# Decompress in-place
ds.decompress()

# Now save as uncompressed
ds.save_as('uncompressed.dcm', write_like_original=False)

Compression

Compressing DICOM Files

import pydicom

ds = pydicom.dcmread('uncompressed.dcm')

# Compress using JPEG 2000 Lossless
ds.compress(pydicom.uid.JPEG2000Lossless)
ds.save_as('compressed_j2k.dcm')

# Compress using RLE Lossless (no additional dependencies)
ds.compress(pydicom.uid.RLELossless)
ds.save_as('compressed_rle.dcm')

# Compress using JPEG Baseline (lossy)
ds.compress(pydicom.uid.JPEGBaseline8Bit)
ds.save_as('compressed_jpeg.dcm')

Compression with Custom Encoding Parameters

import pydicom
from pydicom.encoders import JPEGLSLosslessEncoder

ds = pydicom.dcmread('uncompressed.dcm')

# Compress with custom parameters
ds.compress(pydicom.uid.JPEGLSLossless, encoding_plugin='pylibjpeg')

Installing Compression Handlers

Different transfer syntaxes require different Python packages:

JPEG Baseline/Extended

pip install pylibjpeg pylibjpeg-libjpeg
# Or
pip install pillow

JPEG Lossless/JPEG-LS

pip install pylibjpeg pylibjpeg-libjpeg
# Or
pip install python-gdcm

JPEG 2000

pip install pylibjpeg pylibjpeg-openjpeg
# Or
pip install python-gdcm
# Or
pip install pillow

RLE

No additional packages needed - built into pydicom

Comprehensive Installation

# Install all common handlers
pip install pylibjpeg pylibjpeg-libjpeg pylibjpeg-openjpeg python-gdcm

Checking Available Handlers

import pydicom

# List available pixel data handlers
from pydicom.pixel_data_handlers.util import get_pixel_data_handlers
handlers = get_pixel_data_handlers()

print("Available handlers:")
for handler in handlers:
    print(f"  - {handler.__name__}")

Best Practices

1. Use Explicit VR Little Endian for maximum compatibility when creating new files
2. Use JPEG 2000 Lossless for good compression with no quality loss
3. Use RLE Lossless if you can't install additional dependencies
4. Check Transfer Syntax before processing to ensure you have the right handlers
5. Test decompression before deploying to ensure all required packages are installed
6. Preserve original transfer syntax when possible using write_like_original=True
7. Consider file size vs. quality tradeoffs when choosing lossy compression
8. Use lossless compression for diagnostic images to maintain clinical quality

Common Issues

Issue: "Unable to decode pixel data"

Cause: Missing compression handler Solution: Install the appropriate package (see Installing Compression Handlers above)

Issue: "Unsupported Transfer Syntax"

Cause: Rare or unsupported compression format Solution: Try installing python-gdcm which supports more formats

Issue: "Pixel data decompressed but looks wrong"

Cause: May need to apply VOI LUT or rescale Solution: Use apply_voi_lut() or apply RescaleSlope/RescaleIntercept

References

• DICOM Standard Part 5 (Data Structures and Encoding): https://dicom.nema.org/medical/dicom/current/output/chtml/part05/PS3.5.html
• Pydicom Transfer Syntax Documentation: https://pydicom.github.io/pydicom/stable/guides/user/transfer_syntaxes.html
• Pydicom Compression Guide: https://pydicom.github.io/pydicom/stable/old/image_data_compression.html