qptifffile 0.0.1

A package for working with Quantitative Phase TIFF files

QPTiffFile

A Python package for working with Quantitative Phase TIFF (QPTIFF) files, commonly used in multiplex imaging and digital pathology.

Overview

QPTiffFile provides tools for reading, processing, and analyzing QPTIFF image files. The package offers:

• Automatic extraction of biomarker/fluorophore information
• Memory-efficient tools for extracting regions of interest from large images
• Support for multi-channel and multi-resolution imagery

Installation

From PyPI (Coming soon)

pip install qptifffile

From Source (The only way currently)

git clone https://github.com/grenkoca/qptifffile.git
cd qptifffile
pip install -e .

Example images

Example .qptiff files are supplied by Akoya Biosciences (formerly owned by Perkin-Elmer): link

Additionally, a .qptiff file specification document can be found here: link

System Requirements

For full functionality including compressed TIFF support, you'll need:

macOS

# For Apple Silicon
brew install libaec

# For Intel Macs
brew install libaec

note: on Apple Silicon chips, you may need to install libaec via conda: https://anaconda.org/conda-forge/libaec/

Linux

# Ubuntu/Debian
sudo apt-get install libaec-dev

# CentOS/RHEL
sudo yum install libaec-devel

Dependencies

Core dependencies:

• tifffile
• numpy

Optional dependencies:

• imagecodecs (recommended for compressed TIFF support)

Usage Examples

Basic QPTIFF File Reading

from qptiff import QPTiffFile

# Open a QPTIFF file
qptiff = QPTiffFile('example_image.qptiff')

# Display available biomarkers
print(qptiff.get_biomarkers())

# Print summary of all channels
qptiff.print_channel_summary()

# Read specific biomarker channels
dapi_image = qptiff.read_region('DAPI')
cd8_image = qptiff.read_region('CD8')

# Read multiple biomarkers
markers = qptiff.read_region(['DAPI', 'CD8', 'PD-L1'])

Working with Regions of Interest

# Extract a specific region (x, y starting position and width, height)
region = qptiff.read_region(
    layers=['DAPI', 'CD8', 'PD-L1'],
    pos=(1000, 2000),
    shape=(500, 500)
)

# Work with lower resolution pyramid levels
overview = qptiff.read_region(
    layers=['DAPI'],
    level=1  # Lower resolution pyramid level
)

Citation

If you use this software in your research, please cite:

@software{qptifffile,
  author = {Grenko, Caleb},
  title = {QPTiffFile: A Python package for working with Quantitative Phase TIFF files},
  url = {https://github.com/grenkoca/qptifffile},
  year = {2025},
}

Contact

The best way to get in touch is via email: grenko.caleb (at) mayo.edu

Acknowledgments

• Based on the excellent tifffile library by Christoph Gohlke