ITKIOOMEZarrNGFF

Overview

This is ITK remote module for IO of images stored in zarr-backed OME-NGFF file format.

Build/install

C++ uses CMake as the build system. Python packages can be installed from PyPI:

pip install itk-ioomezarrngff

Usage

Usage from C++ should not require any special action. In special situations, you might need to invoke:

itk::OMEZarrNGFFImageIOFactory::RegisterOneFactory();

In Python, we need to explicitly specify the IO, otherwise DICOM IO will be invoked because it is the built-in default for directories. Example:

import sys
import itk
imageio = itk.OMEZarrNGFFImageIO.New()
image = itk.imread(sys.argv[1], imageio=imageio)
itk.imwrite(image, sys.argv[2], imageio=imageio, compression=False)

Acknowledgements

ITKIOOMEZarrNGFF was developed in part by with support from:

• NIH NIMH BRAIN Initiative under award 1RF1MH126732.
• The Allen Institute for Neural Dynamics (AIND).