ome-tiff-pyramid-tools

Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.

pyramid_assemble.py

Combine several separate TIFF files into an OME-TIFF legacy pyramid. Will use all available CPU cores to speed up the image down-sampling process.

Example:

pyramid_assemble.py channel-1.tif channel-2.tif channel-3.tif pyramid.ome.tif --pixel-size 0.65

Requirements

• Python 3.6 or higher
• tifffile>=2020.9.28
• scikit-image
• zarr

pryamid_upgrade.py

Upgrade legacy OME-TIFF pyramids to the BioFormats 6 OME-TIFF pyramid format. Also can optionally add channel names to the OME-XML metadata. Does not read or modify pixel data at all so it runs more or less instantaneously. Note that it modifies the input file in place so make your own backups if you want to retain the original version.

Example:

pyramid_upgrade.py pyramid.ome.tif -n name1 name2 name3

Requirements

Python 3.7 or higher, or Python 3.6 with the dataclasses backport installed.

Todo

• Split out TiffSurgeon into its own package with better documentation and rationale.
• Include a small example input file for testing.