ZenReg documentation

ZenReg is a Python package for fast, memory-efficient, and modular microscopy image registration.

ZenReg’s philosophy is to make common microscopy registration tasks available through one convenient wrapper while keeping the internals modular enough for new backends and contributions. The package is therefore designed around one main workflow and a set of modular backends that can be used:

from zenreg import load_stack, register_stack, save_stack

image, metadata = load_stack("image.ome.tif", return_metadata=True)

registered, details = register_stack(
    image,
    registration_channel=0,
    method="phase_cross_correlation",
    return_shifts=True,
    return_details=True)

save_stack("image_registered.ome.tif", registered, metadata=metadata, registration_details=details)

At the same time, the package is built for reproducible outputs: Registered OME-TIFFs can be saved together with shift tables, settings YAML files, and summary plots. This enables users to easily share their results and reproduce them later.

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