ConvertToOmeTiff

ConvertToOmeTiff reads an image file and converts it to OME-TIFF using tifffile. It is a focused converter for the common workflow step where an intermediate TIFF or selected analysis plane must be normalized for viewers or downstream tools that expect OME metadata.

Inputs

• input_image: image file to convert.

• dimension_order: optional OME axis order. When omitted, the tool infers YX, ZYX, CZYX, or TCZYX from dimensionality.

Outputs

• output_image: converted OME-TIFF image, defaulting to {input_image.stem}.ome.tiff.

Dependencies and Core Libraries

BioImageFlow core APIs, imageio for reading, tifffile for OME-TIFF writing, and NumPy through the image stack.

Assumptions

The input image has already been selected or arranged into the axis order declared by dimension_order. This converter writes a single OME-TIFF image and does not perform pyramid generation, intensity normalization, or Bio-Formats metadata translation.

Minimal Example

from bioimageflow_core import Arguments
from bioimageflow_io_tools import ConvertToOmeTiff

ConvertToOmeTiff().process_row(
    Arguments(
        input_image="selected_plane.tif",
        output_image="selected_plane.ome.tiff",
        dimension_order="YX",
    )
)

Expected Results

The OME-TIFF exists, preserves the input pixel values, and tifffile reports the requested series axes.

Failure Modes

Unreadable inputs, invalid axis metadata, unsupported dimensionality without an explicit dimension_order, and filesystem write failures stop execution.