BioIOConvertImage

BioIOConvertImage converts microscopy image file formats using bioio and installed bioio plugins. It can read broad plugin-backed formats such as CZI, OME-Zarr, OME-TIFF, TIFF, PNG, and similar sources, then write an output format selected by the output suffix.

Use BioIOConvertImage when the input requires bioio reader plugins or broad microscopy format coverage. Use ConvertImageFormat for lightweight workflow-local conversion through imageio, tifffile OME-TIFF, or the package’s minimal OME-Zarr writer.

Inputs are input_image, dim_order, optional scene, optional channel, optional z, and optional timepoint. Output is output_image, whose extension controls the writer. The tool prints source dimensions and squeezes singleton leading dimensions after optional selection.

from bioimageflow_io_tools import BioIOConvertImage

converted = BioIOConvertImage()(
    input_image="sample.czi",
    scene=0,
    channel=1,
    output_image="sample_ch1.ome.tiff",
)

Expected result: the selected scene/channel/Z/timepoint is written to the requested output format.

Dependencies and Core Libraries

BioImageFlow core APIs, bioio, bioio OME-TIFF and OME-Zarr writers, bioio CZI/ImageIO/TIFF plugins, NumPy, Pillow, and tifffile.

Assumptions

The requested bioio reader and writer plugins are installed and the selected dimension order matches the source image.

Failure Modes

Missing plugins, invalid scene/channel/Z/T indexes, unsupported extensions, or writer errors stop execution.