bioimageflow-io-tools¶
bioimageflow-io-tools is the optional ingestion and conversion package for
microscopy image selection, axis slicing, and simple OME-compatible output.
It is focused on file layout and format handling rather than biological analysis.
Core lightweight libraries are imageio, NumPy, tifffile, and a minimal OME-Zarr writer in the package code.
BioIOConvertImage uses an explicit bioio/plugin-backed environment for broad microscopy formats such as CZI and OME-Zarr.
Tools¶
BioIOConvertImage: broad bioio/plugin-backed format conversion for CZI, OME-Zarr, OME-TIFF, TIFF, PNG, and similar formats.
ReadImageMetadata: report shape, dtype, dimensionality, and a lightweight axes guess.
ValidateImageLayout: check declared layout length, required axes, and optional minimum sizes.
ConvertImageFormat: select optional scene, channel, Z, or T dimensions and convert to imageio outputs, OME-TIFF, or minimal OME-Zarr by output suffix.
ConvertToOmeTiff: convert an image file to OME-TIFF with axis metadata.
ConvertToOmeZarr: convert an image file to a single-scale OME-Zarr v2 directory.
SelectScene: extract scene 0 from ordinary images or a TIFF series by index.
SelectTimepoint: select one T index from a declared layout.
SelectChannel: select one C index from a declared layout.
SelectZRange: select a start-inclusive, stop-exclusive Z slab from a declared layout.
SelectDimensions: select a channel, z plane, or timepoint from declared axis layouts.
Workflow Use¶
Use BioIOConvertImage when a workflow needs OME-aware scene, channel, Z, timepoint, or dimension-order handling.
Use ConvertImageFormat for lightweight TIFF/imageio format changes and simple slicing.