Metadata-Version: 2.5
Name: bioimageflow-io-tools
Version: 0.2.0
Summary: Lightweight image IO tools for BioImageFlow
Project-URL: Homepage, https://github.com/Inria-SAIRPICO/bioimageflow
Project-URL: Documentation, https://bioimageflow.readthedocs.io/latest/
Project-URL: Repository, https://github.com/Inria-SAIRPICO/bioimageflow
Project-URL: Issues, https://github.com/Inria-SAIRPICO/bioimageflow/issues
Author: BioImageFlow Contributors
License-Expression: BSD-4-Clause
License-File: LICENSE
Keywords: bioimage-analysis,bioimageflow,microscopy,workflow
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Requires-Dist: bioimageflow-core<0.4,>=0.3.0
Requires-Dist: imageio>=2.31.0
Requires-Dist: numpy>=1.23.5
Requires-Dist: tifffile>=2023.7.10
Description-Content-Type: text/markdown

# bioimageflow-io-tools

Optional BioImageFlow package for image ingestion, metadata inspection, axis validation, slicing, lightweight format conversion, and explicit bioio/plugin-backed conversion.

Core libraries for lightweight tools are imageio, NumPy, and tifffile.
`BioIOConvertImage` and `ConvertToOmeZarr` declare a separate pinned BioIO/plugin-backed runtime for broad microscopy formats and maintained OME-Zarr writing.

## Tools

- `ReadImageMetadata`
- `ValidateImageLayout`
- `ConvertImageFormat`
- `BioIOConvertImage`
- `ConvertToOmeTiff`
- `ConvertToOmeZarr`
- `SelectScene`
- `SelectTimepoint`
- `SelectChannel`
- `SelectZRange`
- `SelectDimensions`

Use `BioIOConvertImage` for microscopy formats that need scene, channel, Z, timepoint, or dimension-order handling.
Use `ConvertImageFormat` only for ordinary imageio conversions.
Use the dedicated OME-TIFF and OME-Zarr tools for OME output; they use reader-provided axes when unambiguous and otherwise require `dimension_order`.
