OMIO: A policy-driven Python library for reproducible microscopy image I/O ============================================================================ .. figure:: _static/figures/OMIO_figures.png :alt: MotilA pipeline overview :align: center :figwidth: 100% .. image:: https://badgen.net/badge/icon/GitHub%20repository?icon=github&label :target: https://github.com/FabrizioMusacchio/omio/ :alt: GitHub Repository .. image:: https://img.shields.io/github/v/release/FabrizioMusacchio/omio :alt: GitHub Release .. image:: https://img.shields.io/pypi/v/omio-microscopy.svg :target: https://pypi.org/project/omio-microscopy/ :alt: PyPI version .. image:: https://img.shields.io/badge/License-GPL%20v3-green.svg :target: https://omio.readthedocs.io/en/latest/overview.html#license :alt: GPLv3 License .. image:: https://github.com/FabrizioMusacchio/omio/actions/workflows/omio_tests.yml/badge.svg :alt: Tests .. image:: https://img.shields.io/github/last-commit/FabrizioMusacchio/omio :target: https://github.com/FabrizioMusacchio/omio/commits/main/ :alt: GitHub last commit .. image:: https://img.shields.io/codecov/c/github/FabrizioMusacchio/omio?logo=codecov :target: https://codecov.io/gh/fabriziomusacchio/omio :alt: codecov .. image:: https://img.shields.io/github/issues/FabrizioMusacchio/omio :target: https://github.com/FabrizioMusacchio/omio/issues :alt: GitHub Issues Open .. image:: https://img.shields.io/github/issues-closed/FabrizioMusacchio/omio?color=53c92e :target: https://github.com/FabrizioMusacchio/omio/issues?q=is%3Aissue%20state%3Aclosed :alt: GitHub Issues Closed .. image:: https://img.shields.io/github/issues-pr/FabrizioMusacchio/omio :target: https://github.com/FabrizioMusacchio/omio/pulls :alt: GitHub Issues or Pull Requests .. image:: https://readthedocs.org/projects/omio/badge/?version=latest :target: https://omio.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status .. image:: https://img.shields.io/github/languages/code-size/fabriziomusacchio/omio :alt: GitHub code size in bytes .. image:: https://img.shields.io/pypi/dm/omio-microscopy?logo=pypy&label=PiPY%20downloads&color=blue :target: https://pypistats.org/packages/omio-microscopy :alt: PyPI Downloads .. image:: https://static.pepy.tech/personalized-badge/omio-microscopy?period=total&units=INTERNATIONAL_SYSTEM&left_color=GRAY&right_color=BLUE&left_text=PiPY+total+downloads :target: https://pepy.tech/projects/omio-microscopy :alt: PyPI Total Downloads .. image:: https://img.shields.io/badge/Example%20Datasets-10.5281%2Fzenodo.18078231-blue :target: https://doi.org/10.5281/zenodo.18078231 :alt: Example Datasets on Zenodo .. image:: https://img.shields.io/badge/Zenodo%20Archive-10.5281%2Fzenodo.18030883-blue :target: https://doi.org/10.5281/zenodo.18030883 :alt: Zenodo Archive `OMIO (Open Microscopy Image I/O) `_ is a policy-driven Python library for reading, organizing, merging, visualizing, and exporting multidimensional microscopy image data under explicit OME-compliant axis and metadata semantics. OMIO is designed as an infrastructure layer between heterogeneous microscopy file formats and downstream analysis or visualization workflows. It provides a unified I/O interface that enforces consistent axis ordering, metadata normalization, and memory-aware data handling across NumPy, Zarr, Dask, napari, and OME-TIFF. .. note:: **NOTE:** OMIO is **currently under active development**. The API and feature set may change in future releases. We also welcome feedback, feature requests, and contributions via `GitHub issues `_. Please report any bugs or inconsistencies you encounter. .. toctree:: :maxdepth: 3 :caption: Contents overview installation usage api changelog contributing `OMIO `_ is `free and open-source software (FOSS) `_ distributed under the :ref:`GPL-3.0 license `.