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bioRxiv · 10.64898/2026.06.09.731118

OMIO: A policy-driven Python library for reproducible microscopy image I/O

Musacchio, F.·Antony, H.·Crux, S.·Fuhrmann, F.·Gockel, N.·Hoffmann, D. M.·Mercan, D.·Nebeling, F. C.·Fuhrmann, M.
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Abstract

Modern fluorescence and multiphoton microscopy workflows operate within a heterogeneous ecosystem of file formats, partially overlapping metadata standards, and reader-specific conventions. In practice, this frequently leads to silent axis misinterpretations, loss or corruption of physical voxel size information, and laboratory-specific glue code that is fragile, poorly documented, and difficult to reproduce. OMIO, short for Open Microscopy Image I/O, addresses these issues by providing a lightweight, policy-driven image I/O layer for Python that enforces a canonical, OME-compatible data representation at the API boundary. The central contribution of OMIO is the explicit separation of low-level format access from semantic normalization. Existing reader libraries are used as interchangeable backends for extracting pixel data and available metadata, while OMIO enforces axis conventions, metadata interpretation, and fallback decisions in a centralized and auditable policy layer. This design allows heterogeneous microscopy inputs to be converted into a stable representation without propagating backend-specific assumptions into downstream analysis code. The core design principles of OMIO include canonical axis semantics (TZCYX), robust metadata normalization with explicit and auditable fallbacks, memory-aware operation via optional Zarr-based backends, and workflow-level semantics that extend beyond individual files to folder stacks and BIDS-like project structures. This architecture allows OMIO to orchestrate existing reader libraries into a coherent and reproducible I/O pipeline without replacing or duplicating their functionality. OMIO is implemented as an open-source and community-oriented system in which support for additional file formats and metadata conventions can be added incrementally through modular reader backends. By encouraging the contribution of example datasets, backend extensions, and feature requests, OMIO is designed to evolve alongside emerging acquisition systems while preserving strict semantic guarantees at the interface level. The resulting standardized OME-TIFF outputs are immediately suitable for downstream quantitative analysis and interactive inspection in scientific Python workflows, including workflows based on ImageJ and Napari. By standardizing image data at the I/O boundary, OMIO supports FAIR-aligned data sharing and reproducible microscopy analysis while facilitating the development of interoperable downstream tools.

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Musacchio, F., Antony, H., Crux, S., Fuhrmann, F., Gockel, N., Hoffmann, D. M., Mercan, D., Nebeling, F. C., Fuhrmann, M.. 2026-06-11. OMIO: A policy-driven Python library for reproducible microscopy image I/O. https://doi.org/10.64898/2026.06.09.731118

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