If you work with #microscopy images 🧠🔬 in #Python 🐍👨💻, you may know the situation: Different file formats, readers, axis conventions, metadata structures... At least I found this increasingly frustrating. So I built #OMIO (Open Microscopy Image I/O), a unified microscopy image reader & writer for #Python:
🌍 https://omio.readthedocs.io/
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A major goal of #OMIO is to make image semantics explicit:
✓ normalizes axis order
✓ preserves singleton dimensions
✓ extracts physical scales when available
✓ keeps metadata accessible
✓ warns when critical metadata are missing
No more guessing whether the array is TZCYX, ZCYX, CZYX, ...
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For large microscopy datasets (e.g. >1 GB): #OMIO can materialize images directly as disk-backed #Zarr stores. This allows #MemoryMapped, slice-wise access w/o loading the entire dataset into RAM. And: It fully integrates with #Napari workflows ✌️
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#OMIO provides three main entry points:
• imread() → read microscopy data
• imwrite() → write standardized OME-TIFF
• imconvert() → convert between formats in a single step
The idea is simple: Read almost anything, normalize semantics, write OME-TIFF 🤗
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Working with large microscopy collections, e.g., full experiment series? #OMIO includes #BIDS-like batch conversion workflows that can traverse project trees and convert datasets automatically while applying the same semantic rules to every file. No format-specific batch scripts required.
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#OMIO is fully #OpenSource:
👨💻 https://github.com/FabrizioMusacchio/omio/
Documentation, tutorials, example data, and a #bioRxiv #preprint are also available:
📚 https://omio.readthedocs.io/en/latest/
📈 https://zenodo.org/records/18078231
📑 https://doi.org/10.64898/2026.06.09.731118
#BioimageAnalysis #Microscopy #Neuroscience
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If you'd like to contribute 🤝, report 🐞, request features 🚀 or new file format support 🗳️, feel free to contact me via #OMIO's GitHub issues:
👨💻 https://github.com/FabrizioMusacchio/omio/
#OpenSource #Python #Microscopy
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@FabMusacchio Neat!
Is the data stored in the order in which it is in the file, and then you just reorder the dimensions without copying, or do you store the data in your forced TZCYX order? I’m asking because it can have implications on processing efficiency.
I have been using https://bioio-devs.github.io/bioio/index.html until now, the successor of AICSImageIO, which handles in Python a substantial amount of Bio-Formats. But it has its issues. I will have to check OMIO!
Fabrizio Musacchio
Cris Luengo
Virgile Andreani