#omio — Public Fediverse posts

@neuroinformatics Btw, the built-in batch converter in #OMIO and several of my other tools already assume a #BIDS-like data structure. Thus, #datashuttle feels like a very good match ✌️

🌍 https://omio.readthedocs.io/en/latest/usage_batch_conversion.html

@albertcardona True. I deliberately avoided #BioFormats for #OMIO, though.

The #Python bindings rely on the #Java Bio-Formats library/ #JVM, and one of OMIO’s goals is to stay lightweight and avoid the additional installation and cross-platform complexity of a Java dependency. However, OMIO is extensible: Whenever support for another format is requested and a dedicated pure-Python library exists or can reasonably be implemented, we’re happy to add it, sure.

🚀 #MotilA now runs with #OMIO!

Today’s version release v1.1.2 adds much more flexible image I/O: #TIFF/ OME-TIFF, #CZI, #LSM & #Thorlabs RAW are now read via OMIO and normalized to #OME-compliant TZCYX axis-order, automatically. So, no more manual axis reordering before analysis 🤗

🌍 https://motila.readthedocs.io/en/latest/changelog.html#motila-v1-1-2

#microglia #motility #Bioimageanalysis #Python

#OMIO is meanwhile at v0.2.9 🚀

The main focus this past week was making #Thorlabs RAW handling more robust: Better #XML/ #YAML #metadata fallback, support for batch-friendly error handling, and clearer diagnostics when metadata doesn’t match the RAW data.

🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-9
⚙️ https://omio.readthedocs.io/en/latest/usage_file_format_supported.html#reading-thorlabs-raw-files

#BioimageAnalysis #Python

Today’s release of #OMIO (v0.2.6) is again a small update, but it brings memory-efficient OME-TIFF writing for Zarr-backed workflows. When imwrite receives a disk-cached #Zarr array, OMIO now streams it plane by plane instead of materializing the full store in RAM.

🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-6

#BioimageAnalysis #Neuroscience #Python

Today's release of #OMIO (v0.2.5) is just a small update, but brings a useful option: configurable disk-cache locations for imread(). Ideal when large #microscopy files live e.g. on a server, while you want OMIO's disk-backed #Zarr cache stored locally for smoother and faster processing and reuse ✌️

🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-5

#BioimageAnalysis #Neuroscience #Python

#OMIO is now at version v0.2.4. This maintenance release brings cleaner API docs, disk-backed empty image creation, and a more convenient #napari opener with automatic layer names, custom channel labels, and configurable blending ✌️

🌍 https://omio.readthedocs.io/en/latest/changelog.html#omio-v0-2-4
📚 https://omio.readthedocs.io/en/latest/usage_template_functions.html#creating-empty-images-as-on-disk-zarr-arrays
📚 https://omio.readthedocs.io/en/latest/usage_core_functions.html#opening-images-in-napari-and-metadata-modification

#bioimageanalysis #Neuroscience

#Omio #Travel - 12% #Gutscheincode #Rabattcode #Coupon #Reisen | MKW: - https://www.preishals.de/gutscheine/omio/

By embedding OpenAI Codex across the entire software development lifecycle, Omio reduced quarter-long engineering sprints into single-month, single-developer deployments. https://www.artificialintelligence-news.com/news/omio-scales-travel-product-development-using-openai-models/ #omio #ai #openai #travel #enterpriseai #technology

I just pushed #OMIO to version v0.2.2. You can now reuse existing disk-backed #Zarr caches instead of rebuilding them every time an image is opened. OMIO stores cache metadata directly in the Zarr store and validates compatibility automatically before reuse ✌️

🌍 https://omio.readthedocs.io/en/latest/usage_large_files.html#reuse-an-existing-on-disk-omio-cache
👨‍💻 https://github.com/FabrizioMusacchio/omio

#Microscopy #BioimageAnalysis #Python #OpenScience

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

🧵8/8

#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

🧵7/8

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.

🧵6/8

#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 🤗

🧵5/8

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 ✌️

🧵4/8

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, ...

🧵3/8

#OMIO currently supports: #TIFF, #OMETIFF, #TIFFseries, #ZEISS #LSM and #CZI, #Thorlabs RAW. All inputs are mapped to a unified representation with #OME-compatible axis semantics and standardized metadata handling.

🧵2/8

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/

🧵1/8

#BioimageAnalysis

2/ OK. Hab's gebucht. War auch nicht so einfach. Immerhin war die ursprüngliche Planung einfach. Das ging mit #DB. Aber buchen konnte ich die Göteborg-Oslo-Voss-Strecke nicht. Auch meine üblichnen Verdächtigen wie #Trainline und #Omio wollten nicht. Manche kannten Voss nicht. Bei der Schwedischen Bahn habe ich rausgefunden, dass Göteborg-Oslo nicht von ihnen ist und nach einigem Suchen dann festgestellt, dass das #Vy ist und die haben dann auch Oslo-Voss gemacht. Lustig ist, dass der Zug nach Oslo fast ausgelastet ist. Nur noch ein paar Plätze in der ersten Klasse und die nehmen dann mal eben 90€ für die Platzreservierung. Wahrscheinlich findet man immer einen Platz, aber who knows.

#Bahn #BahnBubble #staygrounded #amBodenBleiben

#Omio #Travel - 12% #Gutscheincode #Rabattcode #Coupon #Reisen | MKW: - https://www.preishals.de/gutscheine/omio/

@bahnoev Weiß jemand, ob #Omio ein seriöser Anbieter für #Deutschlandtickets's ist? Ein Zugbegleiter einer NE-Bahn hat mir das neulich angepriesen, da könne man ohne die sonst übliche Kündigungsfrist D-Tickets abbestellen – kann eigentlich nicht wahr sein, oder?

Echtzeitinfos in anderen Apps: Bahn schließt neue Verträge

https://bahnblogstelle.com/220976/echtzeitinfos-in-anderen-apps-bahn-schliesst-neue-vertraege/

#Echtzeitinfo #App #Ticket #Auskunft #Vertrag #Omio #Trainline #DeutscheBahn #Bahn

Cuidado con #Avlo y #Omio. No sé en qué momento de la compra aparece la confusión, pero en un viaje de ida y vuelta a Valencia creímos haber incluido el equipaje y para volvernos a Madrid hemos tenido que apoquinar 90 euros. 🥴

Para ir nadie te dice nada, pero para volver tienen apostados a tres armarios con patas que te preguntan con violencia si has adquirido el suplemento. 🤡

Omio takes $100M to shuttle through the coronavirus crisis - Multimodal travel platform Omio (formerly GoEuro) has raised $100M in late stage funding to help see... - http://feedproxy.google.com/~r/Techcrunch/~3/1r2UiRwyLd0/ #consumerproducts #fundings&exits #transportation #kleinerperkins #travelindustry #unitedkingdom #goldmansachs #northamerica #unitedstates #coronavirus #carrentals #carsharing #narenshaam #transport #covid-19 #kinnevik #rome2rio #germany #temasek #europe #berlin #omio

Three travel startups tell us how they’re responding to the coronavirus crisis - With the globalized world going into partial or complete lock down over the Covid-19 pandemic, start... more: http://feedproxy.google.com/~r/Techcrunch/~3/MqjcZV9wwDk/ #bookingplatforms #getyourguide #onlinetravel #coronavirus #travelperk #startups #covid-19 #europe #omio #tc

Travel aggregator Omio hops over the pond to launch in North America - Travel aggregator Omio, which operates a multimodal transport planning and booking platform for inte... more: http://feedproxy.google.com/~r/Techcrunch/~3/A3OTZ22Uim8/ #travelaggregator #transportation #unitedairlines #deltaairlines #travelplanner #northamerica #unitedstates #narenshaam #transport #europe #amtrak #berlin #canada #goeuro #travel #omio #tc

Omio buys Rome2Rio to build out its global travel aggregator business - Omio (née GoEuro) has acquired multimodal travel veteran Rome2rio as it works on building out a glo... more: http://feedproxy.google.com/~r/Techcrunch/~3/32pp3w73p-I/ #travelaggregator #fundings&exits #transportation #narenshaam #australia #melbourne #transport #rome2rio #europe #goeuro #travel #apps #omio