In ngff-zarr, we released a new Model Context Protocol (MCP) server 🧬🔬
This means you can now use natural language to:

✅ Convert datasets to OME-Zarr format
✅ Optimize compression codecs automatically
✅ Configure intelligent sharding
✅ Generate Python scripts for batch processing
✅ Validate OME-Zarr stores

https://ngff-zarr.readthedocs.io/en/latest/mcp.html

#ScientificImaging #OMEZarr #AI #ResearchSoftware #ReproducibleResearch #MCP

Know someone looking for a new start in 2025? 🔍 #getfedihired

🚀 We're hiring! Join the @GerBI Team as a Software Developer!

💻 Build scalable #bioimaging solutions

🌍 Collaborate globally

🎯 Contribute to open science through
#OMEZarr

@ome @zarr

Remote, full-time. Apply by 31 Jan 2025:

https://bit.ly/3Zrd4SR

🚀 **Join the 3rd Get Your Brain Together Hackathon!** 🧠

🔍 **Purpose:**
Our focus: advancing **OME-Zarr spatial transformations**!

Enhancing:
- **Reproducibility**: Consistent transformations across platforms.
- **Workflow Integration**: Seamless image analysis steps.
- **Accuracy**: Reduced resampling errors.
- **Flexibility**: Supports diverse research needs.

More: https://insightsoftwareconsortium.github.io/GetYourBrainTogether/HCK03_2024_UNC_Hybrid/

#Neuroimaging #Bioimaging #OMEZarr #Hackathon #OpenSource #ScientificResearch

OME's next Annual Community Meeting is May 29-31, 2024 in sunny Dundee!!! Spend 2 days with the community talking all things #OMERO, #OMEZarr, and public bioimage #FAIRdata resources. More info and registration:

https://www.openmicroscopy.org/events/ome-community-meeting-2024/

OME-ZARR is a possible candidate for a standard IR/Raman file format.

[from Twitter]
We look forward to this Friday's #VirtualPub with @joel_luethi, Friedrich Miescher Institute for Biomedical Research, and Bugra Özdemir of Euro-BioImaging.
They will take us on an "Exploration and Analysis of Image Data using #OMEZarr." All are welcome! https://www.eurobioimaging.eu/about-us/virtual-pub

[from Twitter]
We look forward to this Friday's #VirtualPub with @joel_luethi, Friedrich Miescher Institute for Biomedical Research, and Bugra Özdemir of Euro-BioImaging.
They will take us on an "Exploration and Analysis of Image Data using #OMEZarr." All are welcome! https://www.eurobioimaging.eu/about-us/virtual-pub

"How open-source software could finally get the world’s microscopes speaking the same language"

@Nature Technology Feature out now covering #OMEZarr with thoughts by @joshmoore, @bethcimini, @BogovicJohn, and more.

https://www.nature.com/articles/d41586-023-03064-9

I am very happy to see this piece and the growing adoption of OME-Zarr. It is the key to make image analysis scalable and interoperable, even for the largest images. With @webknossos we build software to make it easy to work with #OMEZarr.

https://www.nature.com/articles/d41586-023-03064-9

Let's discuss how to adopt the new Zarr version 3 into OME-Zarr so that we can use sharding and the extensible structure! Join the discussion on https://forum.image.sc/t/adopt-zarr-v3-in-ome-zarr/84786 #omezarr @zarr @ome

@normanrz @ome @zarr

Hot off the presses! 📖🔬📣

@DrHenningFalk@twitter.com's #OMEZarr drawings are now in print. Very timely for the first #volumeEM #GordonConf. ❤️

Discover remarkable datasets from the scientific community in our gallery!

https://zarr.webknossos.org/

All datasets are available as OME-Zarr, now. Contact us if you would like to publish your dataset here. @zarr #OMEZarr

... and special apologies for the lack of open access.

For the next 50 days (until 2023-04-28) you can access the chapter on using #OMEZarr in #VolumeEM under:

https://authors.elsevier.com/a/1gjIc,25QIopF6

👏👏👏#VolumeEM @VolumeEM1
---
RT @notjustmoore
"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚

https://doi.org/10.1016/bs.mcb.2023.01.016

Special thanks to co-authors @normanrz & @BogovicJohn, co-artist @DrHenningFalk, and volume (ha!) editors @EM_STP @KedarNarayan2 & @PaulVerkade
https://twitter.com/notjustmoore/status/1633865042025127937

"Toward #scalable reuse of #vEM data: #OMEZarr to the rescue" just hit the shelves!📚

https://doi.org/10.1016/bs.mcb.2023.01.016

Special thanks to co-authors @normanrz & @BogovicJohn@twitter.com, co-artist @DrHenningFalk@twitter.com, and volume (ha!) editors Lucy Collinson, Kedar Narayan, & Paul Verkade

Not to mention @ome + @zarr

Love to see @webknossos in such great company! #OMEZarr
---
RT @notjustmoore
#OMEZARR co-authors 2/3

@markkitti, Gabor, Aybüke, Albane, @BioinfoTongLI, Prisca, Melissa, Dominik, @joel_luethi, @JMaitinShepard, @trevmanz, @thewtex, Khaled, @will_j_moore, Bugra, @cppape, Lucas, Martin, @pietzscht, @preibischs, @normanrz, @DavidRStirling, ...
https://twitter.com/notjustmoore/status/1628096218340421634

One thing that shows just how fast the community is moving: I only learned about #OMEZarr a bit more than a year ago with the Nature methods paper on #OMENGFF, which convinced me that this was the way forward: https://www.nature.com/articles/s41592-021-01326-w
(2/5)

Super happy that the preprint for the #OMEZarr paper is out now! If you want to know where bioimage analysis is going: I think this will be the direction! Standardization & open source for the win!

Find the #bioRxiv preprint here: https://www.biorxiv.org/content/10.1101/2023.02.17.528834v1

And Josh's main thread about it here: https://fediscience.org/@joshmoore/109904124384328635

Thread (1/5)

Latest report from the #OMENGFF #Community describing #OMEZARR, a #CloudOptimized #BioImaging #DataFormat, is out now on #bioRxiv!

If you are having trouble with big, slow, or otherwise unwieldy imaging data, reach out or take a look for a #FAIR-er option.

https://www.biorxiv.org/content/10.1101/2023.02.17.528834v1

What could be a better end of the year present than a poster that brings together #NASA, #openmicroscopy, and #zarr? 🚀🦠🔬🖥️🎁

Kudos to https://twitter.com/ryantscott and team for taking us where no #OMEZARR has been before...

#OpenScience #DataRepository

https://agu2022fallmeeting-agu.ipostersessions.com/default.aspx?s=C6-2E-73-3A-75-35-51-8D-EA-94-0A-70-87-CB-6A-81