Streaming OME-Zarr data directly into syGlass for #3DThursday🌍🔬
With #syGlass v2.6.0, datasets can stream from disk, S3, or HTTPS with no massive downloads required.
Huge thanks to the community building open imaging standards:
@openmicroscopy.org
#OMEZarr #Microscopy #OpenScience #Bioimaging
If you've been wondering what our current obsession with OME-Zarr and lego blocks is about, I have good news for you: the Fractal preprint is out!
Thanks to @joelluethi.bsky.social , all co-authors, and the Fractal developers and users community for making this beautiful project a reality ❤️
Help shape the future of @openmicroscopy.org! 🔮
The OME 2026 community survey is open—tell us what’s working, what isn’t, and what you'd like to see next.
Takes just a few minutes 👇
forum.image.sc/t/ome-2026-c...
Thanks @will-j-moore.bsky.social ! The supplementary videos are available in the supplementary materials tab: www.biorxiv.org/content/10.6...
They are also available on YouTube:
1: www.youtube.com/watch?v=uhv4...
2: www.youtube.com/watch?v=t2Fj...
3: www.youtube.com/watch?v=5Sg1...
Calling all OME Community members, contributors, and lurkers! Please take a minute to answer the OME 2026 Community Survey (docs.google.com/forms/d/e/1F...) to help us prepare for discussing the future of OME governance during the OME 2026 Community Meeting at the end of April.
@ccp-volumeem.bsky.social I'm very glad we got this out before the hackathon, so I can focus on learning more about the #volumeEM needs, chat & hack with all the participants there! Looking forward to meeting everyone tomorrow & thanks for organising this nice event!
Looking forward to learning more about this and how it can be used for #volumeEM at the #CCPvolumeEM #NGFF hackathon at @ebi.embl.org this week!
#BioImageAnalysis @cosec-ukri.bsky.social #OMEZarr
Part 2 of the coauthors:
@priscaliberali.bsky.social , @lucaspelkmans.bsky.social & @virginieuhlmann.bsky.social
Also, many thanks to Exact lab, all the Fractal task developers, community collaborators, and core services & facilities at UZH & @fmiscience.bsky.social
Many thanks to all coauthors:
Part 1:
@lorenzocerrone.bsky.social , Tommaso Comparin, Max Hess, @rhornb.bsky.social , Adrian Tschan, Gustavo Quintas Glasner de Medeiros, @nrepina.bsky.social , Loredana Cantoni, Fabio Steffen, Jean-Pierre Bourquin
& part 2 in next post
Are you also processing OME-Zarrs or developing image analysis methods? Join the community of Fractal task developers or Fractal platform users!
fractal-analytics-platform.github.io
Want to see how Fractal looks in action? Check out our public server here: fractal-demo.mls.uzh.ch
Finally, we demonstrate that Fractal results in highly-reproducible analysis workflows, enabling drug response profiling in clinical settings
We illustrate how Fractal enables the analysis of large and complex bioimage datasets: multiplexed, multiscale, 3D, and 4D
We also demonstrate how a computational platform can leverage this spec to make building and running workflows at scale on HPC clusters accessible through a simple web interface
youtu.be/uhv4rSc_6gs
In our preprint, we first introduce a task specification for interoperable image analysis on OME-Zarr files, where inputs & outputs are OME-Zarr. We already have over 100 publicly available processing units implemented following this spec: fractal-analytics-platform.github.io/fractal_tasks/
This is the main project we’ve been working on at the BioVisionCenter over the past years. Why?
- Enable interoperable processing steps
- Make image analysis on HPC clusters more accessible
- Scale image processing to TB-sized microscopy datasets
- Increase the reproducibility of bioimage analysis
We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows.
Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis.
(1 / 10🧵)
www.biorxiv.org/content/10.6...
Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:
- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports
github.com/imaging-form...
v0.0.rc1 on PyPI
🚀 We’re hiring! The Structural Biology Platform is seeking a Project Leader to advance cryo-electron tomography and expand capabilities at the FMI. Join a vibrant research community at the interface of structural biology, cell biology & disease mechanisms. Apply at: www.fmi.ch/education-ca...
We are hiring a Research Software Engineer to enhance and maintain the SpatialData framework.
We will work together with colleagues at EMBL, DKFZ, GSK, and across the scverse community.
🔗 Deadline: 15/02/2026
embl.wd103.myworkdayjobs.com/en-US/EMBL/d...
19th #OME Community Meeting, Düsseldorf · 28–30 April 2026
Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools.
Details & registration (deadline: 31 March 2026):
gerbi-gmb.de/event/ome-20...
Big news! The Data Management team/Data Science Centre at EMBL (i.e. my team) is hiring for a position based in Heidelberg (but working across all sites!). We are looking for a scientific workflows developer that will focus on multimodal pipelines. embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...
I am still digesting all the info from the OME-NGFF hackathon last week.
So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.
CZI --> OME-ZARR with some options ...
By far not perfect but still fun!
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
Go read Joel's thread on the hackathon last week in Zürich! If you have any level of interest in OME-NGFF, there are so many exciting things happening. I had a great time meeting some of my favorite people in the world - It was equal parts rewarding, fun and exhausting 🙃️
