We are looking for an experienced light microscopy specialist, motivated to support our users in the Advanced Light Microscopy Facility at EMBL Heidelberg.
embl.wd103.myworkdayjobs.com/en-US/EMBL/j... -closing date 11 May 2026 @eurobioimaging.bsky.social @globalbioimaging.bsky.social

🚨🔬🚨🔬🚨
We are pleased to announce that registration for the 7th edition of the Crick BioImage Analysis Symposium #CBIAS 2026 is now open!
🕐November 23rd-24th, 2026📍The Francis Crick Institute, London. We look forward to seeing as many of you as possible there (or online 😀)

‘Why is publishing so expensive?’ For many of us who work in scientific publishing, the title of this Editorial is a question we hear all the time when we're out talking to academics. And it's a perfectly reasonable one. After all, re...

A question I get asked all the time by @dev-journal.bsky.social authors "Why does it cost so much to publish a paper?"

We break down the finances and explain where the money goes

Spoiler: quality publishing takes a village (people + infrastructure)

journals.biologists.com/dev/article/...

We have just released the latest Fractal update: Bringing workflow template support to Fractal with Fractal server 2.20

This allows users to create workflow templates & share it with others.

Learn more about it here: fractal-analytics-platform.github.io/news/2026-03...

napari 0.7.0 is available now! 🚀🎉

It's a BIG release so read the full release notes, with highlights: https://napari.org/stable/release/release_0_7_0.html

We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant […]

[Original post on fosstodon.org]

Open Bioimaging Practices Meetup: March 2026

🔬 Next Open Bioimaging Practices Meetup (OBPM) – Mar 31, 16:00 CET
Hybrid: FMI Basel & Zoom

Talk by @jo-soltwedel.bsky.social :
Transforming OME-Zarr: What’s coming in v0.6

Plus short updates from the BVC & time for discussion

www.biovisioncenter.uzh.ch/en/events/Up...

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software.

image.coop/blog/posts/2...

The Human Organ Atlas The Human Organ Atlas provides open access to 3D images of human anatomy spanning whole organs to cellular scale resolution.

The paper that sums up what I've been working on and running for the last three years was published this week 🎉

www.science.org/doi/10.1126/...

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 ❤️

OME 2026 Community Survey Calling all OME Community members, contributors, and lurkers! This year in April, the 19th OME Community Meeting will be gathering to determine the "Future and Governance of OME" during the final mee...

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

Fractal web: Accessible workflow building & OME-Zarr data interaction YouTube video by Joel Lüthi

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...

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

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...

Research Software Engineer - Spatial-omics The Oliver Stegle team and the Bioimage Analysis Support Team at EMBL Heidelberg are looking for a research software engineer to contribute to the development and maintenance of highly-used open-sourc...

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 - German BioImaging Join us for the 19th Open Microscopy Environment (OME) Community Meeting from 28.-30.4.2026, in the Haus der Universität Düsseldorf. Invited Speakers Carole Goble – Keynote – Jean-Marie Burel Josh Moo...

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...

Scientific Workflows Developer The European Molecular Biology Laboratory (EMBL) is Europe’s life sciences laboratory – an intergovernmental organisation with more than 110 independent research groups and service teams covering the ...

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...