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]

🔬 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 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 ❤️

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...

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.

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

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 🙃️

Very happy to share some more pics! What an amazing week! I am still recovering! Thank you so much to you all❤️‍🩹🥲

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

What an incredible two days! Reposting this with so much appreciation for everyone who made the 2025 International OME-NGFF workshop such a special event. Thanks everyone for coming & especially everyone of the BVC team to help pull this off!

This is what hacking *actually* looks like. #OME_NGFF_Hackathon

The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head: jobs.uzh.ch/job-vacancie... It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬 Application deadline: December 15, 2025.

Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊 Huge kudos to Max Hess for this PhD milestone! 💪 @lucaspelkmans.bsky.social shorturl.at/cO0u7 Let's zoom in!

The #mesoSPIM symposium really opened my eyes to the power of open source hardware. I've highlighted some of the surprising outcomes in a new blog post: How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium www.syglass.io/blog/how-ope...

Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!

We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...

The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social www.biorxiv.org/content/10.1...

🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️ jobs.helsinki.fi/job/Helsinki... #jobopening

Job opportunity at the University of Zurich! 📢 We are looking for a 𝐋𝐚𝐛𝐨𝐫𝐚𝐭𝐨𝐫𝐲 𝐓𝐞𝐜𝐡𝐧𝐢𝐜𝐢𝐚𝐧 / 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐀𝐬𝐬𝐢𝐬𝐭𝐚𝐧𝐭 (𝟒𝟎%) to join our Microscopy Innovation Platform (MIP), an open-source initiative focused on advancing and making light-sheet and multiphoton microscopy accessible to researchers. 1/3

@nfdi4bioimage.bsky.social Task Area Leaders Josh Moore and Christian Tischer will introduce participants to the history and basics of OME-Zarr at the international 2025 OME-NGFF Symposium from November 10–11 in Zurich, SW. Register here: 👉 www.ema.uzh.ch/de/register/... Picture by BioVisionCenter

Job alert! We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? See also on the forum: forum.image.sc/t/research-e...

We’re looking for an enthusiastic postdoc to join our team. 😊 The project focuses on protein design and cryo-EM applied to cancer research. 🔬🧪 The position is fully funded for 3 years. Please share 🙏 Job description and application details (deadline: October 11th): www.cnio.es/en/empleo/po...

napari 0.6.5 is out! 🚀 Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: napari.org/dev/release/...

BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)

Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...

Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org @tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev

Are you working with OME-Zarrs in Switzerland? We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)

Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...

We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊 📄 joss.theoj.org/papers/10.2110… (1/3)

Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden Wednesday, 27th of August, 2pm CEST

Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

I'll be there! Giving a talk! and hacking on _something_ for a few days!

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)