Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io

🌟Enhancements🌟 The proofreading tool got smarter: you can now define multiple segments around a desired split, and it will automatically pick the optimal split point.

🌟Enhancements🌟 Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀

#Nanoimaging symposium @crick.ac.uk! At #CrickXrays25 we'll tackle: 💫synchrotron upgrades 📈current limits in throughput, volume, resolution 🧪sample preparation for X-ray PC imaging 🧠♥️applications in neuroscience and tissue life science 🗓️13th October 2025 🇬🇧🌐 London & online tinyurl.com/crickxrays25

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...

🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com! Community-driven standards to make bioimage data AI-ready & reusable. 👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata

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...

#preprint: We optimised the preparation of tissues for #X-ray phase contrast imaging. Drying tissue samples (instead of embedding them) brings more signal in #X-ray phase contrast images. The process largely preserves #ultrastructure. @safekhan.bsky.social @andreas-t-schaefer.bsky.social

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 🧵)

🌟Enhancements🌟 ICYMI: Webknossos viewports are now rotatable. Use keyboard shortcuts to rotate the orthogonal viewport. Try Shift + Left, Shift + Right, Shift + Up and Shift + Down. Learn more about keyboard shortcuts: docs.webknossos.org/webknossos/u...

🌟Big new feature🌟 Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.

🌟Enhancement🌟 Make the 3D meshes of your segments translucent. Great for revealing inner segments, such as as cell organelles. Also, translucent meshes look really cool 😎

Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST! Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...

OME-Zarr 4 life

You can now apply until the 4th of June !! #EMBOBioImage www.embl.org/about/info/c...

#preprint: We mapped the structure and function of olfactory bulb circuits with in vivo 2-photon microscopy and synchrotron #Xray holographic nanotomography. doi.org/10.1101/2025... @yuxinzhang.bsky.social @andreas-t-schaefer.bsky.social @apacureanu.bsky.social @crick.ac.uk @esrf.fr

My PhD project is out as a preprint! We combined 2P and synchrotron X-ray to understand mouse olfactory bulb circuits, linking physiology to structure in 3 animals! doi.org/10.1101/2025... 🙌 @carlesbosch.bsky.social, @apacureanu.bsky.social, @andreas-t-schaefer.bsky.social, @esrf.fr, @crick.ac.uk

Super happy that our papers #2 and #3 from our 3-person lab just went online on bioRxiv! First large-scale 3D EM dataset from mouse hippocampus CA1 www.biorxiv.org/content/10.1... - check out the beautiful data on webknossos wklink.org/7023 ! …

If you want to learn the latest developments in volumeEM from the experts, with hands-on experience on our instruments @embl.org, this course is for you! 🔬

🚀 Advancing Retinal Connectomics! Prof. David Berson from Brown University discussed strategies for large-scale segmentation in retinal connectomics at the vEM Data Challenges Symposium. 🎥 Watch the recorded session here: (youtu.be/vO8lro_wlz8?...)

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀 Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich. 🔗 Read the preprint: osf.io/preprints/bi... 🧵 (1/15)

🚀 Starting in a few hours! Join leading experts as they share insights on handling large #VolumeEM datasets & improving collaborative workflows. 📅 March 6 | 5-7PM CET | Online | Free 🔗 Register now: buff.ly/TZRYGcL.

⏳ 4 more days to go! Don't miss our online symposium on #VolumeEM data challenges - practical solutions for massive datasets & collaboration. 📅 March 6, 2025 | 5-7PM CET | Free registration 🔗 Sign up: buff.ly/LaZw4aA.

Luke Noon from CIPF will speak at our symposium on vEM data challenges about pioneering vEM workflows beyond the brain. Learn how his team maps liver and peripheral tissues with innovative annotation & collaboration strategies! 📅 March 6, 2025 | 5-7PM CET | Online www.eventbrite.de/e/volume-em-...

@carlesbosch.bsky.social from the Francis Crick Institute presents his work at our symposium on vEM data challenges, showcasing how correlative 2-photon and X-ray imaging reveals neural computation in olfactory circuits. 📅 March 6, 2025 | 5-7PM CET | Free registration | https://buff.ly/42gkyv4

In our symposium on vEM data challenges, Prof. David Berson from Brown University will explore strategies for large-scale segmentation in retinal connectomics. Register now and get reminders! 📅 March 6, 2025 | 5-7PM CET | Free registration 📖 Full abstract and sign up link: https://buff.ly/42gkyv4

X-ray nanotomography can be your new friend for neuronal imaging. In our new #preprint (tinyurl.com/nanoXneuro) we present advances that push the spatial resolution limit for X-ray holographic nanotomography (XNH). We can now resolve synapses. 🧵

🐣 New feature 🐣 You can now activate “Selective Visibility” in WEBKNOSSOS to highlight only the active segment or the ones you hover over. This is great to quickly track cell extensions in complex segmentations. Try it out now on webknossos.org!

Receive an email as soon as you can register! mailchi.mp/embl/bia25-01 @ahklemm.bsky.social @iarganda.bsky.social @virginieuhlmann.bsky.social @jytinevez.bsky.social @bethcimini.bsky.social @haesleinhuepf.bsky.social @brittavelten.bsky.social @tischi.bsky.social

And now, support for Zarr v3 & sharding is released as an OME-Zarr specification! 🎉 forum.image.sc/t/ngff-0-5-r... #NGFF #BioImaging #Formats @openmicroscopy.org @zarr.dev

✨ 2024 Feature Highlights ✨ As we step into 2025, let’s look back at last year’s big developments in WEBKNOSSOS! From AI-powered analysis to 3D quick-select, we’ve streamlined volume EM workflows. Stay tuned for the full feature series or read more: https://buff.ly/3DZLHYR

If you missed the Zarr-Python 3 release party last week, no worries because today, we released zarr-python 3.0.1 and numcodecs 0.15.0. release notes 👉 zarr.readthedocs.io/en/stable/re...

We haven't done much performance tuning but the early results are looking really good.

Check out Joe's blog post about what is in the new zarr-python release!

🎉 Zarr-Python 3 is here! 🎉 - Full support for Zarr v3 spec - Chunk-sharding for more efficient data storage - Major performance boosts with async I/O & parallel compression 💻 pip install --upgrade zarr 💻 conda install --channel conda-forge zarr Blog post: https://buff.ly/3C3OwYw

We just released zarr-python 3.0! It ships with support for sharding, performance improvements, better extensibility and a fully modernized code base. Check out the docs for details: zarr.readthedocs.io/en/stable/ I want to thank everybody who helped with this big lift! It was a pleasure. @zarr.dev

Hi, Zarr community! 👋 🚨 Big news: Zarr-Python 3.0 is dropping next week! 🚨 If your project depends on Zarr-Python, make sure to check out the migration guide to get ready for the update. Guide: https://buff.ly/3W0cLxd More updates soon! 🧑🏻‍💻

Happy holidays from all of us at WEBKNOSSOS! ❄️🎄 We’re grateful for your trust and collaboration in 2024. Here’s to a New Year full of discoveries and progress! 🧠

Oh yes, we did! Here are our new postcards - educational outreach material that pinpoints challenges in bioimaging #RDM complexity. Turn them around to find out about solutions and support! And all illustrations are free for reuse (CC-BY). doi.org/10.5281/zeno... Many thanks to Henning Falk!

At #AGU24 last week, I gave a talk titled "Seamless Arrays: A Full Stack, Cloud-Native Architecture for Fast, Scalable Data Access". Slides and some summary below 👇 doi.org/10.6084/m9.f...

Please help the #Zarr community welcome @normanrz.bsky.social as the newest member of the Steering Council! 👏🏼 zarr.dev/blog/steerin...