Working on correlative microscopy workflows? Use skeletons to align landmarks and combine light microscopy and vEM data directly in WEBKNOSSOS. Example dataset (Drawitsch et al., eLife 2018): webknossos.org/links/tNaRtC...

Creating animations in WEBKNOSSOS? You can now include skeletons in your renders. Generate clearer videos for publications, presentations, or sharing your reconstructions. Try it out at webknossos.org now!

We spoke with @inperience.bsky.social from Miami University about using WEBKNOSSOS in a cell biology course built around real C. elegans vEM data. 48 students annotated cells, generated AI training data, and even contributed to a biological discovery. Read the interview: buff.ly/MckCdVY

Start with a small test bounding box. Validate the segmentation, inspect errors, and only then run the model on the full dataset. A controlled workflow for large-scale EM analysis.

“Users can leave Hamburg and continue inspecting their datasets the same day without transferring large volumes of data.” At the P14 beamline, tomography datasets appear in WEBKNOSSOS minutes after reconstruction, allowing users to explore them remotely in the browser. medium.com/webknossos/f...

Segmentation errors often reflect gaps in the training data. Review the ground truth, add missing examples, retrain, and iterate. Custom model training gives you direct control over model behavior. Guidelines for ground truth annotation: buff.ly/w41Ip9e

“And from a facility perspective, everything is automated. No one has to manually convert, upload, organize, or assign permissions.” At EMBL P14, reconstructed tomography datasets are automatically converted and transferred to WEBKNOSSOS through the API. Read more: medium.com/webknossos/f...

At the EMBL P14 beamline, tomography datasets are automatically transferred into WEBKNOSSOS minutes after reconstruction. Angelika Svetlove explains how the team built this pipeline - and why analysis, not acquisition, is now the main bottleneck. Read the interview:

Run pre-trained segmentation models for SEM data in WEBKNOSSOS. Test on small bounding boxes, inspect merge and split errors, and run on the full dataset once validated. View the tutorial: youtu.be/lZS2tOJYErw

We annotated ground truth data and trained an instance segmentation model for mitochondria detection on a 140 GB mouse cortex dataset (Motta et al., 2019) in WEBKNOSSOS. See the workflow and results: medium.com/webknossos/c...

The first syGlass feature release of the year is here! Meet syGlass v2.6.0: 🖥️ Spatial Reality Display support 🛜 Stream/read OME-Zarr directly 🖌️ Partition surfaces via 3D brush ⌨️ Enter text via in-VR keyboards www.syglass.io/blog/syglass...

Last year brought many great new features to WEBKNOSSOS ✨ Over the next days, we’ll share a series of feature highlights. Stay tuned!

🚨Gearing up for #NGFF 0.6! 🚨 Help us give this a final push over the finish line and join us in ironing out the last flaws on the way! More information here 👇 forum.image.sc/t/ngff-weekl...

Our Method of the Year 2025 is...drumroll please...EM-based connectomics!! Our Editorial introduces our choice and highlights six Comments and other related content in this special issue. Please join us in celebrating EM-based connectomics! 🎉🧠🔬 www.nature.com/articles/s41...

Connectomics is Method of the Year 2025!! @natmethods.nature.com just released the news nature.com/articles/s41... In my perspective piece, I afford some predictions into the future and compare how we are doing vs. genomics www.nature.com/articles/s41...

Maybe @normanrz.com can provide more @webknossos.org socks to help with the shoe-filling?

#paper! X-rays can resolve #ultrastructure in tissues non-destructively. www.nature.com/articles/s41... Shoutout to key collaborators at @crick.ac.uk and @psich.bsky.social Ana Diaz, @adrianawanner.bsky.social and @andreas-t-schaefer.bsky.social, and to the whole team that made this possible.

Happy to share the first paper from my journey at @psich.bsky.social towards X-ray connectomics, now out in @natmethods.nature.com: www.nature.com/articles/s41...

Our new paper showcasing molecular connectomics with pan-expansion microscopy is out in @natbiotech.nature.com! www.nature.com/articles/s41... This wonderful collaboration with @bewersdorflab.bsky.social was led by Ons M'Saad (now founder/CEO of Panluminate) and @allisonphysics.bsky.social. (1/5)

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

#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