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Norman Rzepka

@normanrz.com
142 followers 96 following 13 posts

Co-Founder of scalable minds. Building WEBKNOSSOS, a tool visualizing, annotation, managing and sharing of large 3D images. Contributing to OME-Zarr. he/him @normanrz@mastodon.social

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Reposted by Norman Rzepka
Josh Moore @joshmoore.bsky.social · 25/09/2026
ICYMI: OME-Zarr 0.6 is out! 🎉 This is big, years in the making. @bogovicj.bsky.social & @jo-soltwedel.bsky.social perseverance brought transformations into this next major step on the road to OME-Zarr 1.0. 👏👏👏 Huge congratulations to the Johns — and to everyone who helped get us here! 🥳🙌
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WEBKNOSSOS @webknossos.org · 20/08/2026
Maximum Intensity Project is now available in WEBKNOSSOS 🐣 MIP renders your dataset directly in the 3D viewport, by projecting a layer through the volume and keeping the brightest value along each ray. Read the article: home.webknossos.org/blog/mip
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Joel Lüthi @joelluethi.bsky.social · 14/08/2026
We're excited to announce the 2026 OME-Zarr hackathon 🎉 📅 Date: November 2nd - November 6th 2026 📍 Location: University of Zurich, Zurich, Switzerland 💻 Virtual participation: possible for Monday afternoon, 1:00 PM CET 6:00 PM CET biovisioncenter.notion.site/2026-ome-zar... (1/6 🧵)
2025 OME-Zarr hackathon
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Kyle Barron @kylebarron.dev · 13/08/2026
Zarrista: a new, faster Python library for working with Zarr data! 1.9x to 2.7x faster than Zarr-Python for reading local data. developmentseed.org/zarrista/lat...
developmentseed.org
Zarrista: Faster Zarr for Python - zarrista
A low-level Zarr API for Python, powered from Rust by zarrs.
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John Bogovic @bogovicj.bsky.social · 17/07/2026
It's an exciting day for #Fiji users! Now read and write @zarr.dev v3 and #OMEZarr v0.5. Don't want a million tiny files in your #zarr? Shard that sucker! Read the details here forum.image.sc/t/fiji-can-r...
forum.image.sc
Fiji can read and write Zarr3 & OME-Zarr v0.5 (new N5 release!)
Updating your Fiji-Latest installation will give you the newest versions of the N5 library, enabling OME-Zarr v0.5 / Zarr v3 support with sharding! What's new? Reading zarr 3 datasets (sharded and u...
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WEBKNOSSOS @webknossos.org · 19/06/2026
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...
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WEBKNOSSOS @webknossos.org · 04/06/2026
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!
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WEBKNOSSOS @webknossos.org · 15/05/2026
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
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WEBKNOSSOS @webknossos.org · 22/04/2026
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.
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WEBKNOSSOS @webknossos.org · 15/04/2026
“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...
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WEBKNOSSOS @webknossos.org · 01/04/2026
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
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WEBKNOSSOS @webknossos.org · 26/03/2026
“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...
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WEBKNOSSOS @webknossos.org · 12/03/2026
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:
medium.com
From Beamline to Browser: Automating High-Throughput X-ray Imaging with WEBKNOSSOS at EMBL P14
At the European Molecular Biology Laboratory (EMBL) in Hamburg, the X-ray imaging team working at the P14 beamline on Petra III at DESY has…
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WEBKNOSSOS @webknossos.org · 05/03/2026
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
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WEBKNOSSOS @webknossos.org · 26/02/2026
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...
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Nathan Spencer @nathantspencer.bsky.social · 17/02/2026
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...
syglass.io
syGlass Winter 2026 Release: v2.6.0 — syGlass
Although it comes on the heels of our last feature release less than three months ago, syGlass v2.6.0 has no shortage of new content to help create new workflows and streamline old ones. Read on to se...
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Reposted by Norman Rzepka
WEBKNOSSOS @webknossos.org · 15/01/2026
Last year brought many great new features to WEBKNOSSOS ✨ Over the next days, we’ll share a series of feature highlights. Stay tuned!
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Johannes Soltwedel @jo-soltwedel.bsky.social · 09/01/2026
🚨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...
forum.image.sc
NGFF weekly dev update thread
🏁 Sprint to 0.6 🏁 Dear NGFF-community, it's been some time since the last release of a mjor version of the NGFF-specification. Since then, many of you engaged with the community which resulted in a lo...
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Nature Methods @natmethods.nature.com · 08/12/2025
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...
nature.com
Method of the Year 2025: electron microscopy-based connectomics - Nature Methods
A large network of interconnected neurons serves as the basis of brain function and of behavior. Methodological advances have enabled the reconstruction of large-scale and even whole-brain connectomes...
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Moritz Helmstaedter @mhlab.bsky.social · 08/12/2025
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...
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Dave Barry @david-j-barry.bsky.social · 04/12/2025
Maybe @normanrz.com can provide more @webknossos.org socks to help with the shoe-filling?
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Carles Bosch @carlesbosch.bsky.social · 27/11/2025
#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.
nature.com
Nondestructive X-ray tomography of brain tissue ultrastructure - Nature Methods
Optimizations of X-ray nanotomography including the choice of resin allows high-resolution imaging of mouse brain tissue, approaching the resolution of volume electron microscopy. Since it does not re...
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Adrian Wanner @adrianawanner.bsky.social · 27/11/2025
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...
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Aaron Kuan @kuanawanda.bsky.social · 27/11/2025
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)
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David Stansby @dstansby.bsky.social · 04/11/2025
Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io
ome-zarr-book.readthedocs.io
An Introduction to OME-Zarr for Big Bioimaging Data
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WEBKNOSSOS @webknossos.org · 09/10/2025
🌟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.
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WEBKNOSSOS @webknossos.org · 18/09/2025
🌟Enhancements🌟 Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀
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Carles Bosch @carlesbosch.bsky.social · 23/09/2025
#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
tinyurl.com
Hard X-ray imaging of biological soft tissues symposium 2025
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Joel Lüthi @joelluethi.bsky.social · 18/09/2025
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...
forms.gle
2025 OME-NGFF Workflows Hackathon application
The 2025 OME-NGFF Workflows Hackathon has a limited number of seats. A selected number of applicants will be invited to participate by the organizing committee from their application. The hackathon is...
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The BioImage Archive @bioimagearchive.bsky.social · 15/09/2025
🎉 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
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Daniel Krentzel @danielkrentzel.bsky.social · 10/09/2025
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...
nature.com
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
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Carles Bosch @carlesbosch.bsky.social · 10/09/2025
#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
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Joel Lüthi @joelluethi.bsky.social · 25/08/2025
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 🧵)
Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland
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WEBKNOSSOS @webknossos.org · 14/08/2025
🌟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...
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WEBKNOSSOS @webknossos.org · 31/07/2025
🌟Big new feature🌟 Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.
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WEBKNOSSOS @webknossos.org · 17/07/2025
🌟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 😎
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Virginie Uhlmann @virginieuhlmann.bsky.social · 03/06/2025
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...
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Rita Strack @ritastrack.bsky.social · 13/05/2025
OME-Zarr 4 life
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Perrine Paul-Gilloteaux @perrinegil.bsky.social · 05/05/2025
You can now apply until the 4th of June !! #EMBOBioImage www.embl.org/about/info/c...
embl.org
Advanced methods in bioimage analysis
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Carles Bosch @carlesbosch.bsky.social · 01/05/2025
#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
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Yuxin Zhang @yuxinzhang.bsky.social · 01/05/2025
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
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Helene Schmidt @helenelab.bsky.social · 23/04/2025
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 ! …
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Paolo Ronchi @paoloronchi.bsky.social · 24/04/2025
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! 🔬
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WEBKNOSSOS @webknossos.org · 25/03/2025
🚀 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?...)
youtu.be
David Berson on Large scale Retinal Connectomics
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Joel Lüthi @joelluethi.bsky.social · 11/03/2025
🚀 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)
osf.io
OSF
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WEBKNOSSOS @webknossos.org · 06/03/2025
🚀 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.
buff.ly
Volume EM data challenges
Learn from leading experts as they share practical solutions for handling massive Volume EM datasets and improving collaborative workflows.
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WEBKNOSSOS @webknossos.org · 03/03/2025
⏳ 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.
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WEBKNOSSOS @webknossos.org · 26/02/2025
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-...
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WEBKNOSSOS @webknossos.org · 26/02/2025
@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 | buff.ly/42gkyv4
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WEBKNOSSOS @webknossos.org · 24/02/2025
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: buff.ly/42gkyv4
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