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 🧵)

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...

Zarrista: Faster Zarr for Python - zarrista

A low-level Zarr API for Python, powered from Rust by zarrs.

developmentseed.org

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...

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...

forum.image.sc

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:

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…

medium.com

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...

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...

syglass.io

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...

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...

forum.image.sc

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...

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...

nature.com

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

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

Hard X-ray imaging of biological soft tissues symposium 2025

tinyurl.com

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...

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...

forms.gle

Joel Lüthi@joelluethi.bsky.social · 12mo ago

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 🧵)

🎉 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...

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...

nature.com

#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

Safe Khan@safekhan.bsky.social · 11mo ago

Our pre-print is out! Critical point drying of brain tissue for x-ray phase contrast imaging. @apeart.bsky.social @yuxinzhang.bsky.social @jkbrmn.bsky.social @apacureanu.bsky.social @andreas-t-schaefer.bsky.social @carlesbosch.bsky.social @esrf.fr @crick.ac.uk bioarXiv: doi.org/10.1101/2025...