“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...
I guess they pair well with these socks: bsky.app/profile/davi... @webknossos.org
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?
Thanks so much for all your work organizing this great symposium series over the years!
I am already looking forward to next year’s edition.
#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
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
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
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...
