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...
OME-Zarr 4 life
You can try it on webknossos.org and if you want to set it up on your own, check out docs.webknossos.org/webknossos/o...
You can now apply until the 4th of June !!
#EMBOBioImage www.embl.org/about/info/c...
See you there!
#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
