Author | Lightnews

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · 25d

🌟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.

1 5

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Sep 18

🌟Enhancements🌟

Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀

1 3

Reposted by Norman Rzepka

Carles Bosch @carlesbosch.bsky.social · Sep 23

#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

1 7 9

Reposted by Norman Rzepka

Joel Lüthi @joelluethi.bsky.social · Sep 18

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...

11 11

Reposted by Norman Rzepka

The BioImage Archive @bioimagearchive.bsky.social · Sep 15

🎉 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

1 8 16

Reposted by Norman Rzepka

Daniel Krentzel @danielkrentzel.bsky.social · Sep 10

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...

www.nature.com

2 20 43

Reposted by Norman Rzepka

Carles Bosch @carlesbosch.bsky.social · Sep 10

#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 · Sep 10

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...

Critical point drying of brain tissue for X-ray phase contrast imaging

X-ray phase contrast tomography is emerging as a powerful method for imaging large volumes of brain tissue at sub-cellular resolution. However, current sample preparation methods are largely inherited...

doi.org

1 4 9

Reposted by Norman Rzepka

Joel Lüthi @joelluethi.bsky.social · Aug 25

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

1 32 40

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Aug 14

🌟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...

1 1

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Jul 31

🌟Big new feature🌟

Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.

1 4

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Jul 17

🌟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 😎

1 7

Reposted by Norman Rzepka

Virginie Uhlmann @virginieuhlmann.bsky.social · Jun 3

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...

10 10

Reposted by Norman Rzepka

Rita Strack @ritastrack.bsky.social · May 13

OME-Zarr 4 life

1 3 9

Norman Rzepka @normanrz.com · May 12

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...

WEBKNOSSOS: Visualize, share and annotate your large 3D images online

Visualize, share, and annotate your large 3D images online. Upload your data and share links with colleagues. Collaboratively create skeleton and volume annotations, all from your browser. Optimized f...

webknossos.org

2

Reposted by Norman Rzepka

Perrine Paul-Gilloteaux @perrinegil.bsky.social · May 5

You can now apply until the 4th of June !!
#EMBOBioImage www.embl.org/about/info/c...

10 9

Norman Rzepka @normanrz.com · May 1

See you there!

1 1

Reposted by Norman Rzepka

Carles Bosch @carlesbosch.bsky.social · May 1

#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

1 22 62

Reposted by Norman Rzepka

Yuxin Zhang @yuxinzhang.bsky.social · May 1

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

4 21 63

Reposted by Norman Rzepka

Helene Schmidt @helenelab.bsky.social · Apr 23

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 ! …

3 9 38

Reposted by Norman Rzepka

Paolo Ronchi @paoloronchi.bsky.social · Apr 24

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! 🔬

EMBL Events @events.embl.org · Apr 10

🔬 The practical course #EMBOvEM is open for registration 👉 https://s.embl.org/vem25-01-bl

You will gain theoretical and hands-on knowledge on the three main techniques for volume EM – microtome-based serial block-face SEM, focused ion beam SEM, and array tomography.

#vEM #Microscopy

12 19

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Mar 25

🚀 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?...)

David Berson on Large scale Retinal Connectomics

youtu.be

1 5

Reposted by Norman Rzepka

Joel Lüthi @joelluethi.bsky.social · Mar 11

🚀 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

osf.io

1 22 43

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Mar 6

🚀 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.

Volume EM data challenges

Learn from leading experts as they share practical solutions for handling massive Volume EM datasets and improving collaborative workflows.

buff.ly

1 2

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Mar 3

⏳ 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.

1 1

Reposted by Norman Rzepka

WEBKNOSSOS @webknossos.org · Feb 26

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-...

2 1