Norman Rzepka
@normanrz.com
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
he/him @normanrz@mastodon.social
Reposted by Norman Rzepka
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
ome-zarr-book.readthedocs.io
November 4, 2025 at 3:33 PM
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
Reposted by Norman Rzepka
🌟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.
The proofreading tool got smarter: you can now define multiple segments around a desired split, and it will automatically pick the optimal split point.
October 9, 2025 at 12:48 PM
🌟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.
The proofreading tool got smarter: you can now define multiple segments around a desired split, and it will automatically pick the optimal split point.
Reposted by Norman Rzepka
🌟Enhancements🌟
Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀
Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀
September 18, 2025 at 12:48 PM
🌟Enhancements🌟
Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀
Shared annotations got a big upgrade: they now update live—see your collaborators’ changes as they happen. Simultaneous editing is on the horizon 👀
Reposted by Norman Rzepka
#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
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
September 23, 2025 at 10:43 AM
#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
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
Reposted by Norman Rzepka
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...
September 18, 2025 at 9:42 AM
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...
Reposted by Norman Rzepka
🎉 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
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
September 15, 2025 at 9:57 AM
🎉 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
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata
Reposted by Norman Rzepka
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...
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
September 10, 2025 at 9:37 AM
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...
www.nature.com/articles/s41...
Reposted by Norman Rzepka
#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
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
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.
@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
September 10, 2025 at 3:51 PM
#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
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
Reposted by Norman Rzepka
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 🧵)
📅 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 🧵)
August 25, 2025 at 9:07 AM
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 🧵)
📅 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 🧵)
Reposted by Norman Rzepka
🌟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...
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...
August 14, 2025 at 3:47 PM
🌟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...
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...
Reposted by Norman Rzepka
🌟Big new feature🌟
Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.
Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.
July 31, 2025 at 3:06 PM
🌟Big new feature🌟
Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.
Rotate the viewports. You can now freely rotate the orthogonal viewports. Trace your objects in the best angle.
Reposted by Norman Rzepka
🌟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 😎
Make the 3D meshes of your segments translucent. Great for revealing inner segments, such as as cell organelles. Also, translucent meshes look really cool 😎
July 17, 2025 at 2:27 PM
🌟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 😎
Make the 3D meshes of your segments translucent. Great for revealing inner segments, such as as cell organelles. Also, translucent meshes look really cool 😎
Reposted by Norman Rzepka
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...
Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
June 3, 2025 at 10:17 AM
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...
Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...
Reposted by Norman Rzepka
Reposted by Norman Rzepka
May 5, 2025 at 5:54 PM
Reposted by Norman Rzepka
#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
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
May 1, 2025 at 1:39 PM
#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
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
Reposted by Norman Rzepka
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
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
May 1, 2025 at 12:20 PM
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
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
Reposted by Norman Rzepka
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 ! …
April 23, 2025 at 7:20 AM
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 ! …
Reposted by Norman Rzepka
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! 🔬
🔬 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
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
April 24, 2025 at 12:17 PM
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! 🔬
Reposted by Norman Rzepka
🚀 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?...)
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
March 25, 2025 at 12:30 PM
🚀 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?...)
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?...)
Reposted by Norman Rzepka
🚀 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)
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
March 11, 2025 at 11:59 AM
🚀 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)
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)
Reposted by Norman Rzepka
🚀 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.
📅 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
March 6, 2025 at 11:00 AM
🚀 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.
📅 March 6 | 5-7PM CET | Online | Free
🔗 Register now: buff.ly/TZRYGcL.
Reposted by Norman Rzepka
⏳ 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.
📅 March 6, 2025 | 5-7PM CET | Free registration
🔗 Sign up: buff.ly/LaZw4aA.
March 3, 2025 at 5:01 PM
⏳ 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.
📅 March 6, 2025 | 5-7PM CET | Free registration
🔗 Sign up: buff.ly/LaZw4aA.
Reposted by Norman Rzepka
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-...
📅 March 6, 2025 | 5-7PM CET | Online www.eventbrite.de/e/volume-em-...
February 26, 2025 at 9:53 AM
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-...
📅 March 6, 2025 | 5-7PM CET | Online www.eventbrite.de/e/volume-em-...
Reposted by Norman Rzepka
@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 | https://buff.ly/42gkyv4
📅 March 6, 2025 | 5-7PM CET | Free registration | https://buff.ly/42gkyv4
February 26, 2025 at 3:27 PM
@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 | https://buff.ly/42gkyv4
📅 March 6, 2025 | 5-7PM CET | Free registration | https://buff.ly/42gkyv4