Guillaume Witz
@guiwitz.bsky.social
Curious scientist and classical music enthusiast. Currently Bioimage Analyst and Data Scientist at the Data Science Lab of the University of Bern. Previously @epfl, @harvard, @biozentrum
Reposted by Guillaume Witz
Community information is here napari.org/stable/commu...
Community
There are several different ways to be a part of the napari community. From being a code or documentation contributor, to creating educational content or examples, you are welcome to help develop and ...
napari.org
October 31, 2025 at 3:17 AM
Community information is here napari.org/stable/commu...
Reposted by Guillaume Witz
Happy Halloween from the napari team!
October 31, 2025 at 2:20 PM
Happy Halloween from the napari team!
It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!
Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!
October 30, 2025 at 4:14 PM
It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!
This was a very interesting talk! If you work in a core facility you’ll find plenty of good ideas about organisation and/or be reassured that certain things, like planning workload, are difficult for everyone, even the best organized.
Hi all. This is the recording of the online seminar I gave following the kind invitation of #GLOBIAS.
I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social
research.pasteur.fr/en/team/imag...
⬇️
I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social
research.pasteur.fr/en/team/imag...
⬇️
October 13, 2025 at 2:26 PM
This was a very interesting talk! If you work in a core facility you’ll find plenty of good ideas about organisation and/or be reassured that certain things, like planning workload, are difficult for everyone, even the best organized.
Reposted by Guillaume Witz
Hi all. This is the recording of the online seminar I gave following the kind invitation of #GLOBIAS.
I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social
research.pasteur.fr/en/team/imag...
⬇️
I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social
research.pasteur.fr/en/team/imag...
⬇️
October 13, 2025 at 8:10 AM
Hi all. This is the recording of the online seminar I gave following the kind invitation of #GLOBIAS.
I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social
research.pasteur.fr/en/team/imag...
⬇️
I share what we have learned delivering #BioimageAnalysis services in the IAH core facility of the @institutpasteur.bsky.social
research.pasteur.fr/en/team/imag...
⬇️
Reposted by Guillaume Witz
Job alert!
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
forum.image.sc
October 7, 2025 at 12:39 PM
Job alert!
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?
See also on the forum:
forum.image.sc/t/research-e...
Reposted by Guillaume Witz
napari 0.6.5 is out! 🚀
Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: https://napari.org/dev/release/release_0_6_5.html
Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: https://napari.org/dev/release/release_0_6_5.html
October 2, 2025 at 11:45 AM
napari 0.6.5 is out! 🚀
Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: https://napari.org/dev/release/release_0_6_5.html
Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: https://napari.org/dev/release/release_0_6_5.html
Reposted by Guillaume Witz
BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...
Bioimage Analysis Specialist | King's College London
www.kcl.ac.uk
September 29, 2025 at 9:48 AM
BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...
Reposted by Guillaume Witz
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Reposted by Guillaume Witz
We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
September 4, 2025 at 4:07 PM
We (with @nicolasdray.bsky.social @zenlabpasteur.bsky.social) are happy to release officially FishFeats, our #napari plugin to streamline 3D smFish/RNA quantification! 🎊
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Reposted by Guillaume Witz
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
September 16, 2025 at 7:46 AM
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
Reposted by Guillaume Witz
Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030
abo.rekrytointi.com/paikat/index...
abo.rekrytointi.com/paikat/index...
University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030
abo.rekrytointi.com
September 10, 2025 at 11:28 AM
Come and work with us 5-year position available for a University Researcher in Bioimaging 1.11.2025-31.12.2030
abo.rekrytointi.com/paikat/index...
abo.rekrytointi.com/paikat/index...
Post an image from your summer that confers peace
August 31, 2025 at 7:18 PM
Post an image from your summer that confers peace
Reposted by Guillaume Witz
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...
August 21, 2025 at 8:16 PM
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...
Reposted by Guillaume Witz
“New paper out 🎉 We built a system to automate optogenetic cell control across scales. For the demo, we made the cells spell my name — because if you can’t use science to feed your ego, what’s the point? 😎🧫✨”
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...
August 22, 2025 at 2:41 PM
“New paper out 🎉 We built a system to automate optogenetic cell control across scales. For the demo, we made the cells spell my name — because if you can’t use science to feed your ego, what’s the point? 😎🧫✨”
A very good idea! I’m deeply skeptical current models can find “new physics” but this would be a good test. Surprised nobody has done this yet. Probably not in the interest of most model trainers to highlight their limits and dehype them. Clarification: I do think that LLMs can be very useful tools!
Fun idea for thought experiment from conversation at UCL AI for data intensive science conference: train LLM only on physics papers from before, say, 1920. See what it predicts for new theory. Could this be done? Might be more useful than arguing about if AI will ‘do’ physics in next 2-3 years.
June 30, 2025 at 6:19 PM
A very good idea! I’m deeply skeptical current models can find “new physics” but this would be a good test. Surprised nobody has done this yet. Probably not in the interest of most model trainers to highlight their limits and dehype them. Clarification: I do think that LLMs can be very useful tools!
You thought the publication business had reached the bottom with predatory journals, insane publication fees, data harvesting etc? No, it can dig deeper 🎉! #justpreprint
New from The Strain Team:
🎊 Springer Nature Discovers MDPI 🎊
Springer Nature has spawned a copycat journal series called "Discover" mimicking #MDPI journal titles and citation behaviours. We even made a browser game to prove it (see 🔗).
Gross! 😀 1/n
#ResearchIntegrity #SciPub #AcademicSky
🎊 Springer Nature Discovers MDPI 🎊
Springer Nature has spawned a copycat journal series called "Discover" mimicking #MDPI journal titles and citation behaviours. We even made a browser game to prove it (see 🔗).
Gross! 😀 1/n
#ResearchIntegrity #SciPub #AcademicSky
Spinger Nature Discovers MDPI – The Strain on Scientific Publishing
Home page for the paper ‘The Strain on Scientific Publishing’ by Mark A Hanson, Dan Brockington, Paolo Crosetto and Pablo Gomez Barreiro
the-strain-on-scientific-publishing.github.io
June 10, 2025 at 7:00 PM
You thought the publication business had reached the bottom with predatory journals, insane publication fees, data harvesting etc? No, it can dig deeper 🎉! #justpreprint
Reposted by Guillaume Witz
"a fascinating case study on the limits of AI in biology and the harms of current publishing incentives" rachel.fast.ai/posts/2025-0...
Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored
an AI researcher going back to school for immunology
rachel.fast.ai
June 4, 2025 at 3:53 PM
"a fascinating case study on the limits of AI in biology and the harms of current publishing incentives" rachel.fast.ai/posts/2025-0...
Reposted by Guillaume Witz
New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
May 12, 2025 at 11:16 AM
New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
Reposted by Guillaume Witz
To look into: a Python alternative to ZEMAX... github.com/HarrisonKram...
GitHub - HarrisonKramer/optiland: Comprehensive optical design, optimization, and analysis in Python, including GPU-accelerated and differentiable ray tracing via PyTorch.
Comprehensive optical design, optimization, and analysis in Python, including GPU-accelerated and differentiable ray tracing via PyTorch. - HarrisonKramer/optiland
github.com
May 2, 2025 at 10:56 PM
To look into: a Python alternative to ZEMAX... github.com/HarrisonKram...
Reposted by Guillaume Witz
And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵
a woman in a hat is crying and says " i 've traveled a good many miles to get here "
Alt: Charlotte from the Sanditon TV series, emotionally exclaiming, "I've traveled a good many miles to get here!"
media.tenor.com
May 1, 2025 at 2:08 PM
And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵
Reposted by Guillaume Witz
CellPhePy is now available 🎉🎉🎉 in the journal of #microscopy. A python version for #CellPhe.
See doi.org/10.1111/jmi....
Thanks @ukri.org and @wellcometrust.bsky.social for funding
@globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social
See doi.org/10.1111/jmi....
Thanks @ukri.org and @wellcometrust.bsky.social for funding
@globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social
CellPhePy: A python implementation of the CellPhe toolkit for automated cell phenotyping from microscopy time‐lapse videos
We previously developed the CellPhe toolkit, an open-source R package for automated cell phenotyping from ptychography time-lapse videos. To align with the growing adoption of python-based image anal...
doi.org
April 28, 2025 at 12:50 PM
CellPhePy is now available 🎉🎉🎉 in the journal of #microscopy. A python version for #CellPhe.
See doi.org/10.1111/jmi....
Thanks @ukri.org and @wellcometrust.bsky.social for funding
@globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social
See doi.org/10.1111/jmi....
Thanks @ukri.org and @wellcometrust.bsky.social for funding
@globias.bsky.social @globalbioimaging.bsky.social @eurobioimaging.bsky.social @bioimaginguk.bsky.social
Reposted by Guillaume Witz
🚀 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 Guillaume Witz
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 23, 2025 at 2:06 PM
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Guillaume Witz
Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.
February 11, 2025 at 6:15 AM
Announcing PathoSAM, our foundation model for nucleus segmentation in histopathology. PathoSAM supports interactive and automatic nucleus segmentation (instance and semantic). See segmentation on a WSI from openslide, check out arxiv.org/abs/2502.00408 or read on for details.