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Guillaume Witz

@guiwitz.bsky.social
597 followers 277 following 53 posts

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

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Reposted by Guillaume Witz
napari @napari.org · 26/08/2026
🚨🚨🚨 napari 0.9.0 is out! 🚨🚨🚨 This is a huge release for us and for our community, with over 30 people contributing new features, improvements, and bug fixes in the 6 weeks since 0.8.0! Release notes here: napari.org/stable/relea... and some highlights in the thread below! 👇
napari.org
napari 0.9.0
Tue, Aug 25, 2026 We’re happy to announce the release of napari 0.9.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing l...
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Guillaume Witz @guiwitz.bsky.social · 12/08/2026
Eclipseset?
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Reposted by Guillaume Witz
Joel Lüthi @joelluethi.bsky.social · 24/07/2026
Do you want to learn more about OME-Zarr viewers, where they stand today and what's being developed at the moment? On August 24th at 4pm CEST, we will hear about 3 different OME-Zarr viewers and user stories for each. www.biovisioncenter.uzh.ch/en/events/Up... (1/5 🧵)
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup August 2026
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SciPy Conference 2026 @scipyconf.bsky.social · 03/06/2026
🔬 Tutorial Spotlight: Build custom image analysis tools without starting from scratch. Tim shows you napari's power for microscopy, satellite data, and everything between 🛰️ Extend, visualize, annotate like a pro! #SciPy2026 🔗 scipy2026.scipy.org
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Guillaume Witz @guiwitz.bsky.social · 02/06/2026
Very interesting job with very nice people! What’s more to ask?
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Guillaume Witz @guiwitz.bsky.social · 02/04/2026
I’m trying to figure out (like everyone else) how to reasonably use LLMs both for my work and teaching. This is fantastically written and clearly articulates a lot of ideas and concerns I had vaguely in mind. I’m considering suggesting this as a read to participants in my scientific coding courses.
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Reposted by Guillaume Witz
napari @napari.org · 11/03/2026
🔬 Registration is open for our pilot Introduction to napari Workshop! napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast. #napari #Python #ImageAnalysis #DataScience #OpenSource
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Jean-Yves Tinevez @jytinevez.bsky.social · 09/03/2026
Let's get ready for a full month of training in image analysis in @pasteur.fr , this summer! Are you interested in learning how to do bioimage analysis? For light microscopy? for cryo-EM? And for cellular cryo-EM? Stay tuned, Pasteur offers access to THREE courses, this June. 👇🎓
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Guillaume Witz @guiwitz.bsky.social · 21/01/2026
Sounds like this could be a very cool (in all meanings of the word 😅) postdoc!
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Reposted by Guillaume Witz
Guillaume Jacquemet @guijacquemet.bsky.social · 15/01/2026
🚨 Job Alert! 🚨 We have an opening at our Microscopy Core Facility in Turku 🇫🇮. If you love imaging 🔬 and helping scientists succeed, we want you! 👇 abo.rekrytointi.com/paikat/index... #Microscopy #ScienceJobs #CoreFacility #Imaging @turkubioscience.bsky.social
abo.rekrytointi.com
Laboratory Engineer (Senior), in Advanced Imaging, 1.5.2026-31.12.2028
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Dave Barry @david-j-barry.bsky.social · 15/01/2026
Time is running out to apply for this year's @royalmicrosoc.bsky.social Intro to Image Analysis course in Cardiff - deadline is tomorrow! Spread the word!
media.tenor.com
two men are sitting in front of a large clock that shows a time of 11:55
ALT: two men are sitting in front of a large clock that shows a time of 11:55
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Lucien Hinderling @lhinderling.bsky.social · 18/12/2025
Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff: Paper: doi.org/10.1242/jcs.... Code: github.com/pertzlab/arc... Plugin: github.com/pertzlab/arc...
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Jacob Tomlinson @jacobtomlinson.dev · 18/11/2025
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing. I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow. jacobtomlinson.dev/posts/2025/p...
jacobtomlinson.dev
Python package managers: uv vs pixi?
When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I don’t hear much ab...
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Joel Lüthi @joelluethi.bsky.social · 17/11/2025
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵
Hackathon participants group picture
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Yohsuke T. Fukai @fukaity.bsky.social · 31/10/2025
Community information is here napari.org/stable/commu...
napari.org
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 ...
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Reposted by Guillaume Witz
napari @napari.org · 31/10/2025
Happy Halloween from the napari team!
Special edition of the napari logo for Halloween. The island is white and looks like a ghost, and there are spiderwebs.
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Guillaume Witz @guiwitz.bsky.social · 30/10/2025
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!
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Guillaume Witz @guiwitz.bsky.social · 13/10/2025
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.
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Reposted by Guillaume Witz
Jean-Yves Tinevez @jytinevez.bsky.social · 13/10/2025
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... ⬇️
research.pasteur.fr
Image Analysis Hub - Research
The Image Analysis Hub is an open-access / equal-access core facility committed to sharing bioimage analysis services expertise with the scientific community. What we do The IAH works by collaborating...
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Jean-Yves Tinevez @jytinevez.bsky.social · 07/10/2025
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...
forum.image.sc
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...
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Reposted by Guillaume Witz
napari @napari.fosstodon.org.ap.brid.gy · 02/10/2025
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: napari.org/dev/release/release_0_6_…
Image depicting the napari viewer in grid mode with scale bars and color bars enabled
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Siân Culley @superresolusian.bsky.social · 29/09/2025
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-...
kcl.ac.uk
Bioimage Analysis Specialist | King's College London
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Ignacio Arganda-Carreras @iarganda.eurosky.social · 30/09/2025
📣 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...
cvpd.github.io
📢 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...
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Gaëlle Letort @gaellel.bsky.social · 04/09/2025
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/
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Joel Lüthi @joelluethi.bsky.social · 16/09/2025
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)
Flyer for the Open Bioimaging Practices Meetups.
1. September 24th at 4pm: Guest presentation by Charlotte Soneson & Silvia Barbiero
2. October 28th at 4pm: Guest presentation by Marvin Albert
3. November 26th at 4pm: Guest presentations by Giliane Rochat & Flurin Sturzenegger
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Guillaume Jacquemet @guijacquemet.bsky.social · 10/09/2025
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
University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030
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Guillaume Witz @guiwitz.bsky.social · 31/08/2025
Post an image from your summer that confers peace
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Lucien Hinderling @lhinderling.bsky.social · 21/08/2025
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...
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Olivier Pertz @olivierpertz.bsky.social · 22/08/2025
“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? 😎🧫✨”
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Guillaume Witz @guiwitz.bsky.social · 30/06/2025
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!
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Guillaume Witz @guiwitz.bsky.social · 10/06/2025
You thought the publication business had reached the bottom with predatory journals, insane publication fees, data harvesting etc? No, it can dig deeper 🎉! #justpreprint
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Reposted by Guillaume Witz
Richard Sever @richardsever.bsky.social · 04/06/2025
"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.fast.ai
Rachel Thomas, PhD - Deep learning gets the glory, deep fact checking gets ignored
an AI researcher going back to school for immunology
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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/05/2025
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🔺:
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Adam Glaser @adamkglaser.bsky.social · 02/05/2025
To look into: a Python alternative to ZEMAX... github.com/HarrisonKram...
github.com
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
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napari @napari.org · 01/05/2025
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: 🧵
media.tenor.com
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!"
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Peter O'Toole @yorkbioimaging.bsky.social · 28/04/2025
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
doi.org
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...
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Joel Lüthi @joelluethi.bsky.social · 11/03/2025
🚀 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.io
OSF
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Lucien Hinderling @lhinderling.bsky.social · 23/02/2025
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...
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Constantin Pape @cppape.bsky.social · 11/02/2025
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.
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Robert Haase @haesleinhuepf.bsky.social · 21/01/2025
I recently visited TU Dresden for two guest lectures about Prompt Engineering, RAG, Agents and Multi-Modal #LLMs. thanks to Simon Razniewski @scadsai.bsky.social for having me! My slides are available #openaccess 💻🤖🔓 zenodo.org/records/1469...
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Guillaume Witz @guiwitz.bsky.social · 18/01/2025
Very useful thread on how to efficiently use LLMs to write. As usual, reality is not a binary choice between “let the model write your entire paper” and “never ever use a model”.
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Erik van Nimwegen @erikvannimwegen.bsky.social · 15/01/2025
What do bacterial cells do when they run out of nutrients? Although most bacterial studies focus on cells in exponentially growing states, in the wild bacteria likely spend most of their time slowly starving to death. 1/n www.biorxiv.org/content/10.1...
biorxiv.org
E. coli prepares for starvation by dramatically remodeling its proteome in the first hours after loss of nutrients
It is widely believed that due to nutrient limitations in natural environments, bacteria spend most of their life in non-growing states. However, very little is known about how bacteria change their p...
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Gabriel Krens @gkrens.bsky.social · 15/01/2025
The Image & Optics Facility @ Institute of Science and Technology Austria is expanding it’s image analysis services and has a vacant position for a service oriented *Image Analysis Specialist* with a strong interest for data infrastructure organization🔬🧑‍💻📈 - sharing is much appreciated
ista.ac.at
Job details
Job details
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Philip Ball @philipcball.bsky.social · 14/01/2025
Has AI really learnt "the language of life"? If we compare "sequence prediction" AI with actual research on genomic mechanisms, we get a sense of what "understanding" does and doesn't mean.
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Guillaume Witz @guiwitz.bsky.social · 07/01/2025
Interesting discussion and an important point as I think these two aspects are often conflated: scientists are not software engineers and are not supposed to create perfect code. But it should be usable! Packaging can be daunting, so ask a researcher software engineer at your university for help!
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/12/2024
Really a no brainer. Another thing one can do: when asked to review a paper that is not pre-printed, tell editor you only review preprinted papers and suggest authors submit a preprint first.
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Erik van Nimwegen @erikvannimwegen.bsky.social · 17/12/2024
Forget the click-baity title. This almost 4 hour long collection of short musical fragments with fun commentary is a wonderful guide through the last 400 years of Western music. Bet you'll discover something wonderful you hadn't known about. www.youtube.com/watch?v=qEzm...
youtube.com
Every Major Composer's Greatest Melody (in my opinion)
YouTube video by Caleb Hu
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Guillaume Witz @guiwitz.bsky.social · 17/12/2024
After science, time for music! In honour of Beethoven's baptism day (it's unclear when exactly he was born) a short thread in the spirit of @loveinner.bsky.social of some of my favourite recordings (and I don't pretend to any absolute truth!)
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Josiah Passmore @jpassmore.bsky.social · 17/12/2024
For more details, check out the preprint www.biorxiv.org/content/10.1... - or ask anything here! (+here's a bonus movie that didn't quite make the cut) 🌀
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Guillaume Witz @guiwitz.bsky.social · 16/12/2024
I just made a long overdue update to microfilm guiwitz.github.io/microfilm now 0.3.0! Beyond adaptations to recent Python and Matplotlib, I added support for the great cmap library cmap-docs.readthedocs.io by @talleylambert.bsky.social for easy access to the best (and most psychedelic) colormaps!1/2
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