Thank you!! ๐
Are FMs actually FMing? โ๏ธ๐ฌ
Thrilled to share that our paper on Foundational Models for mitochondria segmentation in EM is heading to the
@iclr-conf.bsky.social
2026 LMRL Workshop! ๐
Check out the full work here:
๐ ArXiv: arxiv.org/abs/2602.08505
๐ OpenReview: openreview.net/forum?id=Bba...
The paper that sums up what I've been working on and running for the last three years was published this week ๐
www.science.org/doi/10.1126/...
Weโre excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows.
Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis.
(1 / 10๐งต)
www.biorxiv.org/content/10.6...
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating).
A brief ๐งต (carried over from the old place)
๐จ ๐๐ ๐ฆ๐๐๐ญ๐ฌ ๐๐ ๐๐ซ๐ฎ๐ ๐๐ข๐ฌ๐๐จ๐ฏ๐๐ซ๐ฒ!
Imaging ๐ถ. ๐๐๐ข๐ก๐๐๐๐๐ข๐ (a model for ๐. ๐ก๐ข๐๐๐๐๐ข๐๐๐ ๐๐ ) + deep learning reveals known, unseen, and novel antibiotic modes of action from images alone, a leap for TB drug discovery.
โ๏ธ @awehenkel.bsky.social & coll.
๐ shorturl.at/9QPDy
#Tuberculosis #MicroSky
One week left to register to the Bioimage Analysis with AI course in Pasteur!
This June, 1 - 5.
I give a bit more details in the thread below
๐
Very excited to be advertising this project with the excellent cosupervision of Peter Mergaert through @i2bcparissaclay.bsky.social and @uniexecec.bsky.social.
This position is open to international applicants and will involve stints in both Penryn UK and Paris France. Please share!
Apply: adum.fr
Our preprint outlining a deep learning-based phenotypic screening approach for the discovery of new TB drugs is out on bioRxiv now ๐๐ฆ
๐ doi.org/10.64898/202...
Thank you @awehenkel.bsky.social @chzimmer.bsky.social @spetrella.bsky.social @curieuseny.bsky.social and everyone else not on bsky (yet)๐
"In repeating that colleges have 'gone soft,' pundits are, in some sense, telling universities what they want to hear. Schools would much rather wring their hands over vague cultural 'softness' than admit the obvious: that their revenue-maximizing logic is actively undermining educational quality."
๐จ Hiring Alert! ๐จMy lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: ๐ฆ Synthetic Biology and๐ก๏ธ Bacterial Immunity. Come do great science with us in the middle of Paris! ๐ซ๐ท๐ฅ research.pasteur.fr/en/job/postd...
Two postdoc positions opened in my team @pasteur.fr in Paris on the development of machine learning methods for single-cell multi-omics spatiotemporal data.
See the announcement for all details emploi.cnrs.fr/Offres/CDD/U...
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris ๐ซ๐ท, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! Itโs 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 ๐งต
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 ๐งต)
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris ๐ซ๐ท, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular #mycobacteria
(doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection)
@lkremer1.bsky.social
#DrugDevelopment
** Now seeking postdocs **
Join our interdisciplinary and transnational team in Wรผrzburg (Germany) or Paris (France) to drive projects in translational biology and antibiotic drug discovery.
Backgrounds in computational biology, AI, physics, or microbiology are all welcome. Please spread the word.
๐จ 1 week left to apply for the Pasteur-Paris University International PhD Program (PPU)!
Join an international community of scientists at the Institut Pasteur ๐ Dedicated support, mentorship & world-class labs included.
๐
Deadline: Oct 20, 2025
๐Program start: October 2026
๐ Apply: bit.ly/CallPPU
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...
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social ๐ SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
๐ arxiv.org/pdf/2507.01009 (1/N)
We're excited to announce the first of two prize winners in our #biologists100 #sustainable #travel blog competition. Read Leaโs experience of travelling via four trains from France to Liverpool.
www.biologists.com/stories/my-j...
Stay tuned for next weekโs post from winner two.
#Sustainability
Beautiful work from @danielkrentzel.bsky.social here!
Correlative EM-LM made easy!
Really grateful to be part of the team.
Thank you so much for having been part of the journey ๐
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data.
www.nature.com/articles/s41...
Awesome to see this out. Thank you for bringing us in the journey @em-stp.bsky.social and @martinjones.bsky.social. Keep rocking @danielkrentzel.bsky.social!
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). ๐
#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
Thank you!
Finally, I want to give a massive thanks to the amazing team behind CLEM-Reg ๐
@matous-elphick.bsky.social, @lainebioimaging.bsky.social @henriqueslab.bsky.social, @em-stp.bsky.social, @martinjones.bsky.social, MC, Chris and Cameron
