Le 02 octobre à l'occasion de la Fête de la Science, j'interviendrai à l'Isart Digital pour parler de "sciences & jeux vidéo" ! Ca aura lieu à 18h. J'espère vous y voir nombreuses et nombreux ! Il faut s'inscrire par ici: www.eventbrite.fr/e/isart-digi...

Webinar on Sept. 29 at 9:30 and 18:00 CEST about the new Cellpose 4 (SAM) implementation and Spot Detection in Huygens: svi.nl/webinarinvit... Simple installation - Improved segmentation - Additional Object Filtering - Direct access to Statistics and Data Plotting. #FluoresenceFriday

Most requested feature: applying the same viewfinder crop to several panels is now built in FigSpace.

Our collaborative paper, with Daria Bonazzi and @dumenillab.bsky.social is finally out in Nat Comms! Using microfluidic confiners, amazing Laure Leblanc found that confined growth of E. coli uncouples growth and division, as well as pressure and biomass production. tinyurl.com/4zdwrp39

🚨New preprint alert 🚨 "Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction" www.biorxiv.org/content/10.6...

Infected macrophages are heterogeneous and bulk metabolomics hides this diversity. Thus, we developed SpatialMetProfiler: MALDI mass-spectrometry imaging + microscopy + image registration → linking the metabolic spectrum of each macrophage to its infection status. We profiled >11,000 single cells

New preprint in the lab! "Single-cell metabolomics reveals infection-specific metabolic reprogramming of human macrophages". Led by Paula Martínez, with @cbuch.bsky.social , Sandrine Aros and @jytinevez.bsky.social How does Legionella pneumophila reshape host metabolism at the single-cell scale? 🧵👇

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w ago

Single-cell metabolomics reveals infection-specific metabolic reprogramming of human macrophages https://www.biorxiv.org/content/10.64898/2026.09.03.749052v1

The final version of the paper presenting our tool EpiCure is now online: journals.biologists.com/dev/article/... !! Thanks again to all collaborators in this project

EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation

Summary: EpiCure is a napari plugin designed to optimise epithelia segmentation and tracking curation through automatic errors detection and ergonomic correction while being easily interoperable with ...

journals.biologists.com

Gaëlle Letort@gaellel.bsky.social · 6mo ago

I'm happy to present our new tool, EpiCure, a napari plugin to ease correction of segmentation and tracking of epithelia movies, developed in @devstempasteur.bsky.social

New version of #Mastodon-SC, the Fiji plugin to track and lineage cells in gigantic movies! What is Mastodon? 👉 in the preprint linked to the quote post What's new? 👇

@paveltomancak.bsky.social · 9mo ago

#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you. www.biorxiv.org/content/10.6...

🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️

Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals

Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...

biorxiv.org

"Det vi kaller hjem, er der hjertet vårt er"

Every. Single. Time.

🔬🔦In our latest Imaging spotlight, Pierre Parutto and Edward Avezov @avezovlab.bsky.social explain single-particle tracking (SPT) and present FidlTrack, their new method for benchmarking and optimising SPT. Check out their advice for optimising your SPT experiments ⤵️

Imaging spotlight: FidlTrack - FocalPlane

Imaging spotlight: FidlTrack - News

focalplane.biologists.com

Join us tomorrow! Marvin Albert (ETH Zurich) will present 𝗺𝘂𝗹𝘁𝗶𝘃𝗶𝗲𝘄-𝘀𝘁𝗶𝘁𝗰𝗵𝗲𝗿, a Python package for scalable stitching/alignment/fusion of multi-view, tiled & multimodal image acquisitions at the #NGFFCafe. 🕚️ 11 am CEST 📍 Online Register⤵️ us02web.zoom.us/meeting/regi...

🔬 Meet Michalis Averof, ZooCELL PI at IGFL @michalis-averof.bsky.social What sparked his interest in EvoDevo? What keeps him curious after all these years? And what does he hope to discover next? 🧵 Read on to get to know Michalis through his own words. #ZooCELL#EvoDevo#genomics#IGFL#MSCA

It's an exciting day for #Fiji users! Now read and write @zarr.dev v3 and #OMEZarr v0.5. Don't want a million tiny files in your #zarr? Shard that sucker! Read the details here forum.image.sc/t/fiji-can-r...

Fiji can read and write Zarr3 & OME-Zarr v0.5 (new N5 release!)

Updating your Fiji-Latest installation will give you the newest versions of the N5 library, enabling OME-Zarr v0.5 / Zarr v3 support with sharding! What's new? Reading zarr 3 datasets (sharded and u...

forum.image.sc

FBI 2026 Tech Transfer results👀 FBI aims to provide the community with access to innovative technologies. To do this, developments from R&D teams need to be transferred to facilities. Since 2021, FBI has supported this process through dedicated calls. Discover the laureates⬇️

At the next #NGFFCafe, Marvin Albert (ETH Zurich) will present 𝗺𝘂𝗹𝘁𝗶𝘃𝗶𝗲𝘄-𝘀𝘁𝗶𝘁𝗰𝗵𝗲𝗿, a Python package for scalable stitching/alignment/fusion of multi-view, tiled & multimodal image acquisitions. Join us! 🗓️ Thursday, July 30 🕚️ 11 am CEST 📍 Online Register⤵️ us02web.zoom.us/meeting/regi...

Happy Birthday to the great Woody Guthrie, born Woodrow Wilson Guthrie 114 years ago today

📣 Tracking cells through time – including divisions – is a core problem in live-imaging microscopy. We built HOCT, an edge-centric Transformer that hits state-of-the-art on the Cell Tracking Challenge without a pretrained image encoder. Work led by @jookuma.bsky.social arxiv.org/abs/2607.11754 🧪🔬💻

I'm super happy to be awarded the cnrs cristal medal dedicated to research support staff🥳🏅!! Even more delighted by the reactions to the announcement, huge thanks to all, I m lucky to work within such a nice community🫶!! Especially the welcoming amazing subgroup of core facility bioimage analysts🤩

CNRS@cnrs.fr · 2mo ago

#TalentsCNRS 🏅 Le CNRS décerne ses médailles de cristal et cristal collectif 2026, récompensant des femmes et des hommes ayant contribué à l’avancée des savoirs et à l’excellence de la recherche française. Félicitations 👏 👉 www.cnrs.fr/fr/actualite... 👉 www.cnrs.fr/fr/actualite...

And also, for the story: www.iledefrance-meudon.cnrs.fr/fr/personne/...

Jean-Yves Tinevez@jytinevez.bsky.social · 2mo ago

Congratulations to superstar and awesome colleague Gaëlle Letort @gaellel.bsky.social, bioimage analyst extraordinaire for THE CRYSTAL MEDAL OF THE CNRS 2026!!! 🥳🎉🕺🦄🥳 We work with amazing people www.insb.cnrs.fr/fr/personne/...

Congratulations to superstar and awesome colleague Gaëlle Letort @gaellel.bsky.social, bioimage analyst extraordinaire for THE CRYSTAL MEDAL OF THE CNRS 2026!!! 🥳🎉🕺🦄🥳 We work with amazing people www.insb.cnrs.fr/fr/personne/...

Congratulation @gaellel.bsky.social for the crystal medal ! So well deserved, you've been transformative for the democratisation of image analysis and deep learning. www.insb.cnrs.fr/fr/talents/c...

CNRS@cnrs.fr · 2mo ago

#TalentsCNRS 🏅 Le CNRS décerne ses médailles de cristal et cristal collectif 2026, récompensant des femmes et des hommes ayant contribué à l’avancée des savoirs et à l’excellence de la recherche française. Félicitations 👏 👉 www.cnrs.fr/fr/actualite... 👉 www.cnrs.fr/fr/actualite...

#TalentsCNRS 🏅 Le CNRS décerne ses médailles de cristal et cristal collectif 2026, récompensant des femmes et des hommes ayant contribué à l’avancée des savoirs et à l’excellence de la recherche française. Félicitations 👏 👉 www.cnrs.fr/fr/actualite... 👉 www.cnrs.fr/fr/actualite...

🎉 Registration is open for the GloBIAS 2026 BioImage Analysts' Workshop! 📍 Dortmund, Germany | 🗓️ 10–13 Nov 2026 Join the BIA community to explore AI, image analysis, training, and the future of BioImage Analysis 👉 www.globias.org/activities/g... #BioImageAnalysis #AI #GloBIAS

SPAOM 2026 is approaching! 🔬 Abstract submission deadline for Selected Talks has been extended to July 8. Join the 10th edition in Vic, near Barcelona, from Oct. 6–9, for a special Workshops Edition dedicated to advanced optical microscopy. 👉 spaom2026.org

No live nuclear label? No problem. Use artificial labelling to infer DAPI-like nuclei, then use #NucleiSky to align your data. For instance, to connect live imaging data to fixed Cell Painting images.

Guillaume Jacquemet@guijacquemet.bsky.social · 3mo ago

Delighted to share our latest preprint "NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations" www.biorxiv.org/content/10.6... Code and App: github.com/CellMigratio...

How do you track thousands of cells in complex systems, in 3D & over time? We are launching a Kaggle challenge to push the frontier of AI-powered cell tracking, building on advances like Ultrack & the DaXi lightsheet microscope from the @loicaroyer.bsky.social lab. bit.ly/4bfdzWE

1/ 🧬🔬 How does one cell become an entire animal? We can now film it in 3D 🐟, but turning those movies into accurate cell tracks is brutally hard. Enter our new #Kaggle challenge: $60K prize pool, to help crack 3D+time cell tracking at scale! 🧵👇 www.kaggle.com/competitions... @biohub.org