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Jean-Yves Tinevez

@jytinevez.bsky.social
2.2K followers 728 following 414 posts

Research engineer and core facility manager at the Institut Pasteur research.pasteur.fr/en/team/image-a… Everything #TrackMate #Mastodon-sc (the tool to track lineages in microscopy videos, not the social networks etc). Views are my own

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Jean-Yves Tinevez @jytinevez.bsky.social · 12h
We have a position open in our core facility in the @pasteur.fr . Please share it and / or apply! forum.image.sc/t/research-e...
forum.image.sc
Research engineer in Bioimage Analysis. Institut Pasteur, Image Analysis Hub - 2026
Dear all Below is an announcement for a permanent position as a Research Engineer in the Institut Pasteur, Paris. There is a flyer attached at the bottom. We are looking ideally for a Bioimage An...
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Guillaume Jacquemet @guijacquemet.bsky.social · 02/10/2026
Thanks to #LabConstrictor our tools are getting easier and easier to distribute and install 😀
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Institut Jacques Monod @ijmonod.bsky.social · 01/10/2026
✍️ The Bonazzi Lab published a new article 📖 @natcomms.nature.com 📃Bacterial growth under confinement requires transcriptional adaptation to resist turgor pressure build-up 🔗 www.nature.com/articles/s41...
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Johannes Soltwedel @jo-soltwedel.bsky.social · 01/10/2026
Just released the napari-clusters-plotter 0.11.0 github.com/BiAPoL/napar..., a little passion-project of mine for interactive exploration of datasets and attached features in @napari.org Two cool things to take note of 👇
github.com
GitHub - BiAPoL/napari-clusters-plotter: A napari plugin for clustering objects according to their properties.
A napari plugin for clustering objects according to their properties. - BiAPoL/napari-clusters-plotter
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UK-BIAS @uk-bias.bsky.social · 17/09/2026
Drowning in Image data? Know there’s a better way to analyse it, but don’t know where to start? 📣 UK-BIAS to the rescue! 👩‍💻🧑‍💻👨‍💻We’re the first dedicated #BioImageAnalysis service in the UK-node of @eurobioimaging.bsky.social bringing together specialists from ten UK institutions. 👩‍💻🧑‍💻👨‍💻
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Jean-Yves Tinevez @jytinevez.bsky.social · 29/09/2026
Made it to beautiful Prague for the wonderful Imaging Principles of Life conference! Looking forward to exciting discussions with great colleagues 🕺 www.czech-bioimaging.cz/activities/c...
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Daniel Krentzel @danielkrentzel.bsky.social · 28/09/2026
Super excited to see the first research article from my PhD @pasteur.fr out in @natcomms.nature.com! Here's a thread on the key results 🧵 @chzimmer.bsky.social @kelvinkho.bsky.social @curieuseny.bsky.social @awehenkel.bsky.social @ivo-boneca.bsky.social www.nature.com/articles/s41...
nature.com
Deep learning recognises antibiotic modes of action from brightfield images - Nature Communications
Authors present a deep learning model that recognises antibiotic modes of action (MoA) directly from brightfield images. Their proposed method complements traditional growth inhibition assays in the s...
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Jean-Yves Tinevez @jytinevez.bsky.social · 27/09/2026
It’s dreadful outside so please help me succeed in getting good Persian rice. Knowledgeable people: what did I miss and how to get it right next time?
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Jean-Yves Tinevez @jytinevez.bsky.social · 23/09/2026
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Jean-Yves Tinevez @jytinevez.bsky.social · 22/09/2026
I'd like to introduce a piece of work we did for the paper of @ines-ssm.bsky.social and colleagues in the lab of Chiara Zurzolo in @pasteur.fr www.nature.com/articles/s41...
nature.com
Tunneling nanotubes regulate mitochondrial homeostasis between glioblastoma and astrocytes, and between tumor cells in vivo - Nature Communications
Tunneling nanotube-like (TNT) connections allow mitochondrial exchange between tumor cells and its tumor microenvironment. Here, the authors show that TNT connections mediate bidirectional mitochondri...
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France-BioImaging @france-bioimaging.bsky.social · 21/09/2026
[CHALLENGE] Light My Cells 2 - The validation phase is now open! The FBI machine learning competition is entering a new phase. Participants now have the opportunity to test up to 5 submissions until Nov. 30, 2026. Interested? Join the competition now!👇 lightmycells2.grand-challenge.org
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Jean-Yves Tinevez @jytinevez.bsky.social · 21/09/2026
An incredible, eye opening piece
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Science Étonnante @scienceetonnante.com · 16/09/2026
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...
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SVI Huygens @svi.nl · 11/09/2026
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
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jmutterer.bsky.social @jmutterer.bsky.social · 08/09/2026
Most requested feature: applying the same viewfinder crop to several panels is now built in FigSpace.
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Delarue Research @delarueresearch.bsky.social · 06/09/2026
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
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Guillaume Jacquemet @guijacquemet.bsky.social · 04/09/2026
🚨New preprint alert 🚨 "Pancreatic cancer cells breach endothelial barriers through protrusion-driven invasion or endothelial retraction" www.biorxiv.org/content/10.6...
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Pedro Escoll @pescoll.bsky.social · 04/09/2026
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
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Pedro Escoll @pescoll.bsky.social · 04/09/2026
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? 🧵👇
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Gaëlle Letort @gaellel.bsky.social · 03/09/2026
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
journals.biologists.com
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 ...
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Jean-Yves Tinevez @jytinevez.bsky.social · 03/09/2026
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? 👇
liveimagetrackingtools.org
geff
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Thibaut Brunet @thibautbrunet.bsky.social · 02/09/2026
🚨 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 🧵⬇️
biorxiv.org
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...
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Jean-Yves Tinevez @jytinevez.bsky.social · 28/08/2026
"Det vi kaller hjem, er der hjertet vårt er"
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Jean-Yves Tinevez @jytinevez.bsky.social · 12/08/2026
Every. Single. Time.
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FocalPlane @focalplane.bsky.social · 10/08/2026
🔬🔦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 ⤵️
focalplane.biologists.com
Imaging spotlight: FidlTrack - FocalPlane
Imaging spotlight: FidlTrack - News
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 29/07/2026
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...
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ZooCELL MSCA-Doctoral Network @zoocell.bsky.social · 21/07/2026
🔬 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
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John Bogovic @bogovicj.bsky.social · 17/07/2026
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...
forum.image.sc
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...
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France-BioImaging @france-bioimaging.bsky.social · 17/07/2026
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⬇️
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 15/07/2026
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...
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Westerns & the Old West @davidlambertart.bsky.social · 14/07/2026
Happy Birthday to the great Woody Guthrie, born Woodrow Wilson Guthrie 114 years ago today
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 14/07/2026
📣 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 🧪🔬💻
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Gaëlle Letort @gaellel.bsky.social · 10/07/2026
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🤩
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Jean-Yves Tinevez @jytinevez.bsky.social · 09/07/2026
And also, for the story: www.iledefrance-meudon.cnrs.fr/fr/personne/...
iledefrance-meudon.cnrs.fr
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Jean-Yves Tinevez @jytinevez.bsky.social · 09/07/2026
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/...
insb.cnrs.fr
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Levayer Lab @levayerr.bsky.social · 09/07/2026
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...
insb.cnrs.fr
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CNRS @cnrs.fr · 09/07/2026
#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...
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GloBIAS @globias.bsky.social · 07/07/2026
🎉 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
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France-BioImaging @france-bioimaging.bsky.social · 03/07/2026
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
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Guillaume Jacquemet @guijacquemet.bsky.social · 02/07/2026
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.
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Biohub @biohub.org · 29/06/2026
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
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 29/06/2026
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
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EMBO Reports @emboreports.org · 26/06/2026
Margot Sahnine, Dorian Obino and co-workers @pasteur.fr show that N. meningitidis induces membrane protrusions with distinct #F-actin networks in epithelial and endothelial cells. The branched network in endothelia depends on Arf1. #Host-pathogen #membrane -> link.springer.com/article/10.1...
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Johannes Soltwedel @jo-soltwedel.bsky.social · 25/06/2026
Just the occasional this-thing-is-really-easy-in-ome-zarr-0.6 kind of post: Stitching in napari @napari.org with napari-stitcher (@m-albert.bsky.social) and napari-ome-zarr (@will-j-moore.bsky.social) (WIP) : (Sample data from the awesome big-stitcher tool github.com/JaneliaSciCo...)
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Jean-Yves Tinevez @jytinevez.bsky.social · 18/06/2026
My office for the day Image analysis open desk at @ijmonod.bsky.social and @pasteur.fr
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 16/06/2026
With a motivating push from @christlet.bsky.social I made a new Fiji plugin, CurveMorph. The idea was to create a tool for kymograph generation along the dynamic (bending/shaking) filament shapes (microtubules, cilia, neurites, etc). The logo was made using the plugin. github.com/UU-cellbiolo...
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Carl Quintanilla @carlquintanilla.bsky.social · 15/06/2026
Dylan, on life in your 80’s, is incredible. @nytimes.com www.nytimes.com/2026/06/14/o...
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christellelangevin.bsky.social @christellelangevin.bsky.social · 15/06/2026
📢 La formation Transparisation & Imagerie 3D d’échantillons biologiques revient ! 📍 IBPS – Paris. 📅 30 nov → 3 déc 2026 Au programme : 🔬 Méthodes de transparisation et imagerie 🧪 Mise en pratique de protocoles 🖥️ Visualisation des données et analyse d’images 3D 👉 Infos + inscriptions
https://cnrsformations.cnrs.fr/catalogue/formation/177/transparisation-et-imagerie-3d-dechantillons-biologiques-epais-et-opaques/
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Institut Pasteur | 130 years of biomedical research @pasteur.fr · 09/06/2026
🏅 Congrats to Elisa Gomez‑Perdiguero & Brice Bathellier, winners of the 2026 Vallery‑Radot Prize ! 👏 Their work advances our understanding of immune cell origins & how the brain processes sound — showcasing Pasteurian excellence. 💙 @labnf.bsky.social
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Harmit Singh Malik @harmitmalik.bsky.social · 04/06/2026
There are two types of people in the world: those who discovered Persepolis and were richer for the experience, and those that still have to. RIP Marjane Satrapi. www.lemonde.fr/en/obituarie...
lemonde.fr
Marjane Satrapi, author of 'Persepolis,' dies at 56
The French-Iranian artist and film director 'died of sadness a little over a year after the death of Mattias Ripa, her husband and the love of her life,' people close to her said.
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