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Stéphane Rigaud

@strigaud.bsky.social
777 followers 328 following 10 posts

Bio-image Analyst, Computer scientist, and plenty of other things that end in «-ist»

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Reposted by Stéphane Rigaud
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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Marco Dalla Vecchia @marcodv.bsky.social · 27/08/2026
Interested in image analysis and a service role in a dynamic and growing facility? Come and joy our image analysis team! Feel free to reach out for any questions or doubts. ista.ac.at/en/job/?titl...
ista.ac.at
Job details
Job details
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Jean-Yves Tinevez @jytinevez.bsky.social · 28/05/2026
Another outcome from the Appose processing hackathon: Cellpose simple tile processing in Fiji, with #imglib2 and #appose only. With @gaellel.bsky.social and @strigaud.bsky.social
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Jean-Yves Tinevez @jytinevez.bsky.social · 27/05/2026
The paper is now published in Current Protocols!! 🎉🥳 currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1... Some personal story below 👇 , and technical details in the linked post that featured the preprint 👉
currentprotocols.onlinelibrary.wiley.com
Automated Optimization of Bacterial Tracking Pipelines With TrackMate 8
Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, ...
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Institute of Molecular Biotechnology @imbavienna.bsky.social · 21/05/2026
We are hiring! Join the BioOptics team as a Microscopy Specialist with a focus on multiphoton intravital microscopy. Link below.👇
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BioImaging North America @bioimagingna.bsky.social · 01/05/2026
#HappyFluorescenceFriday #microscopycommunity-Monday is the last day to submit for I2KxBINA 2026! We’re inviting submissions for workshops, talks, and posters for the I2K portion of I2KxBINA 2026, happening Sept 27 to Oct 2, 2026 in Madison, WI. Deadline: May 4, 12pm PT. buff.ly/CBnw1TG
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Nicolas Rivron @nicolasrivron.bsky.social · 11/04/2026
Hi all! 👋 leeboratory.bsky.social and I are recruiting a VIP³ postdoc to join our teams and decode the genetic logic of how blastoids transit to the post-implantation stage. MolBio, genetics and computational approaches. If this sounds like you (or someone you know), we’d love to hear from you! 🚀
leeboratory.bsky.social
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Estibaliz Gómez de Mariscal, PhD @gomez-mariscal.bsky.social · 09/04/2026
🚨Are you an expert in #proteomics, #metabolomics, #singlecell #spatialomics, or #datascience?🌟 Looking for new opportunities in a growing environment surrounded by scientific excellence (👉 #NIMSB)? And, in Lisbon...🌊🏝️☀️🏄‍♀️...🍍🦐🍷...❤️ Deadline April 20th👇 www.linkedin.com/posts/nimsb_...
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 30/03/2026
🙌 Programme's out for the Image Data Community Days! Check out the amazing plenary sessions & workshops during our 5-day long online event! There's something for everyone - don't miss out. Registration is FREE & open to all⤵️ www.eurobioimaging.eu/events/image...
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Kristina Stapornwongkul @kstapornwongkul.bsky.social · 20/03/2026
We’re looking for a new team member! 🚀 Only 3 more weeks to apply to the fantastic Vienna BioCenter PhD program
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Iván Hidalgo-Cenalmor @ivanhcenalmor.bsky.social · 16/03/2026
Excited to share my first PhD project: LabConstrictor 📒🐍 Have you ever created a Jupyter notebook with all your love 🫶, only for others to be unable to install it 🥲? LabConstrictor, comes to solve this! Check out how it works in the preprint 🔗 arxiv.org/abs/2603.107... or follow this thread ⬇️
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Gaëlle Letort @gaellel.bsky.social · 10/03/2026
Thanks to #Appose hackaton with @jytinevez.bsky.social, @ctrue.bsky.social, @nkiaru.bsky.social, @msphan.bsky.social, @strigaud.bsky.social, Carlos, Thomas and Julie, DeXtrusion can be **INSTALLED** and run to detect cell extrusions directly from Fiji 🤩! Appose is amazing
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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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Nicolas Chiaruttini @nkiaru.bsky.social · 02/03/2026
Appose processing hackathon with @jytinevez.bsky.social, @ctrue.bsky.social, @gaellel.bsky.social, @strigaud.bsky.social, Carlos and Thomas . Simple POC with Java calling python through Appose to flip blocks. Promising!
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Jean-Yves Tinevez @jytinevez.bsky.social · 24/02/2026
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 👇
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Jean-Yves Tinevez @jytinevez.bsky.social · 09/02/2026
New preprint alert! We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin). www.biorxiv.org/content/10.6... 👇🧵
biorxiv.org
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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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Guillaume Jacquemet @guijacquemet.bsky.social · 21/12/2025
I will be recruiting two postdocs early next year. - One image analyst - one biologist interested in working on lymphatics! Reach out if you are interested 👍
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Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...
janelia.org
Deep Learning for Microscopy Image Analysis
Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,
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Jean-Yves Tinevez @jytinevez.bsky.social · 19/12/2025
Happy holidays from an amazing team.
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Guillaume Jacquemet @guijacquemet.bsky.social · 27/11/2025
Interested in Zebrafish brain imaging? We released a 3D printed mold that's is super helpful for us. Check it out Customizable FDM-based zebrafish embryo mold for live imaging www.biorxiv.org/content/10.1... Work by Marcela and Jaakko in the lab
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Jean-Yves Tinevez @jytinevez.bsky.social · 20/11/2025
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:
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Daniel Krentzel @danielkrentzel.bsky.social · 15/11/2025
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 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr research.pasteur.fr/fr/job/open-...
research.pasteur.fr
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 13/11/2025
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
A fluorescent embryo on black text, with the words 
Halfway to I2K: Virtual Tutorials on Image Analysis
November 17-19, 2025
Virtual Conference for beginners to developers
i2kconference.org
Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024
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Camille Berthelot @camilleberthelot.bsky.social · 14/11/2025
Still looking for our perfect doctoral candidate as part of @evomg-dn.bsky.social - come and join us to work on the evolutionary pressures that shape gene expression and disease in the uterus! Please RT (or is it RB? not sure how our lingo has changed!)
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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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Fabrice Senger @senger.bsky.social · 06/10/2025
with lots of pyclesperanto inside
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Guillaume Jacquemet @guijacquemet.bsky.social · 11/09/2025
Anyone interested in getting my job? Do not hesitate to apply, it's a pretty good gig
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Jean-Yves Tinevez @jytinevez.bsky.social · 18/09/2025
Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)? Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.
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Jean-Yves Tinevez @jytinevez.bsky.social · 10/09/2025
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). 👇
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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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Jean-Yves Tinevez @jytinevez.bsky.social · 14/07/2025
Are you developing with TrackMate? If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration. Details on the forum: forum.image.sc/t/upcoming-b...
forum.image.sc
Upcoming breaking changes in TrackMate v8
Hello TrackMate developers, This post is only important if you are developing TrackMate extensions yourself, in particular TrackMate spot detectors and segmentation modules. If not you can skip it en...
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Juliane Glaser @julianeg.bsky.social · 09/07/2025
Finally out! 🥳 Our paper showing how a transposable element (TE) insertion can cause developmental phenotypes is now published @natgenet.nature.com 🧬🦠🐁 Below is a brief description of the major findings. Check the full version of the paper for more details: www.nature.com/articles/s41588-025-02248-5
nature.com
Enhancer adoption by an LTR retrotransposon generates viral-like particles, causing developmental limb phenotypes - Nature Genetics
Activation of an LTR retrotransposon inserted upstream of the Fgf8 gene produces viral-like particles in the mouse developing limb, triggering apoptosis and causing limb malformation. This phenotype c...
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Robert Haase @haesleinhuepf.bsky.social · 10/07/2025
The @globias.bsky.social #preprint 🚨 is out, outlining global needs of BioImage Analysts, presenting how GloBIAS seeks to support and professionalize this role through education, and community building! Congrats Agustin Corbat and the entire team for pulling this through! arxiv.org/abs/2507.06407
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Ricardo Henriques @henriqueslab.bsky.social · 27/06/2025
🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab 📜: zenodo.org/records/1575... 👨‍💻: github.com/HenriquesLab...
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Guillaume Jacquemet @guijacquemet.bsky.social · 23/06/2025
Are you looking for a postdoc? I will be looking for 2-4 people after the summer to join the lab !! Do not hesitate to reach out and disseminate !!
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Jean-Yves Tinevez @jytinevez.bsky.social · 12/06/2025
We have been collaborating with Daria for years and I warmly recommend working with her.
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Stéphane Rigaud @strigaud.bsky.social · 11/06/2025
From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘
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Institut Pasteur Education @pasteuredu.bsky.social · 28/05/2025
🔬Le Cours Pasteur NEUBIAS propose une formation avancée en analyse d’images biologiques intégrant théorie, pratique et IA. Lina El Hajji, post-doc à Sorbonne Université, partage son expérience. La prochaine édition aura lieu en juin 2026 sous le nom « Advanced Bioimage Analysis with AI »
youtube.com
Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS
YouTube video by Institut Pasteur EDUCATION
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Joanna Pylvänäinen @jwpylvanainen.bsky.social · 16/05/2025
Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.
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Gaëlle Letort @gaellel.bsky.social · 16/05/2025
For day 5 of #neubiaspasteur2025 we learned to crash our GPU memory with @strigaud.bsky.social . And also to do efficient image analysis on GPU with #clesperanto
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Stéphane Rigaud @strigaud.bsky.social · 15/05/2025
4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel
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Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 13/05/2025
Thank you very much to @florianjug.bsky.social and The Column for such an amazing talk! It’s always great to hear from you! #neubiaspasteur2025
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Stéphane Rigaud @strigaud.bsky.social · 14/05/2025
3rd day of the #NEUBIASpasteur2025 with a introduction lecture to OMICS by Florian Muller, followed by a full day of #qupath by Thierry Pecot and #ome-zarr / #dask by @m-albert.bsky.social
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Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 13/05/2025
Thank you #neubiaspasteur2025 for the great energy! My slides on AI-based bioimage analysis pipelines (and SAMJ!) are now up on Zenodo. I hope you took away something new! 💡 🔗 zenodo.org/records/1539...
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Daniel Krentzel @danielkrentzel.bsky.social · 13/05/2025
Indeed, the participants formed groups and implemented @napari.org plugins from scratch for tasks like pixel classification or cell tracking. At the end, the groups did a live demo of their plugin 💻 I was super impressed! 🥳 #NEUBIASPasteur2025 📚 Course materials: github.com/Image-Analys...
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Gaëlle Letort @gaellel.bsky.social · 13/05/2025
Second day with Ilastik (@ilastik-team.bsky.social) covered by @MinhSonPhan, with @strigaud.bsky.social and @jytinevez.bsky.social as helpers. How to easily train a pixel classifier to segment focal adhesions..
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Stéphane Rigaud @strigaud.bsky.social · 13/05/2025
Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social
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Joanna Pylvänäinen @jwpylvanainen.bsky.social · 13/05/2025
Just arrived to Institute Pasteur in Paris for Neubias Image analysis course. Todays opening talk about the future of bioimage analysis by @florianjug.bsky.social - very cool week ahead! #neubiaspasteur2025
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