Stéphane Rigaud
@strigaud.bsky.social
Bio-image Analyst, Computer scientist, and plenty of other things that end in «-ist» @pasteur.fr
Reposted by Stéphane Rigaud
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:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
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:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Stéphane Rigaud
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/fr/job/open-...
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...
research.pasteur.fr
November 15, 2025 at 9:22 AM
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/fr/job/open-...
Reposted by Stéphane Rigaud
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)
November 13, 2025 at 2:32 PM
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)
Reposted by Stéphane Rigaud
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!)
Please RT (or is it RB? not sure how our lingo has changed!)
🚨 15 days left to apply!
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu
#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
Be part of EvoMG-DN and advance your PhD career in evolutionary genomics.
👉 www.evomg-dn.eu
#PhD #DoctoralTraining #ResearchCareers #LifeSciences #BiomedicalResearch #Genomics #EvolutionaryBiology #MSCA #HorizonEurope #EUResearch #ResearchOpportunities #PhDPositions
November 14, 2025 at 10:22 AM
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!)
Please RT (or is it RB? not sure how our lingo has changed!)
Reposted by Stéphane Rigaud
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...
⬇️
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...
⬇️
October 13, 2025 at 8:10 AM
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...
⬇️
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...
⬇️
Reposted by Stéphane Rigaud
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...
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...
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...
forum.image.sc
October 7, 2025 at 12:39 PM
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...
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...
Reposted by Stéphane Rigaud
with lots of pyclesperanto inside
Packing-Driven Mechanotransduction: local crowding overrides adhesion and stiffness cues for YAP Activation in Cellular Collectives https://www.biorxiv.org/content/10.1101/2025.10.03.680214v1
October 6, 2025 at 9:46 AM
with lots of pyclesperanto inside
Reposted by Stéphane Rigaud
Anyone interested in getting my job?
Do not hesitate to apply, it's a pretty good gig
Do not hesitate to apply, it's a pretty good gig
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/paikat/index...
University Researcher in Bioimaging / Universitetsforskare med inriktning bioimaging, 1.11.2025-31.12.2030
abo.rekrytointi.com
September 11, 2025 at 10:37 AM
Anyone interested in getting my job?
Do not hesitate to apply, it's a pretty good gig
Do not hesitate to apply, it's a pretty good gig
Reposted by Stéphane Rigaud
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.
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.
Next #GloBIAS seminar is coming up: join us on 22nd of September, 4 pm CEST to hear from Jean-Yves Tinevez about: The scientific added value of a core-facility dedicated to Bioimage Analysis services. Want to register? -> www.globias.org/activities/b...
September 18, 2025 at 9:26 AM
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.
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.
Reposted by Stéphane Rigaud
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). 👇
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). 👇
September 10, 2025 at 12:50 PM
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). 👇
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). 👇
Reposted by Stéphane Rigaud
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/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
September 4, 2025 at 4:07 PM
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/
Available here: github.com/gletort/Fish... user documentation: gletort.github.io/FishFeats/
Reposted by Stéphane Rigaud
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...
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...
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...
forum.image.sc
July 14, 2025 at 8:56 PM
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...
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...
Reposted by Stéphane Rigaud
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
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
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...
www.nature.com
July 9, 2025 at 10:05 AM
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
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
Reposted by Stéphane Rigaud
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
arxiv.org/abs/2507.06407
July 10, 2025 at 1:19 PM
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
arxiv.org/abs/2507.06407
Reposted by Stéphane Rigaud
🧑🔬📰🚀 #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...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
June 27, 2025 at 12:34 PM
🧑🔬📰🚀 #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...
📜: zenodo.org/records/1575...
👨💻: github.com/HenriquesLab...
Reposted by Stéphane Rigaud
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 !!
I will be looking for 2-4 people after the summer to join the lab !!
Do not hesitate to reach out and disseminate !!
June 23, 2025 at 2:29 PM
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 !!
I will be looking for 2-4 people after the summer to join the lab !!
Do not hesitate to reach out and disseminate !!
Reposted by Stéphane Rigaud
We have been collaborating with Daria for years and I warmly recommend working with her.
💼 Postdoctoral Researcher Mechanobiology of Meningococcal Infection
📅 November 1st
📍 Daria Bonazzi's Lab
Apply before June 23st
🔗 www.ijm.fr/post-doc-m-f...
📅 November 1st
📍 Daria Bonazzi's Lab
Apply before June 23st
🔗 www.ijm.fr/post-doc-m-f...
June 12, 2025 at 10:06 AM
We have been collaborating with Daria for years and I warmly recommend working with her.
From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘
Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
🎉✌️
journals.plos.org/ploscompbiol...
So happy about this paper and how the work turned out.
A small thread 👇
#bioimageanalysis #corefacility
F-BIAS: Towards a distributed national core facility for bioimage analysis †
Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...
journals.plos.org
June 11, 2025 at 8:42 AM
From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘
Reposted by Stéphane Rigaud
🔬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 »
Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS
YouTube video by Institut Pasteur EDUCATION
youtube.com
May 28, 2025 at 10:01 AM
🔬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 »
Reposted by Stéphane Rigaud
Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.
May 16, 2025 at 12:06 PM
Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.
Reposted by Stéphane Rigaud
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
May 16, 2025 at 10:03 AM
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
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
May 15, 2025 at 12:33 PM
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
Reposted by Stéphane Rigaud
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
May 13, 2025 at 12:10 PM
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
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
May 14, 2025 at 10:22 AM
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
Reposted by Stéphane Rigaud
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...
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...
May 13, 2025 at 12:36 PM
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...
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...