Stéphane Rigaud
@strigaud.bsky.social
📤 752
📥 309
📝 9
Bio-image Analyst, Computer scientist, and plenty of other things that end in «-ist»
@pasteur.fr
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
6 days ago
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...
⬇️
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
12 days ago
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...
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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...
https://forum.image.sc/t/research-engineer-in-bioimage-analysis-for-the-researchers-of-the-inidex-formula/116903
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reposted by
Stéphane Rigaud
Fabrice Senger
13 days ago
with lots of pyclesperanto inside
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reposted by
Stéphane Rigaud
Guillaume Jacquemet
about 1 month ago
Anyone interested in getting my job? Do not hesitate to apply, it's a pretty good gig
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 1 month ago
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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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 1 month ago
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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reposted by
Stéphane Rigaud
Gaëlle Letort
about 1 month ago
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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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
3 months ago
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...
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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...
https://forum.image.sc/t/upcoming-breaking-changes-in-trackmate-v8/114687
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reposted by
Stéphane Rigaud
Juliane Glaser
3 months ago
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
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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...
https://www.nature.com/articles/s41588-025-02248-5
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reposted by
Stéphane Rigaud
Robert Haase
3 months ago
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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reposted by
Stéphane Rigaud
Ricardo Henriques
4 months ago
🧑🔬📰🚀
#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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reposted by
Stéphane Rigaud
Guillaume Jacquemet
4 months ago
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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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
4 months ago
We have been collaborating with Daria for years and I warmly recommend working with her.
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From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘
add a skeleton here at some point
4 months ago
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reposted by
Stéphane Rigaud
Institut Pasteur Education
5 months ago
🔬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 »
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Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS
YouTube video by Institut Pasteur EDUCATION
https://youtube.com/shorts/3hOTyXfjnrA?feature=share
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reposted by
Stéphane Rigaud
Joanna Pylvänäinen
5 months ago
Final session where we finish our pipeline using
#celltrackscolab
with Laura Xénard.
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reposted by
Stéphane Rigaud
Gaëlle Letort
5 months ago
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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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
5 months ago
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reposted by
Stéphane Rigaud
Caterina Fuster Barceló
5 months ago
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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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
5 months ago
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reposted by
Stéphane Rigaud
Caterina Fuster Barceló
5 months ago
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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reposted by
Stéphane Rigaud
Daniel Krentzel
5 months ago
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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reposted by
Stéphane Rigaud
Gaëlle Letort
5 months ago
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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Kick-starting the
#neubiaspasteur2025
#BioImageAnalysis
courses at
@pasteur.fr
and
@pasteuredu.bsky.social
5 months ago
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reposted by
Stéphane Rigaud
Joanna Pylvänäinen
5 months ago
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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Stéphane Rigaud
Stefania Marcotti
6 months ago
Applications closing on May 6th 2025 for the “Train the Trainers in Bioimage Analysis” workshop, taking place on June 13th 2025 in London! Reach out should you have any questions 👩💻🔬🧫
franciscrickinstitute.github.io/Train_the_tr...
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reposted by
Stéphane Rigaud
GloBIAS
6 months ago
GloBIAS
#BioimageAnalysis
#Conference
2025 – we have opened the registration for our 2025 in-person event. Please check the webpage
www.globias.org/activities/b...
for more information and the link to the registration form.
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
6 months ago
Tomorrow (midnight) is the last day to apply! I am biased but I swear it will be a great course. For instance we were just fine tuning the last 2 days of the ECI track with Laura and
@jwpylvanainen.bsky.social
-
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reposted by
Stéphane Rigaud
7 months ago
Great to see that many noise2void inspired denoising algorithms have been ported to
@pytorch.org
! Kudos to
@florianjug.bsky.social
and many others ...
github.com/CAREamics/ca...
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GitHub - CAREamics/careamics: A deep-learning library for denoising images using Noise2Void and friends (CARE, PN2V, HDN etc.), with a focus on user-experience and documentation.)
A deep-learning library for denoising images using Noise2Void and friends (CARE, PN2V, HDN etc.), with a focus on user-experience and documentation.) - CAREamics/careamics
https://github.com/CAREamics/careamics
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months ago
Team is teaching machine learning at the
@pslqlife.bsky.social
course on cellular dynamics. Lecture from
@gaellel.bsky.social
, practical from Minh-Son with
@strigaud.bsky.social
and me as helpers
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months ago
Preprint (update) alert! F-BIAS: Towards a distributed national core facility for Bioimage Analysis. (
arxiv.org/abs/2409.15009
) 0/ In this paper we discuss our experience in federating ourselves and delivering bioimage analysis services to the scientific community in France. 👇 a short thread
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F-BIAS: Towards a distributed national core facility for Bioimage Analysis.
https://arxiv.org/html/2409.15009v2
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Last days to register!
add a skeleton here at some point
7 months ago
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months ago
Only five days remain to register!* Here is the tentative program: *: it is likely that there won't be a deadline extension.
add a skeleton here at some point
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months ago
Registration deadline extended to the 31st of March.
add a skeleton here at some point
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months ago
Do you want to learn
#BioimageAnalysis
? Do you want to strengthen your skills? We're thrilled to announce the
#NEUBIAS
Pasteur Course on Bioimage Analysis - May 2025! in
@pasteur.fr
Paris!
research.pasteur.fr/en/course/ne...
Details are on the page linked here, some info below 👇
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NEUBIAS Pasteur course on Bioimage Analysis - 2025 - Research
Topics The exact schedule is still being finalized. Here is a description of the course content. Both tracks of the course have a specific focus on hands-on and interactive tutorials. They are meant t...
https://research.pasteur.fr/en/course/neubias-network-of-european-bioimage-analysts/
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reposted by
Stéphane Rigaud
Jean-Yves Tinevez
8 months ago
Do you love and use
#microscopy
? There is a fantastic event taking place at the
@institutpasteur.bsky.social
Paris in 3 weeks, just for you :) 1/ mini symposium on imaging, AND / OR 2/ book demo slots to test the latest microscopes from partners Please share with colleagues, more below👇
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reposted by
Stéphane Rigaud
Constantin Pape
8 months ago
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool.
www.nature.com/articles/s41...
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Stéphane Rigaud
Juliane Glaser
9 months ago
It’s official 🎉 I am excited to share that I will start my lab this spring at the Max Planck Institute for Immunobiology and Epigenetics
@mpi-ie.bsky.social
in beautiful Freiburg 🤩🗻☀️ I am looking forward to new collaborations and working with the fantastic community in Freiburg & its surroundings!
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Stéphane Rigaud
Institut Pasteur | 130 years of biomedical research
9 months ago
The Institut Pasteur has decided to leave X (formerly Twitter) to join BlueSky! 🦋 The Institut Pasteur made this decision due to several serious issues observed on the X platform since its acquisition. Join us here to continue advocating for science.
www.pasteur.fr/en/home/pres...
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Institut Pasteur decides to leave X
The Institut Pasteur, a research organization which for more than 130 years has been committed to tackling infectious diseases, sharing knowledge and defending science, has decided to leave X because ...
https://www.pasteur.fr/en/home/press-area/press-documents/institut-pasteur-decides-leave-x
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reposted by
Stéphane Rigaud
Pierre-François Lenne
over 3 years ago
Our code for force inference in epithelial tissues is available online! Feel free to contact us if you're interested in using it or if you want to collaborate. Code :Ref :
nature.com/articles/s4159…
data.mendeley.com/datasets/78ng4…
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Stéphane Rigaud
Bellaiche Lab
12 months ago
🎓 Join us for our Spring School in Quantitative Biology: "Cell Dynamics in Developmental Systems" ✨ Featuring renowned speakers and hands-on workshops! Learn more and register:
www.edu.bio.ens.psl.eu/spip.php?art...
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Stéphane Rigaud
Institut Pasteur | 130 years of biomedical research
9 months ago
Welcome to the official Bluesky page of the Institut Pasteur! 🔬 Explore with us the frontiers of biomedical research 🧪 Follow us to uncover groundbreaking discoveries 💡 Share knowledge for global health 🌍 Join a community passionate about progress and open science.
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Stéphane Rigaud
Jean-Yves Tinevez
9 months ago
Our excellent colleagues in
@france-bioimaging.bsky.social
are back with the new yearly FBI data challenge. This year it focuses on **fusion algorithms for multi-view images in 3D** that are deep-learning based. You have an idea on how to improve fusion of multi-view, lightsheet data? Register!
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Stéphane Rigaud
Diana Pinheiro
9 months ago
If you are interested in all things stem cells and development, then this is the conference for you 🤩 We have put together an exciting and diverse list of speakers - and you can be a part of it too! 😉 Loking forward hearing from young scientists - for oral presentations register by tomorrow! 🤓 👻
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Stéphane Rigaud
Laurent Guerard
9 months ago
2025 is now well underway and we are happy to announce that ZIDAS is coming to Basel this year !
2025.zidas.org
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ZIDAS 2025
This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.
https://2025.zidas.org
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reposted by
Stéphane Rigaud
Sandrine Lévêque Fort 🔬
9 months ago
#MiFoBio2025
the autumn microscopy school by
@gdrimabio.bsky.social
will take place from 10th to 16th October 2025. The call for workshops to share pratical knowledges is open till 31/01
ateliers-mifobio.fr
We'll bring stuff as usual, stay tuned !
@cnrsingenierie.bsky.social
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reposted by
Stéphane Rigaud
Joel Lüthi
9 months ago
In many cases, you may be able to get Copilot for free, either as a teacher or open source maintainer:
docs.github.com/en/copilot/m...
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Getting free access to Copilot Pro as a student, teacher, or maintainer - GitHub Docs
Learn how to use Copilot Pro for free as a student, teacher, or open-source maintainer.
https://docs.github.com/en/copilot/managing-copilot/managing-copilot-as-an-individual-subscriber/managing-your-github-copilot-pro-subscription/getting-free-access-to-copilot-pro-as-a-student-teacher-or-maintainer
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Stéphane Rigaud
Nicolas Chiaruttini
9 months ago
Finally had a bit of time to play with multi-GPU deconvolution. Using
@truenorth-ia.bsky.social
and
@haesleinhuepf.bsky.social
previous work. Here it is in action in
#BigDataViewer
using async and lazy processing. Look at the two poor laptop GPUs going as fast as they can:
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Stéphane Rigaud
France-BioImaging
9 months ago
The Wellcome Photography Prize is back📢
#WPP25
invites entries from
#microscopy
to medical imaging. Prizes include up to £10,000, your work shown in a public exhibition and global media coverage. 👉Find out more at
wellcome.org/photoprize
Enter by 14 January 2025 for free!
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reposted by
Stéphane Rigaud
Levayer Lab
10 months ago
Looking for a job still connected to acamedia and research ? Do you like interacting with a lot of people, outreach activity, organising scientific events ? Do you have good writing and organisation skills ? We may have a job for you👇 (permanent position)
emploi.pasteur.fr/offre-de-emp...
🙏RT
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