Stéphane Rigaud
@strigaud.bsky.social
📤 758
📥 315
📝 10
Bio-image Analyst, Computer scientist, and plenty of other things that end in «-ist»
reposted by
Stéphane Rigaud
eurobioimaging.bsky.social
6 days ago
🙌 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...
0
7
7
reposted by
Stéphane Rigaud
Kristina Stapornwongkul
15 days ago
We’re looking for a new team member! 🚀 Only 3 more weeks to apply to the fantastic Vienna BioCenter PhD program
add a skeleton here at some point
0
16
17
reposted by
Stéphane Rigaud
Iván Hidalgo-Cenalmor
20 days ago
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 ⬇️
loading . . .
9
112
48
reposted by
Stéphane Rigaud
Gaëlle Letort
25 days ago
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
loading . . .
1
20
10
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
26 days ago
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. 👇🎓
3
29
28
reposted by
Stéphane Rigaud
Nicolas Chiaruttini
about 1 month ago
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!
0
23
5
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 1 month ago
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 👇
add a skeleton here at some point
1
40
30
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 2 months ago
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...
👇🧵
loading . . .
https://www.biorxiv.org/content/10.64898/2026.02.06.704368v1
2
52
20
reposted by
Stéphane Rigaud
Guillaume Jacquemet
3 months ago
🚨 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
loading . . .
Laboratory Engineer (Senior), in Advanced Imaging, 1.5.2026-31.12.2028
https://abo.rekrytointi.com/paikat/index.php?jid=976&key=&o=A_RJ&rspvt=7w3egf12wjs44k8g08gcc4cgsgkc0wc
0
48
76
reposted by
Stéphane Rigaud
Guillaume Jacquemet
3 months ago
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 👍
add a skeleton here at some point
1
54
44
reposted by
Stéphane Rigaud
Florian Jug
3 months ago
🚨 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/...
loading . . .
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.,
https://www.janelia.org/you-janelia/conferences/bootcamp-course-on-deep-learning-for-microscopy-image-analysis
0
78
65
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
4 months ago
Happy holidays from an amazing team.
0
35
1
reposted by
Stéphane Rigaud
Guillaume Jacquemet
4 months ago
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
3
67
26
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
5 months ago
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:
4
182
83
reposted by
Stéphane Rigaud
Daniel Krentzel
5 months ago
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-...
loading . . .
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...
https://research.pasteur.fr/fr/job/open-source-developer-for-deep-learning-antibiotic-discovery-platform/
0
20
14
reposted by
Stéphane Rigaud
Beth Cimini 🔬💻📊
5 months ago
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)
1
53
48
reposted by
Stéphane Rigaud
Camille Berthelot
5 months ago
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!)
add a skeleton here at some point
0
16
24
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
6 months 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...
⬇️
add a skeleton here at some point
1
39
15
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
6 months 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...
loading . . .
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
2
62
88
reposted by
Stéphane Rigaud
Fabrice Senger
6 months ago
with lots of pyclesperanto inside
add a skeleton here at some point
0
5
2
reposted by
Stéphane Rigaud
Guillaume Jacquemet
7 months ago
Anyone interested in getting my job? Do not hesitate to apply, it's a pretty good gig
add a skeleton here at some point
2
22
14
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months 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.
add a skeleton here at some point
0
17
11
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
7 months 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). 👇
3
52
28
reposted by
Stéphane Rigaud
Gaëlle Letort
7 months 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/
loading . . .
1
46
21
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
9 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...
loading . . .
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
0
14
6
reposted by
Stéphane Rigaud
Juliane Glaser
9 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
loading . . .
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
15
294
137
reposted by
Stéphane Rigaud
Robert Haase
9 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
1
4
3
reposted by
Stéphane Rigaud
Ricardo Henriques
9 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...
3
82
40
reposted by
Stéphane Rigaud
Guillaume Jacquemet
10 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 !!
0
70
94
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
10 months ago
We have been collaborating with Daria for years and I warmly recommend working with her.
add a skeleton here at some point
0
6
7
From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘
add a skeleton here at some point
10 months ago
0
6
1
reposted by
Stéphane Rigaud
Institut Pasteur Education
10 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 »
loading . . .
Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS
YouTube video by Institut Pasteur EDUCATION
https://youtube.com/shorts/3hOTyXfjnrA?feature=share
2
9
4
reposted by
Stéphane Rigaud
Joanna Pylvänäinen
11 months ago
Final session where we finish our pipeline using
#celltrackscolab
with Laura Xénard.
0
6
1
reposted by
Stéphane Rigaud
Gaëlle Letort
11 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
0
5
3
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
11 months ago
1
13
6
reposted by
Stéphane Rigaud
Caterina Fuster Barceló
11 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
1
6
2
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
11 months ago
1
14
4
reposted by
Stéphane Rigaud
Caterina Fuster Barceló
11 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...
0
15
8
reposted by
Stéphane Rigaud
Daniel Krentzel
11 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...
add a skeleton here at some point
2
24
10
reposted by
Stéphane Rigaud
Gaëlle Letort
11 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..
1
9
5
Kick-starting the
#neubiaspasteur2025
#BioImageAnalysis
courses at
@pasteur.fr
and
@pasteuredu.bsky.social
11 months ago
1
29
9
reposted by
Stéphane Rigaud
Joanna Pylvänäinen
11 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
3
33
4
reposted by
Stéphane Rigaud
Stefania Marcotti
12 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...
add a skeleton here at some point
1
10
9
reposted by
Stéphane Rigaud
GloBIAS
12 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.
0
23
22
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
12 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
-
add a skeleton here at some point
1
7
5
reposted by
Stéphane Rigaud
about 1 year 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...
loading . . .
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
0
18
9
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 1 year 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
0
12
3
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 1 year 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
loading . . .
F-BIAS: Towards a distributed national core facility for Bioimage Analysis.
https://arxiv.org/html/2409.15009v2
3
36
21
Last days to register!
add a skeleton here at some point
about 1 year ago
0
0
1
reposted by
Stéphane Rigaud
Jean-Yves Tinevez
about 1 year 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
1
4
8
Load more
feeds!
log in