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...
⬇️
13.10.2025 08:10 — 👍 36 🔁 12 💬 1 📌 1
with lots of pyclesperanto inside
06.10.2025 09:46 — 👍 5 🔁 1 💬 0 📌 1
Anyone interested in getting my job?
Do not hesitate to apply, it's a pretty good gig
11.09.2025 10:37 — 👍 22 🔁 14 💬 2 📌 0
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.
18.09.2025 09:26 — 👍 17 🔁 11 💬 0 📌 0
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). 👇
10.09.2025 12:50 — 👍 51 🔁 28 💬 3 📌 0
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/
04.09.2025 16:07 — 👍 46 🔁 21 💬 1 📌 0
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
10.07.2025 13:19 — 👍 4 🔁 3 💬 1 📌 0
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 !!
23.06.2025 14:29 — 👍 67 🔁 87 💬 0 📌 7
We have been collaborating with Daria for years and I warmly recommend working with her.
12.06.2025 10:06 — 👍 6 🔁 7 💬 0 📌 0
From Local to National BioImage Analysis Hub, how to share ressources, knowledge, and especially help each others 🤘
11.06.2025 08:42 — 👍 5 🔁 1 💬 0 📌 0
YouTube video by Institut Pasteur EDUCATION
Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS
🔬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 »
28.05.2025 10:01 — 👍 9 🔁 4 💬 2 📌 0
Final session where we finish our pipeline using #celltrackscolab with Laura Xénard.
16.05.2025 12:05 — 👍 6 🔁 1 💬 0 📌 0
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
16.05.2025 10:03 — 👍 5 🔁 3 💬 0 📌 0
Perfect way to finish the day with ☀️ and warm evening.
Thanks to the teachers and dear colleagues @jwpylvanainen.bsky.social @mambroset.bsky.social @gaellel.bsky.social @m-albert.bsky.social Carlos Garcia-Lopez & Heloise Monnet, and the students that join us !
15.05.2025 12:37 — 👍 7 🔁 2 💬 0 📌 0
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
13.05.2025 12:10 — 👍 6 🔁 2 💬 1 📌 0
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...
13.05.2025 12:36 — 👍 15 🔁 8 💬 0 📌 0
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...
13.05.2025 10:33 — 👍 24 🔁 9 💬 2 📌 1
Repo will be fully updated at the end of the course ;)
13.05.2025 13:41 — 👍 4 🔁 0 💬 0 📌 0
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..
13.05.2025 10:20 — 👍 9 🔁 5 💬 1 📌 0
First day covered #fiji by @mambroset.bsky.social and a mini-@napari.fosstodon.org.ap.brid.gy challenge to develop widgets for image processing by @danielkrentzel.bsky.social
13.05.2025 09:10 — 👍 3 🔁 0 💬 1 📌 1
Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social
13.05.2025 07:57 — 👍 29 🔁 9 💬 1 📌 0
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
13.05.2025 07:46 — 👍 32 🔁 4 💬 3 📌 0
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...
22.04.2025 11:56 — 👍 10 🔁 9 💬 1 📌 0
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.
16.04.2025 19:40 — 👍 24 🔁 19 💬 0 📌 4
The Max Perutz Labs are a joint venture of the University of Vienna and the Medical University of Vienna, dedicated to a mechanistic understanding of fundamental biomedical processes.
https://www.sciencedirect.com/journal/developmental-biology
The Imaging & Optics Facility @ Institute of Science andTechnology Austria (ISTA) supports scientists by providing state-of-the-art services in advanced microscopy applications, image analysis, flow cytometry and optical development solutions
EMBO is the organization of more than 2,100 leading researchers that promotes excellence in life sciences in Europe and beyond.
https://www.embo.org/
Getting to grips with chromosome organisation and dynamics using ‘scopes, sequencing and silicon.
Located at @imbavienna.bsky.social - @viennabiocenter.bsky.social
Fan of dark DNA&RNA, transposons, embryology, 3D genome, big and small adventures
Group Leader at IMBA, Vienna Biocenter
Scientific journal publishing research, overview and commentary across all of biology. All of it!
https://www.cell.com/current-biology/home
Part of CellPress @cellpress.bsky.social
Fascinated by insect-induced plant galls! Cell biologist, interested in solving molecular puzzles in defense & developmental signalling. PI at @gmi Vienna Biocenter
CryoFIB Development and In situ structural biology. NPC and TE enthusiast. Drosophilist but ready to switch to wherever biology takes us
Getting to enjoy science with a group at IMBA/IMP of the Vienna BioCenter https://www.imp.ac.at/groups/sven-klumpe
Research, Education and Business. Vienna BioCenter is a life science cluster that includes IMP, IMBA, GMI, Max Perutz Labs, as well as the Faculty of Life Science & CeMESS (both University of Vienna) and 35+ biotechs.
GMI is the only international center for basic plant research in Austria. Research covers many aspects of molecular and evolutionary genetics.
🇸🇪 Sweden's national center for molecular biosciences
👩🔬 Infrastructure with unique technologies and expertise
👥 Research community
🥼 Life science 🌱
💻 Often data-driven
https://www.scilifelab.se/
https://www.linkedin.com/company/scilifelab/
Dynamics of Host-Pathogen Interactions Unit at @pasteur.fr https://research.pasteur.fr/en/team/dynamics-of-host-pathogen-interactions/
Biologist 🪰 Scientific illustrator 🌿🦠🐛
