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Emmanuel Soubies

@esoubies.bsky.social

CNRS researcher at IRIT. Computational Imaging, Microscopy, Optimization, Machine Learning Website: https://www.irit.fr/~Emmanuel.Soubies/

230 Followers  |  186 Following  |  4 Posts  |  Joined: 20.11.2024
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Posts by Emmanuel Soubies (@esoubies.bsky.social)

Calliopรฉ

We are recruiting four positions connected to Machine Learning, Statistical Learning, and AI for Science in the Applied Mathematics department at ร‰cole polytechnique. Join our vibrant community at IP Paris and Hi! Paris IA center. List below๐Ÿงต tinyurl.com/3jpw9t26

06.02.2026 07:56 โ€” ๐Ÿ‘ 11    ๐Ÿ” 19    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

There is an Associate Professor position in CS at ENS Lyon, with potential integration in my team, starting in sept 2026: DM me in interested!
Details at www.ens-lyon.fr/LIP/images/P...

05.02.2026 09:04 โ€” ๐Ÿ‘ 6    ๐Ÿ” 9    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 1
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Les inscriptions aux journรฉes MODE 2026 ร  Nice sont dรฉsormais ouvertes. Elles se dรฉrouleront du 18 au 20 mars ร  l'Hรดtel Saint-Paul.

Les inscriptions sont ouvertes jusqu'au 1 mars (majoration > 9/02). La deadline pour soumettre une communication est le **15 janvier**.

15.12.2025 08:11 โ€” ๐Ÿ‘ 5    ๐Ÿ” 7    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 1
GRETSI : 20รจme ร‰cole d'ร‰tรฉ en Traitement du Signal et des Images

Ecole d'รฉtรฉ de Peyresq sur les modรจles gรฉnรฉratifs et le transport optimal : www.gretsi.fr/peyresq2026 (cours en franรงais). Date limite de candidature le 27 fรฉvrier

12.12.2025 13:22 โ€” ๐Ÿ‘ 9    ๐Ÿ” 6    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
Prix de thรจse en Signal, Image et Vision dรฉcernรฉ par le Club EEA, le GdR ISIS et le GRETSI

A diffuser : Club EEA, GdR IASIS et #GRETSI dรฉlivrent conjointement un Prix de Thรจse distinguant des travaux originaux et novateurs, pour promouvoir la recherche dans le domaine du Signal, de l'Image et de la Vision. Date limite : 9 mars 2026.
gretsi.fr/prix-de-thes...

08.12.2025 22:35 โ€” ๐Ÿ‘ 5    ๐Ÿ” 1    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Lock-in-SIM, a new approach to reject background and minimize artefacts in structured illumination microscopy (SIM): www.nature.com/articles/s41...
Glad to see @esoubies.bsky.social's FlexSIM is the best opponent in side-by-side comparisons!

02.12.2025 07:42 โ€” ๐Ÿ‘ 28    ๐Ÿ” 8    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

New paper out! Together with my postdoc advisors @esoubies.bsky.social and Cรฉdric Fรฉvotte :)

We study the optimization landscape of L0-Bregman relaxations, which naturally arise when one optimizes non-quadratic fidelity terms coupled with the L0-norm.

1/n

20.11.2025 20:45 โ€” ๐Ÿ‘ 10    ๐Ÿ” 3    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
DeepInverse Joins the PyTorch Ecosystem: the library for solving imaging inverse problems with deep learning โ€“ PyTorch

๐Ÿ’ฅ DeepInverse is now part of the official PyTorch Landscape๐Ÿ’ฅ

We are excited to join an ecosystem of great open-source AI libraries, including @hf.co diffusers, MONAI, einops, etc.

pytorch.org/blog/deepinv...

05.11.2025 17:31 โ€” ๐Ÿ‘ 10    ๐Ÿ” 5    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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#TalentsCNRS ๐Ÿ… | Dรฉcouvrez le Centre International de Rencontres #Mathรฉmatiques, le Cirm, laurรฉat de la mรฉdaille de cristal collectif @cnrs.fr

Reconnu comme un centre incontournable ร  l'international, la mรฉdaille rรฉcompense la qualitรฉ du travail de son รฉquipe.

โžก๏ธ www.insmi.cnrs.fr/fr/cnrsinfo/...

02.09.2025 07:37 โ€” ๐Ÿ‘ 13    ๐Ÿ” 8    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 1
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#Sketchpose is out in @melbajournal.bsky.social !
Go read it if you are interested in training cell segmentation models using few partial annotations ๐Ÿ˜€

25.08.2025 09:28 โ€” ๐Ÿ‘ 4    ๐Ÿ” 2    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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New paper on the generalization of Flow Matching www.arxiv.org/abs/2506.03719

๐Ÿคฏ Why does flow matching generalize? Did you know that the flow matching target you're trying to learn *can only generate training points*?

w @quentinbertrand.bsky.social @annegnx.bsky.social @remiemonet.bsky.social ๐Ÿ‘‡๐Ÿ‘‡๐Ÿ‘‡

18.06.2025 08:08 โ€” ๐Ÿ‘ 55    ๐Ÿ” 17    ๐Ÿ’ฌ 2    ๐Ÿ“Œ 3
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Then why does flow matching generalize?? Because it fails!

The inductive bias of the neural network prevents from perfectly learning u* and overfitting.

In particular neural networks fail to learn the velocity field for two particular time values.

See the paper for a finer analysis ๐Ÿ˜€

18.06.2025 08:15 โ€” ๐Ÿ‘ 5    ๐Ÿ” 3    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Mon article sur les maths de lโ€™IA est paru dans la gazette de la smf smf.emath.fr/publications...
La version en anglais est sur arxiv
arxiv.org/abs/2501.10465

16.05.2025 22:35 โ€” ๐Ÿ‘ 26    ๐Ÿ” 8    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

Seems that here a part of the signal of interest has been attenuated? From my own tests (with the Matlab version on SIM data), maybe this can be improved by playing with the threshold parameter.

16.05.2025 14:20 โ€” ๐Ÿ‘ 0    ๐Ÿ” 0    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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In particular, it handles out-of-focus regions more effectively than traditional OTF attenuation.

15.05.2025 12:31 โ€” ๐Ÿ‘ 9    ๐Ÿ” 2    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0

Nice work! We integrated this dark-sectioning method into our FlexSIM pipeline (github.com/esoubies/Fle...) as an additional option for handling out-of-focus signal. It works remarkably well!

15.05.2025 12:30 โ€” ๐Ÿ‘ 27    ๐Ÿ” 5    ๐Ÿ’ฌ 2    ๐Ÿ“Œ 0
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๐Ÿ”ฅIt's D-day. We're opening pre-registration for #Mifobio2025 today๐Ÿ”ฅ

๐Ÿ‘‰ This is the 11th edition of the Thematic School!

All the relevant information, as well as the pre-registration form, is easily accessible on imabio-cnrs.fr but only if you are logged on this site.

๐Ÿ‘‰Deadline June 10, 2025 โ—

05.05.2025 17:20 โ€” ๐Ÿ‘ 22    ๐Ÿ” 12    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 4
A Visual Dive into Conditional Flow Matching | ICLR Blogposts 2025 Conditional flow matching (CFM) was introduced by three simultaneous papers at ICLR 2023, through different approaches (conditional matching, rectifying flows and stochastic interpolants). <br/> The m...

It was received quite enthusiastically here so time to share it again!!!

Our #ICLR2025 blog post on Flow Matching was published yesterday : iclr-blogposts.github.io/2025/blog/co...

My PhD student @annegnx.bsky.social will present it tomorrow in ICLR, ๐Ÿ‘‰poster session 4, 3 pm, #549 in Hall 3/2B ๐Ÿ‘ˆ

24.04.2025 13:45 โ€” ๐Ÿ‘ 11    ๐Ÿ” 6    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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Our PhD student Louis Romette is optimizing long-term live-cell imaging. He just casually dropped this 65-hour movie of a growing neuron (div 3 to 6) with knocked-in actin ๐Ÿ”ฅ๐Ÿ•ถ๏ธ #realtimemicroscopy

17.04.2025 13:30 โ€” ๐Ÿ‘ 299    ๐Ÿ” 50    ๐Ÿ’ฌ 14    ๐Ÿ“Œ 5
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Advancing Super-Resolution Microscopy: Recent Innovations in Commercial Instruments Abstract. Super-resolution microscopy techniques have accelerated scientific progress, enabling researchers to explore cellular structures and dynamics wit

We have a new review out! In this Microscopy & Microanalysis piece, Louisa Mezache and I survey some of the latest commercially available microscope technologies: Nikon NSPARC, Re-scan Gaia, CSR Biotech MI-SIM, refinements to STED, SMLM from Bruker and Abbelightโ€ฆ Check it out with free access:

09.04.2025 15:47 โ€” ๐Ÿ‘ 107    ๐Ÿ” 44    ๐Ÿ’ฌ 2    ๐Ÿ“Œ 4
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Our NCIS facility and Nikon Center of Excellence for Neuro-nanoimaging is on Bluesky! Follow @ncis-marseille.bsky.social for your stunning images and microscopy news fix by @bertrandvernay.bsky.social and me

12.02.2025 11:19 โ€” ๐Ÿ‘ 40    ๐Ÿ” 8    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
Portail Emploi CNRS - Offre d'emploi - Post-doctorant (H/F) pour le dรฉveloppement de nouveaux concepts en microscopie de fluorescence super-rรฉsolue pour l'observation de cellules vivantes

If you are interested by building or applying new microscopes around single molecule, FLIM, in depth imaging, live-cell+ SMLM, we are opening post-doc positions for various backgrounds funded by ERC grant, donโ€™t hesitate to contact me (flexible start).
shorturl.at/fYNij
shorturl.at/gDQkz

29.01.2025 14:07 โ€” ๐Ÿ‘ 9    ๐Ÿ” 5    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 1
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Our paper "PnP-Flow: Plug-and-Play Image Restoration with Flow Matching" has been accepted to ICLR 2025. Here a short explainer: We want to restore images (i.e., solve inverse problems) using pretrained velocity fields from flow matching. However, using change of variables is super costly.

23.01.2025 10:53 โ€” ๐Ÿ‘ 15    ๐Ÿ” 5    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 2
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Description Please note that job descriptions are not exhaustive, and you may be asked to take on additional duties that align with the key responsibilities ment...

We are hiring at assistant/associate professor level. We are particularly interested in applicants working on AI, Machine Learning (ML), and data sciences in topics relevant to the work of the department. Deadline 12th of February:
www.imperial.ac.uk/jobs/search-....

17.01.2025 09:50 โ€” ๐Ÿ‘ 2    ๐Ÿ” 2    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Open Assistant Professor position in Statistical Learning or Data Science at ร‰cole Polytechnique at Paris/Saclay. Reasonable teaching hours on ML/Stat or DS courses with very good students. Deadline is March 28th 2025, contact us if interested. gargantua.polytechnique.fr/siatel-web/a...

15.01.2025 08:37 โ€” ๐Ÿ‘ 27    ๐Ÿ” 14    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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#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

14.01.2025 15:48 โ€” ๐Ÿ‘ 47    ๐Ÿ” 29    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 1
Strasbourg, Alsace, place Klรฉber en hiver

Strasbourg, Alsace, place Klรฉber en hiver

Colloque #GRETSI, #Strasbourg 25-29 aoรปt 2025
gretsi.fr/colloque2025/
Soumission du 3 fรฉvrier au 21 mars
#GRETSI2025 XXXe Colloque Francophone de Traitement du Signal et des Images (vision, apprentissage, capteurs, communication, modรจles)
Relayez !

13.01.2025 09:41 โ€” ๐Ÿ‘ 1    ๐Ÿ” 3    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0

Videos of the CNRS optimization conference now online (in French):
- Claire Mathieu : www.youtube.com/watch?v=_ZXZ...
- Gabriel Peyrรฉ : www.youtube.com/watch?v=vQOF...
- Jรฉrรดme Bolte : www.youtube.com/watch?v=tjkg...
- Axel Parmentier : www.youtube.com/watch?v=DohO...

Enjoy ๐Ÿ™‚

07.01.2025 06:29 โ€” ๐Ÿ‘ 41    ๐Ÿ” 9    ๐Ÿ’ฌ 0    ๐Ÿ“Œ 0
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Have some curiosity on investigating the well-known PCA (Principal Component Analysis) with a glimpse of sparse optimization? With homogeneous or scale-invariant SOOT/SPOQ norm ratio penalties? Join INRIA for a Master Internship in 2025 (INRIA) Revisiting PCA with norm-ratio sparsity penalties

22.12.2024 14:40 โ€” ๐Ÿ‘ 2    ๐Ÿ” 2    ๐Ÿ’ฌ 1    ๐Ÿ“Œ 0
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New review: together with PhD student Ciarรกn Butler-Hallissey, we provide a comprehensive overview on how super-resolution microscopy can dissect the neuronal cytoskeleton, and the exciting perspectives ahead. Shock full of beautiful images, published or from our lab! www.nature.com/articles/s44...

04.12.2024 11:31 โ€” ๐Ÿ‘ 170    ๐Ÿ” 48    ๐Ÿ’ฌ 6    ๐Ÿ“Œ 5