Emmanuel Soubies
@esoubies.bsky.social
CNRS researcher at IRIT.
Computational Imaging, Microscopy, Optimization, Machine Learning
Website: https://www.irit.fr/~Emmanuel.Soubies/
Computational Imaging, Microscopy, Optimization, Machine Learning
Website: https://www.irit.fr/~Emmanuel.Soubies/
Reposted by Emmanuel Soubies
💥 DeepInverse is now part of the official PyTorch Landscape💥
We are excited to join an ecosystem of great open-source AI libraries, including @hf.co diffusers, MONAI, einops, etc.
pytorch.org/blog/deepinv...
We are excited to join an ecosystem of great open-source AI libraries, including @hf.co diffusers, MONAI, einops, etc.
pytorch.org/blog/deepinv...
DeepInverse Joins the PyTorch Ecosystem: the library for solving imaging inverse problems with deep learning – PyTorch
pytorch.org
November 5, 2025 at 5:31 PM
💥 DeepInverse is now part of the official PyTorch Landscape💥
We are excited to join an ecosystem of great open-source AI libraries, including @hf.co diffusers, MONAI, einops, etc.
pytorch.org/blog/deepinv...
We are excited to join an ecosystem of great open-source AI libraries, including @hf.co diffusers, MONAI, einops, etc.
pytorch.org/blog/deepinv...
Reposted by Emmanuel Soubies
#TalentsCNRS 🏅 | Découvrez le Centre International de Rencontres #Mathématiques, le Cirm, lauréat de la médaille de cristal collectif @cnrs.fr
Reconnu comme un centre incontournable à l'international, la médaille récompense la qualité du travail de son équipe.
➡️ www.insmi.cnrs.fr/fr/cnrsinfo/...
Reconnu comme un centre incontournable à l'international, la médaille récompense la qualité du travail de son équipe.
➡️ www.insmi.cnrs.fr/fr/cnrsinfo/...
September 2, 2025 at 7:37 AM
#TalentsCNRS 🏅 | Découvrez le Centre International de Rencontres #Mathématiques, le Cirm, lauréat de la médaille de cristal collectif @cnrs.fr
Reconnu comme un centre incontournable à l'international, la médaille récompense la qualité du travail de son équipe.
➡️ www.insmi.cnrs.fr/fr/cnrsinfo/...
Reconnu comme un centre incontournable à l'international, la médaille récompense la qualité du travail de son équipe.
➡️ www.insmi.cnrs.fr/fr/cnrsinfo/...
Reposted by Emmanuel Soubies
#Sketchpose is out in @melbajournal.bsky.social !
Go read it if you are interested in training cell segmentation models using few partial annotations 😀
Go read it if you are interested in training cell segmentation models using few partial annotations 😀
August 25, 2025 at 9:28 AM
#Sketchpose is out in @melbajournal.bsky.social !
Go read it if you are interested in training cell segmentation models using few partial annotations 😀
Go read it if you are interested in training cell segmentation models using few partial annotations 😀
Reposted by Emmanuel Soubies
New paper on the generalization of Flow Matching www.arxiv.org/abs/2506.03719
🤯 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 👇👇👇
🤯 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 👇👇👇
June 18, 2025 at 8:08 AM
New paper on the generalization of Flow Matching www.arxiv.org/abs/2506.03719
🤯 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 👇👇👇
🤯 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 👇👇👇
Reposted by Emmanuel Soubies
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 😀
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 😀
June 18, 2025 at 8:15 AM
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 😀
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 😀
Reposted by Emmanuel Soubies
Mon article sur les maths de l’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
La version en anglais est sur arxiv
arxiv.org/abs/2501.10465
May 16, 2025 at 10:35 PM
Mon article sur les maths de l’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
La version en anglais est sur arxiv
arxiv.org/abs/2501.10465
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!
A Dark sectioning algorithm removes background and provides single-frame optical sectioning in fluorescence microscopy, facilitating improved deep-tissue segmentation accuracy.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Dark-based optical sectioning assists background removal in fluorescence microscopy - Nature Methods
The Dark sectioning algorithm removes the background and provides single-frame optical sectioning in fluorescence microscopy. It offers improved quantitative analysis and deep-tissue segmentation accu...
www.nature.com
May 15, 2025 at 12:30 PM
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!
Reposted by Emmanuel Soubies
🔥It's D-day. We're opening pre-registration for #Mifobio2025 today🔥
👉 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.
👉Deadline June 10, 2025 ❗
👉 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.
👉Deadline June 10, 2025 ❗
May 5, 2025 at 5:21 PM
🔥It's D-day. We're opening pre-registration for #Mifobio2025 today🔥
👉 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.
👉Deadline June 10, 2025 ❗
👉 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.
👉Deadline June 10, 2025 ❗
Reposted by Emmanuel Soubies
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, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
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, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
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...
iclr-blogposts.github.io
April 24, 2025 at 1:45 PM
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, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
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, 👉poster session 4, 3 pm, #549 in Hall 3/2B 👈
Reposted by Emmanuel Soubies
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 🔥🕶️ #realtimemicroscopy
April 17, 2025 at 1:30 PM
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 🔥🕶️ #realtimemicroscopy
Reposted by Emmanuel Soubies
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 Abbelight… Check it out with free access:
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
academic.oup.com
April 9, 2025 at 3:47 PM
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 Abbelight… Check it out with free access:
Reposted by Emmanuel Soubies
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
February 12, 2025 at 11:19 AM
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
Reposted by Emmanuel Soubies
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, don’t hesitate to contact me (flexible start).
shorturl.at/fYNij
shorturl.at/gDQkz
shorturl.at/fYNij
shorturl.at/gDQkz
Portail Emploi CNRS - Offre d'emploi - Post-doctorant (H/F) pour le développement de nouveaux concepts en microscopie de fluorescence super-résolue pour l'observation de cellules vivantes
shorturl.at
January 29, 2025 at 2:07 PM
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, don’t hesitate to contact me (flexible start).
shorturl.at/fYNij
shorturl.at/gDQkz
shorturl.at/fYNij
shorturl.at/gDQkz
Reposted by Emmanuel Soubies
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.
January 23, 2025 at 10:53 AM
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.
Reposted by Emmanuel Soubies
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-....
www.imperial.ac.uk/jobs/search-....
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...
www.imperial.ac.uk
January 17, 2025 at 9:50 AM
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-....
www.imperial.ac.uk/jobs/search-....
Reposted by Emmanuel Soubies
Open Assistant Professor position in Statistical Learning or Data Science at École 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...
January 15, 2025 at 8:37 AM
Open Assistant Professor position in Statistical Learning or Data Science at École 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...
Reposted by Emmanuel Soubies
#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
We'll bring stuff as usual, stay tuned ! @cnrsingenierie.bsky.social
January 14, 2025 at 3:48 PM
#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
We'll bring stuff as usual, stay tuned ! @cnrsingenierie.bsky.social
Reposted by Emmanuel Soubies
Colloque #GRETSI, #Strasbourg 25-29 août 2025
gretsi.fr/colloque2025/
Soumission du 3 février au 21 mars
#GRETSI2025 XXXe Colloque Francophone de Traitement du Signal et des Images (vision, apprentissage, capteurs, communication, modèles)
Relayez !
gretsi.fr/colloque2025/
Soumission du 3 février au 21 mars
#GRETSI2025 XXXe Colloque Francophone de Traitement du Signal et des Images (vision, apprentissage, capteurs, communication, modèles)
Relayez !
January 13, 2025 at 9:41 AM
Colloque #GRETSI, #Strasbourg 25-29 août 2025
gretsi.fr/colloque2025/
Soumission du 3 février au 21 mars
#GRETSI2025 XXXe Colloque Francophone de Traitement du Signal et des Images (vision, apprentissage, capteurs, communication, modèles)
Relayez !
gretsi.fr/colloque2025/
Soumission du 3 février au 21 mars
#GRETSI2025 XXXe Colloque Francophone de Traitement du Signal et des Images (vision, apprentissage, capteurs, communication, modèles)
Relayez !
Reposted by Emmanuel Soubies
Videos of the CNRS optimization conference now online (in French):
- Claire Mathieu : www.youtube.com/watch?v=_ZXZ...
- Gabriel Peyré : www.youtube.com/watch?v=vQOF...
- Jérôme Bolte : www.youtube.com/watch?v=tjkg...
- Axel Parmentier : www.youtube.com/watch?v=DohO...
Enjoy 🙂
- Claire Mathieu : www.youtube.com/watch?v=_ZXZ...
- Gabriel Peyré : www.youtube.com/watch?v=vQOF...
- Jérôme Bolte : www.youtube.com/watch?v=tjkg...
- Axel Parmentier : www.youtube.com/watch?v=DohO...
Enjoy 🙂
www.youtube.com
January 7, 2025 at 6:29 AM
Videos of the CNRS optimization conference now online (in French):
- Claire Mathieu : www.youtube.com/watch?v=_ZXZ...
- Gabriel Peyré : www.youtube.com/watch?v=vQOF...
- Jérôme Bolte : www.youtube.com/watch?v=tjkg...
- Axel Parmentier : www.youtube.com/watch?v=DohO...
Enjoy 🙂
- Claire Mathieu : www.youtube.com/watch?v=_ZXZ...
- Gabriel Peyré : www.youtube.com/watch?v=vQOF...
- Jérôme Bolte : www.youtube.com/watch?v=tjkg...
- Axel Parmentier : www.youtube.com/watch?v=DohO...
Enjoy 🙂
Reposted by Emmanuel Soubies
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
December 22, 2024 at 2:39 PM
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
Reposted by Emmanuel Soubies
New review: together with PhD student Ciarán 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...
December 4, 2024 at 11:31 AM
New review: together with PhD student Ciarán 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...
Reposted by Emmanuel Soubies
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
November 27, 2024 at 9:00 AM
Anne Gagneux, Ségolène Martin, @quentinbertrand.bsky.social Remi Emonet and I wrote a tutorial blog post on flow matching: dl.heeere.com/conditional-... with lots of illustrations and intuition!
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
We got this idea after their cool work on improving Plug and Play with FM: arxiv.org/abs/2410.02423
Reposted by Emmanuel Soubies
🔊 Exciting AI Research Opportunity! my team at @czbiohub SF is hiring a Research Scientist to develop foundational AI models for BioImage analysis. Join us to work on cutting-edge ML/CV! 💻🔬🧪🧠
#AIJobs #ML
job-boards.greenhouse.io/chanzuckerbe...
#AIJobs #ML
job-boards.greenhouse.io/chanzuckerbe...
November 26, 2024 at 3:01 AM
🔊 Exciting AI Research Opportunity! my team at @czbiohub SF is hiring a Research Scientist to develop foundational AI models for BioImage analysis. Join us to work on cutting-edge ML/CV! 💻🔬🧪🧠
#AIJobs #ML
job-boards.greenhouse.io/chanzuckerbe...
#AIJobs #ML
job-boards.greenhouse.io/chanzuckerbe...
Reposted by Emmanuel Soubies
I have several positions with my ERC grant MALAGA on the Theory of Graph Machine Learning 🤓 Consider applying!
nkeriven.github.io/malaga/
(if you don't find the position for you but are interested in the topic anyway, contact me!)
nkeriven.github.io/malaga/
(if you don't find the position for you but are interested in the topic anyway, contact me!)
November 21, 2024 at 3:48 PM
I have several positions with my ERC grant MALAGA on the Theory of Graph Machine Learning 🤓 Consider applying!
nkeriven.github.io/malaga/
(if you don't find the position for you but are interested in the topic anyway, contact me!)
nkeriven.github.io/malaga/
(if you don't find the position for you but are interested in the topic anyway, contact me!)