Chloé Roffay
@chloeroffay.bsky.social
From physics to cells to gastruloids • Postdoc in @dianapinheiro.bsky.social • PhD : @rouxlab.bsky.social 🔬🐬 🎨 • alum cpes @psl-univ.bsky.social • she/her • Views my own
Reposted by Chloé Roffay
is there a direct crosstalk between actin and vimentin intermediate filaments? Our work shows that vimentin promotes actin assembly by stabilizing ATP-subunits at the barbed end.
Fantastic work done by @lilianpaty.bsky.social with @romet-jegou-lab.bsky.social
www.biorxiv.org/content/10.1...
Fantastic work done by @lilianpaty.bsky.social with @romet-jegou-lab.bsky.social
www.biorxiv.org/content/10.1...
November 24, 2025 at 10:15 AM
is there a direct crosstalk between actin and vimentin intermediate filaments? Our work shows that vimentin promotes actin assembly by stabilizing ATP-subunits at the barbed end.
Fantastic work done by @lilianpaty.bsky.social with @romet-jegou-lab.bsky.social
www.biorxiv.org/content/10.1...
Fantastic work done by @lilianpaty.bsky.social with @romet-jegou-lab.bsky.social
www.biorxiv.org/content/10.1...
Reposted by Chloé Roffay
📣 New review! Dynamical systems and low-dimensional geometric structures in phase space help rationalize how embryos develop form and function, from large datasets. We focus on morphogenesis, cell differentiation, and their interconnection.
@alex-plum.bsky.social
sciencedirect.com/science/arti...
@alex-plum.bsky.social
sciencedirect.com/science/arti...
June 4, 2025 at 4:46 PM
📣 New review! Dynamical systems and low-dimensional geometric structures in phase space help rationalize how embryos develop form and function, from large datasets. We focus on morphogenesis, cell differentiation, and their interconnection.
@alex-plum.bsky.social
sciencedirect.com/science/arti...
@alex-plum.bsky.social
sciencedirect.com/science/arti...
Reposted by Chloé Roffay
Very happy to share video of 1st lecture @college-de-france.fr on Biological computation 😊. I defend the necessity to access Algorithmic & Computational levels of analysis in cell & developmental biol. proposed by David Marr in neuroscience. Logic & Function matter 🤩.
Video: tinyurl.com/55yejk5f
Video: tinyurl.com/55yejk5f
Qu’est-ce que l’information biologique (suite) ? (1) - Thomas Lecuit (2025-2026)
Enseignement 2025-2026 : Qu’est-ce que l’information biologique (suite) ? Cours du 20 décembre 2025 : Introduction : approche computationelle du vivant Professeur : Thomas Lecuit Chaire Dynamiques du vivant Retrouvez les enregistrements audios et vidéos du cycle : https://www.college-de-france.fr/fr/agenda/cours/qu-est-ce-que-information-biologique Tous les enseignements du Pr Thomas Lecuit : https://www.college-de-france.fr/chaire/thomas-lecuit-dynamiques-du-vivant-chaire-statutaire https://www.youtube.com/playlist?list=PLOj9pZ2YNGZ84uMY6DhPnqpL1rq5qNAVJ Le Collège de France est une institution de recherche fondamentale dans tous les domaines de la connaissance et un lieu de diffusion du « savoir en train de se faire » ouvert à tous. Les cours, séminaires, colloques sont enregistrés puis mis à disposition du public sur le site internet du Collège de France. Découvrez toutes les ressources du Collège de France : https://www.college-de-france.fr Soutenir le Collège de France : https://www.fondation-cdf.fr/faire-un-don Suivez-nous sur : Threads : https://www.threads.net/@collegedefrance Bluesky : https://bsky.app/profile/college-de-france.fr Facebook : https://www.facebook.com/College.de.France Instagram : https://www.instagram.com/collegedefrance LinkedIn : https://fr.linkedin.com/company/coll%C3%A8gedefrance
tinyurl.com
November 24, 2025 at 9:42 AM
Very happy to share video of 1st lecture @college-de-france.fr on Biological computation 😊. I defend the necessity to access Algorithmic & Computational levels of analysis in cell & developmental biol. proposed by David Marr in neuroscience. Logic & Function matter 🤩.
Video: tinyurl.com/55yejk5f
Video: tinyurl.com/55yejk5f
Reposted by Chloé Roffay
Trackastra integration
With Martin Weigert & Benjamin Galluser: Integrated Trackastra as a tracker into TrackMate. This required some changes in Trackastra CLI and a rework of the tracker API of TrackMate.
With Martin Weigert & Benjamin Galluser: Integrated Trackastra as a tracker into TrackMate. This required some changes in Trackastra CLI and a rework of the tracker API of TrackMate.
November 20, 2025 at 11:42 AM
Trackastra integration
With Martin Weigert & Benjamin Galluser: Integrated Trackastra as a tracker into TrackMate. This required some changes in Trackastra CLI and a rework of the tracker API of TrackMate.
With Martin Weigert & Benjamin Galluser: Integrated Trackastra as a tracker into TrackMate. This required some changes in Trackastra CLI and a rework of the tracker API of TrackMate.
Updated Trackmate8, tried out Trackastra! Got some issues with the conda path and numpy not being where it should be but got solved easily thanks to the extensive documentation. Trackastra performed at least as well as the LAP tracker and detected properly several divisions! Investigation ongoing 🤠🤠
Trackastra is part of the brand-new TrackMate v8.
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune 🤖
November 24, 2025 at 7:20 AM
Updated Trackmate8, tried out Trackastra! Got some issues with the conda path and numpy not being where it should be but got solved easily thanks to the extensive documentation. Trackastra performed at least as well as the LAP tracker and detected properly several divisions! Investigation ongoing 🤠🤠
Reposted by Chloé Roffay
More details and images that are not @#$23-up here:
forum.image.sc/t/trackmate-...
forum.image.sc/t/trackmate-...
TrackMate v8 - segmentation editor and Python CLI integration
TrackMate v8: 2D Segmentation Editor & Python CLI Integration Hi everyone, I am excited to announce TrackMate v8, a major update introducing key improvements for both end-users and developers. Mai...
forum.image.sc
November 20, 2025 at 11:44 AM
More details and images that are not @#$23-up here:
forum.image.sc/t/trackmate-...
forum.image.sc/t/trackmate-...
Reposted by Chloé Roffay
The lab’s first pre-print! We investigated how growth-inducing Erk activity waves are regulated in regenerating zebrafish scales. We discovered that Erk waves are followed by waves of expression of their own inhibitors, as predicted by excitable waves theory. tinyurl.com/26r2cmpj
November 20, 2025 at 6:11 PM
The lab’s first pre-print! We investigated how growth-inducing Erk activity waves are regulated in regenerating zebrafish scales. We discovered that Erk waves are followed by waves of expression of their own inhibitors, as predicted by excitable waves theory. tinyurl.com/26r2cmpj
Join us for 2026 #kitpqbio! 🤩
Advanced grad students + postdocs: apply for the 2026 #kitpqbio summer course, "Physical Principles of Morphogenesis in Plants and Animals," at buff.ly/OXXMKEv. Apply by Feb. 1.
Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)
Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)
November 20, 2025 at 5:48 PM
Join us for 2026 #kitpqbio! 🤩
Reposted by Chloé Roffay
Launching celldynamicslab.com, the homepage of our new group at EPFL working on cell fragmentation, membrane and cortex mechanics, FLIM imaging, and microfluidics tools. MSc/PhD or postdocs interested in quantitative cell biology are welcome to reach out. We're also hiring a lab manager in 2026!
Main - Cell Dynamics and Fragmentation Lab
The Cell Dynamics and Fragmentation lab at We study how single cells move and fragment in complex environments using microfluidics. We bring tools and concep...
celldynamicslab.com
November 11, 2025 at 5:10 PM
Launching celldynamicslab.com, the homepage of our new group at EPFL working on cell fragmentation, membrane and cortex mechanics, FLIM imaging, and microfluidics tools. MSc/PhD or postdocs interested in quantitative cell biology are welcome to reach out. We're also hiring a lab manager in 2026!
Reposted by Chloé Roffay
Happy to share our new work from my graduate lab, with friends & colleagues @suewop.bsky.social, Pieter Derksen, Gary Han, Nikolas Claussen, and @streichan.bsky.social! We find that germ layers exhibit persistent, distinct flow patterns during zebrafish gastrulation.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Stationary and germ layer-specific cellular flows shape the zebrafish gastrula
During gastrulation, a sequence of complex processes transforms the blastula into a multilayered embryo. Fixed sample analysis has revealed much about how genetic signaling cascades determine the majo...
www.biorxiv.org
November 13, 2025 at 9:17 PM
Happy to share our new work from my graduate lab, with friends & colleagues @suewop.bsky.social, Pieter Derksen, Gary Han, Nikolas Claussen, and @streichan.bsky.social! We find that germ layers exhibit persistent, distinct flow patterns during zebrafish gastrulation.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Chloé Roffay
Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish https://www.biorxiv.org/content/10.1101/2025.11.12.688039v1
November 13, 2025 at 8:34 PM
Cell type-independent timekeeping gene modules enable embryonic stage prediction in zebrafish https://www.biorxiv.org/content/10.1101/2025.11.12.688039v1
Reposted by Chloé Roffay
We are highlighting Austin Smith, a @biologists.bsky.social Director, @dmmjournal.bsky.social Guest Editor and former @dev-journal.bsky.social Editor, as an extraordinary biologist. #100biologists
@ausmith.bsky.social
@ausmith.bsky.social
November 3, 2025 at 3:49 PM
We are highlighting Austin Smith, a @biologists.bsky.social Director, @dmmjournal.bsky.social Guest Editor and former @dev-journal.bsky.social Editor, as an extraordinary biologist. #100biologists
@ausmith.bsky.social
@ausmith.bsky.social
'AI' is based on training dataset. Dataset are annotated by humans.
This week's @nature.com cover highlights a report of A.I.- mediated distortion
When #ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants nature.com/articles/s41...
When #ChatGPT was asked to rate 40,000 résumés, it ranked the older male candidates as better quality than the younger female applicants nature.com/articles/s41...
November 3, 2025 at 6:47 AM
'AI' is based on training dataset. Dataset are annotated by humans.
Reposted by Chloé Roffay
And another great gut epithelium story from our cool neighbors !!!😎 @cbitoulouse.bsky.social
Ever wondered how adult organs preserve epithelial barrier integrity while continuously exposed to mechanical stress? We tackled this question in our new preprint – led by our brilliant PhD student Vishnu Krishnakumar! (1/11)
🔗 www.biorxiv.org/content/10.1...
🔗 www.biorxiv.org/content/10.1...
Robust pan-junctional reinforcement preserves the gut epithelial barrier under mechanical stress
Epithelia are specialized tissue barriers that safeguard the organism's internal milieu from the hostile external environment, a function critically dependent on intercellular junctions. In the colon,...
www.biorxiv.org
October 30, 2025 at 2:48 PM
And another great gut epithelium story from our cool neighbors !!!😎 @cbitoulouse.bsky.social
Reposted by Chloé Roffay
Our ForSys method to infer the mechanical state of a tissue in space and time is published now in @cp-iscience.bsky.social !
www.cell.com/iscience/ful...
(1/10)
www.cell.com/iscience/ful...
(1/10)
October 20, 2025 at 1:03 PM
Our ForSys method to infer the mechanical state of a tissue in space and time is published now in @cp-iscience.bsky.social !
www.cell.com/iscience/ful...
(1/10)
www.cell.com/iscience/ful...
(1/10)
Reposted by Chloé Roffay
Zebrafish embryo undergoing gastrulation. Credit to Dr. Gopi Shah at EMBL. #ZebrafishZunday 🧪
October 19, 2025 at 9:24 AM
Zebrafish embryo undergoing gastrulation. Credit to Dr. Gopi Shah at EMBL. #ZebrafishZunday 🧪
Reposted by Chloé Roffay
A lot of pressure on the different grant schemes, and pretty much independent of career stage.
October 17, 2025 at 10:20 AM
A lot of pressure on the different grant schemes, and pretty much independent of career stage.
Reposted by Chloé Roffay
October 17, 2025 at 9:22 AM
Reposted by Chloé Roffay
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
qedscience.com
October 15, 2025 at 12:22 PM
Reposted by Chloé Roffay
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains
1/
doi.org/10.1101/2025...
1/
doi.org/10.1101/2025...
October 8, 2025 at 1:05 PM
New preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains
1/
doi.org/10.1101/2025...
1/
doi.org/10.1101/2025...
Reposted by Chloé Roffay
🚨 New preprint out!
“Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM” with Tithi Mandal and @rouxlab.bsky.social
We benchmark and describe step-by-step Flipper-TR FLIM measurements across different set-ups and and strategies.
www.biorxiv.org/content/10.1...
“Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM” with Tithi Mandal and @rouxlab.bsky.social
We benchmark and describe step-by-step Flipper-TR FLIM measurements across different set-ups and and strategies.
www.biorxiv.org/content/10.1...
Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM
Flipper-TR is a membrane dye sensitive to lipid packing widely used to probe membrane tension in live cells via fluorescence lifetime imaging microscopy (FLIM). However, no consensus currently exists ...
www.biorxiv.org
October 5, 2025 at 4:04 PM
🚨 New preprint out!
“Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM” with Tithi Mandal and @rouxlab.bsky.social
We benchmark and describe step-by-step Flipper-TR FLIM measurements across different set-ups and and strategies.
www.biorxiv.org/content/10.1...
“Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM” with Tithi Mandal and @rouxlab.bsky.social
We benchmark and describe step-by-step Flipper-TR FLIM measurements across different set-ups and and strategies.
www.biorxiv.org/content/10.1...
Reposted by Chloé Roffay
First, check out my recent bioRxiv preprint w/ @oweinerlab.bsky.social: www.biorxiv.org/content/10.1...
We find contractility shifts the proportion of implantation-competent embryos from young and aged females. Keep reading this for more info!
We find contractility shifts the proportion of implantation-competent embryos from young and aged females. Keep reading this for more info!
A mechanical origin for implantation defects in embryos from aged females
Women over 35 experience a marked reduction in fertility. The origin of these fertility defects appears to reside in the implantation capacity of the embryo itself, but the mechanistic basis of this i...
www.biorxiv.org
October 1, 2025 at 6:21 PM
First, check out my recent bioRxiv preprint w/ @oweinerlab.bsky.social: www.biorxiv.org/content/10.1...
We find contractility shifts the proportion of implantation-competent embryos from young and aged females. Keep reading this for more info!
We find contractility shifts the proportion of implantation-competent embryos from young and aged females. Keep reading this for more info!
Reposted by Chloé Roffay
I have a PhD student and an undergrad student positions open at the Institute of Biotechnology @helsinki.fi We are using reconstitution, cell and structural biology to study protein-membrane interactions and membrane microdomain formation. Links to calls below! Feel free to drop a message and share!
September 29, 2025 at 3:45 PM
I have a PhD student and an undergrad student positions open at the Institute of Biotechnology @helsinki.fi We are using reconstitution, cell and structural biology to study protein-membrane interactions and membrane microdomain formation. Links to calls below! Feel free to drop a message and share!
Reposted by Chloé Roffay
I’m not sure as a community we **truely** acknowledged how powerful the #CellMigrationSeminarSeries series was at keeping us connected at such an uncertain time. Thank-you @ankita13jha.bsky.social @adamshellard.bsky.social @drjenmitchell.bsky.social & @simplythebex.bsky.social
September 29, 2025 at 2:07 AM
I’m not sure as a community we **truely** acknowledged how powerful the #CellMigrationSeminarSeries series was at keeping us connected at such an uncertain time. Thank-you @ankita13jha.bsky.social @adamshellard.bsky.social @drjenmitchell.bsky.social & @simplythebex.bsky.social
Reposted by Chloé Roffay
Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM https://www.biorxiv.org/content/10.1101/2025.09.23.678124v1
September 26, 2025 at 2:49 AM
Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM https://www.biorxiv.org/content/10.1101/2025.09.23.678124v1