Fabrice Senger
@senger.bsky.social
Mechanobiology / Multi-cellular assemblies
Reposted by Fabrice Senger
I won't talk about NMeth @natmethods.nature.com forever (probably), but I do want to brag a bit about the November focus issue on cell segmentation and tracking, which is many ways is my last hurrah (and final editorial) for the journal. I am so proud of these papers!! www.nature.com/nmeth/volume...
November 13, 2025 at 8:49 PM
I won't talk about NMeth @natmethods.nature.com forever (probably), but I do want to brag a bit about the November focus issue on cell segmentation and tracking, which is many ways is my last hurrah (and final editorial) for the journal. I am so proud of these papers!! www.nature.com/nmeth/volume...
Reposted by Fabrice Senger
What a wonderful surprise this morning to see our work highlighted. Thanks @juanmartin-serrano.bsky.social and @jcb.org !
Spotlight: @juanmartin-serrano.bsky.social highlights work from Dam, Moreno, Brownlow, @longchrom.bsky.social et al. (rupress.org/jcb/article/...), which reveals how Srs2/PARI act as a missegregated chromatin sensor for NoCut, delaying cytokinetic abscission. rupress.org/jcb/article/...
#Cytokinesis
#Cytokinesis
November 13, 2025 at 11:32 AM
What a wonderful surprise this morning to see our work highlighted. Thanks @juanmartin-serrano.bsky.social and @jcb.org !
Reposted by Fabrice Senger
#Autophagy #Mechanobiology
Interesting evidence on opposite effects of ⏫matrix stiffness on Autophagy of #EndothelialCell⏬ vs #SmoothMuscleCell⏫
280~480 kPa, crosslinked poly(L-lysine)-hyaluronic acid film on coverglass
#BioactiveMat 2021
www.sciencedirect.com/science/arti...
Interesting evidence on opposite effects of ⏫matrix stiffness on Autophagy of #EndothelialCell⏬ vs #SmoothMuscleCell⏫
280~480 kPa, crosslinked poly(L-lysine)-hyaluronic acid film on coverglass
#BioactiveMat 2021
www.sciencedirect.com/science/arti...
November 12, 2025 at 7:59 PM
#Autophagy #Mechanobiology
Interesting evidence on opposite effects of ⏫matrix stiffness on Autophagy of #EndothelialCell⏬ vs #SmoothMuscleCell⏫
280~480 kPa, crosslinked poly(L-lysine)-hyaluronic acid film on coverglass
#BioactiveMat 2021
www.sciencedirect.com/science/arti...
Interesting evidence on opposite effects of ⏫matrix stiffness on Autophagy of #EndothelialCell⏬ vs #SmoothMuscleCell⏫
280~480 kPa, crosslinked poly(L-lysine)-hyaluronic acid film on coverglass
#BioactiveMat 2021
www.sciencedirect.com/science/arti...
Reposted by Fabrice Senger
A game changer in our hands... www.nature.com/articles/s41...
Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods
u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...
www.nature.com
November 11, 2025 at 6:48 PM
A game changer in our hands... www.nature.com/articles/s41...
Reposted by Fabrice Senger
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 Fabrice Senger
Just out! Our work on active transport in epithelial tissues. Congrats to Huiqiong Wu, Greg Arkowitz and Ranjith Chilupuri in collaboration with C. Duclut and J. Prost!
PNAS www.pnas.org/doi/10.1073/...
PNAS www.pnas.org/doi/10.1073/...
November 11, 2025 at 11:01 PM
Just out! Our work on active transport in epithelial tissues. Congrats to Huiqiong Wu, Greg Arkowitz and Ranjith Chilupuri in collaboration with C. Duclut and J. Prost!
PNAS www.pnas.org/doi/10.1073/...
PNAS www.pnas.org/doi/10.1073/...
Reposted by Fabrice Senger
Talking about impostor syndrome.....
I'll be a teacher in the EMBO "Hack your Microscope" together with some of the very best researchers in the field.
5.5 days of hacking and microscope/fluidics shenanigans in Portugal.
You can apply here: meetings.embo.org/event/26-mic... #EMBOmicroscope
I'll be a teacher in the EMBO "Hack your Microscope" together with some of the very best researchers in the field.
5.5 days of hacking and microscope/fluidics shenanigans in Portugal.
You can apply here: meetings.embo.org/event/26-mic... #EMBOmicroscope
Hack your microscope
Recent advances in open-source microscopy have made high-resolution, customizable imaging systems more accessible, allowing researchers to overcome the constraints of traditional commercial solutions…
meetings.embo.org
November 11, 2025 at 11:39 AM
Talking about impostor syndrome.....
I'll be a teacher in the EMBO "Hack your Microscope" together with some of the very best researchers in the field.
5.5 days of hacking and microscope/fluidics shenanigans in Portugal.
You can apply here: meetings.embo.org/event/26-mic... #EMBOmicroscope
I'll be a teacher in the EMBO "Hack your Microscope" together with some of the very best researchers in the field.
5.5 days of hacking and microscope/fluidics shenanigans in Portugal.
You can apply here: meetings.embo.org/event/26-mic... #EMBOmicroscope
Reposted by Fabrice Senger
This is happening TODAY 2:30 pm!
Next Monday, 10th November, at 2:30 PM, we are delighted to welcome @maitrejl.bsky.social from Institut Curie. Don’t forget to subscribe to our mailing list to receive the Zoom link!
See you all there! 😊
See you all there! 😊
November 10, 2025 at 8:22 AM
This is happening TODAY 2:30 pm!
Reposted by Fabrice Senger
A fantastic paper by my @hhmijanelia.bsky.social colleague and friend Heejun Choi (who is on the job market!). Another elegant use of the Janelia Fluor dyes for cellular imaging. www.nature.com/articles/s41...
Secretome translation shaped by lysosomes and lunapark-marked ER junctions - Nature
Live-cell imaging of mRNA encoding secretome proteins and translated nascent peptide markers show that secretome translation occurs at endoplasmic reticulum junctions near lysosomes, requires lun...
www.nature.com
November 6, 2025 at 2:24 PM
A fantastic paper by my @hhmijanelia.bsky.social colleague and friend Heejun Choi (who is on the job market!). Another elegant use of the Janelia Fluor dyes for cellular imaging. www.nature.com/articles/s41...
Very interesting discussion here
I am honnestly a bit worried by the latest fuss about qed (the IA driven review). While the results are indeed quite impressive (it is very good at listing the claim and finding potential improvement), I don't quite see how this will eventually reduce the reviewing burden or help us
November 7, 2025 at 10:26 AM
Very interesting discussion here
Reposted by Fabrice Senger
Diatoms – microscopic algae found almost everywhere there’s water – make up ~25% of Earth’s annual oxygen production.🌎
EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬
www.cell.com/current-biol...
EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬
www.cell.com/current-biol...
November 6, 2025 at 1:28 PM
Diatoms – microscopic algae found almost everywhere there’s water – make up ~25% of Earth’s annual oxygen production.🌎
EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬
www.cell.com/current-biol...
EMBL researchers have now found a way to easily reveal their inner structures by combining cryo-fixation with ultrastructural expansion microscopy 🔬
www.cell.com/current-biol...
Reposted by Fabrice Senger
Janelia is hosting a course on DL for bioimage analysis www.janelia.org/you-janelia/...
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.,
www.janelia.org
November 6, 2025 at 5:02 PM
Janelia is hosting a course on DL for bioimage analysis www.janelia.org/you-janelia/...
Reposted by Fabrice Senger
November 6, 2025 at 12:09 PM
Reposted by Fabrice Senger
Laurence Wilson and Martin Bees use high-speed 3D holographic imaging to capture the flagellar beat of single algal cells, revealing changes in the ‘handedness’ of the flagellar shapes at different points in their cycle.
#JCSciliaSI
journals.biologists.com/jcs/article/...
#JCSciliaSI
journals.biologists.com/jcs/article/...
November 6, 2025 at 9:05 AM
Laurence Wilson and Martin Bees use high-speed 3D holographic imaging to capture the flagellar beat of single algal cells, revealing changes in the ‘handedness’ of the flagellar shapes at different points in their cycle.
#JCSciliaSI
journals.biologists.com/jcs/article/...
#JCSciliaSI
journals.biologists.com/jcs/article/...
Reposted by Fabrice Senger
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
November 4, 2025 at 10:40 PM
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
Reposted by Fabrice Senger
In the New and Notable "Single-cell memory matters in collective migration ," Ruihan Hou and Jinglei Hu highlight the paper "Time-dependent active force drives periodic reversal in collective cell migration."
Single-cell memory matters in collective migration
The coordinated migration of collective cells within confluent tissues is essential for various physiological and pathological processes, including embryogenesis, wound healing, and cancer metastasis…
www.cell.com
November 5, 2025 at 7:01 PM
In the New and Notable "Single-cell memory matters in collective migration ," Ruihan Hou and Jinglei Hu highlight the paper "Time-dependent active force drives periodic reversal in collective cell migration."
Reposted by Fabrice Senger
Out now: Simulating Organogenesis in #COMSOL: Tissue Patterning with Directed Cell Migration
We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis.
arxiv.org/pdf/2509.08930
We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis.
arxiv.org/pdf/2509.08930
September 12, 2025 at 5:23 AM
Out now: Simulating Organogenesis in #COMSOL: Tissue Patterning with Directed Cell Migration
We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis.
arxiv.org/pdf/2509.08930
We provide a detailed walkthrough of how to implement #DCM partial integro-differential equation models - enabling accessible simulations of tissue patterning and morphogenesis.
arxiv.org/pdf/2509.08930
i clustered some stuff
November 5, 2025 at 4:20 PM
i clustered some stuff
Reposted by Fabrice Senger
We have observed a beautifully strange phenomenon of phase separation by human monocytes placed on soft matrix, which do it for survival.
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
Mechano-induced patterned domain formation by monocytes - Nature Materials
Human primary monocytes reversibly phase separate into regular, multicellular, multilayered domains on soft matrices with physiological stiffness due to local activation and global inhibition processe...
www.nature.com
November 5, 2025 at 12:41 PM
We have observed a beautifully strange phenomenon of phase separation by human monocytes placed on soft matrix, which do it for survival.
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
Reposted by Fabrice Senger
If necessary Pierre NASSOY's talk 😜 :
👉 youtu.be/ye-i6deGO1Q?...
@univbordeaux.bsky.social @cnrs.fr
#Mifobio2025 #GDRimabio
👉 youtu.be/ye-i6deGO1Q?...
@univbordeaux.bsky.social @cnrs.fr
#Mifobio2025 #GDRimabio
November 4, 2025 at 5:13 PM
If necessary Pierre NASSOY's talk 😜 :
👉 youtu.be/ye-i6deGO1Q?...
@univbordeaux.bsky.social @cnrs.fr
#Mifobio2025 #GDRimabio
👉 youtu.be/ye-i6deGO1Q?...
@univbordeaux.bsky.social @cnrs.fr
#Mifobio2025 #GDRimabio
Have a look, i love it. The code is super well annotated !
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Adventures in Code VII: getting started with napari – quantixed
quantixed.org
November 4, 2025 at 12:37 PM
Have a look, i love it. The code is super well annotated !
Reposted by Fabrice Senger
We've now discovered some neat cell culture dishes that feature a 50 micron thick film of a proprietary polymer with refractive index even closer to water than FEP. They work just as well as our homemade FEP assembly and are available in multiwell plate format too!
www.sarstedt.com/en/products/...
www.sarstedt.com/en/products/...
October 28, 2025 at 8:27 PM
We've now discovered some neat cell culture dishes that feature a 50 micron thick film of a proprietary polymer with refractive index even closer to water than FEP. They work just as well as our homemade FEP assembly and are available in multiwell plate format too!
www.sarstedt.com/en/products/...
www.sarstedt.com/en/products/...
Reposted by Fabrice Senger
Good documentation makes open hardware accessible, reusable & extensible.
Join the next GOSH Community Call with Julien Colomb, who’ll share his new Hardware Documentation Guide & lead a discussion on documenting for collaboration & reuse.
🗓 Nov 20 · 12:00 UTC
🔗 us06web.zoom.us/meeting/regi...
Join the next GOSH Community Call with Julien Colomb, who’ll share his new Hardware Documentation Guide & lead a discussion on documenting for collaboration & reuse.
🗓 Nov 20 · 12:00 UTC
🔗 us06web.zoom.us/meeting/regi...
November 3, 2025 at 12:59 PM
Good documentation makes open hardware accessible, reusable & extensible.
Join the next GOSH Community Call with Julien Colomb, who’ll share his new Hardware Documentation Guide & lead a discussion on documenting for collaboration & reuse.
🗓 Nov 20 · 12:00 UTC
🔗 us06web.zoom.us/meeting/regi...
Join the next GOSH Community Call with Julien Colomb, who’ll share his new Hardware Documentation Guide & lead a discussion on documenting for collaboration & reuse.
🗓 Nov 20 · 12:00 UTC
🔗 us06web.zoom.us/meeting/regi...
Reposted by Fabrice Senger
With SNAP benefits suspended for now, I just donated to my local food bank. If you can, you should consider donating to your local food bank. No one should be going hungry in this day and age
November 1, 2025 at 2:41 PM
With SNAP benefits suspended for now, I just donated to my local food bank. If you can, you should consider donating to your local food bank. No one should be going hungry in this day and age
Reposted by Fabrice Senger
Just tried q.e.d. by @odedrechavi.bsky.social et al. with a few papers including by myself & others where I knew a claim within was flawed based on a misunderstanding of the signal.
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
q.e.d Science
Critical Thinking AI for constructive criticism and science evaluation
www.qedscience.com
November 1, 2025 at 12:15 PM
Just tried q.e.d. by @odedrechavi.bsky.social et al. with a few papers including by myself & others where I knew a claim within was flawed based on a misunderstanding of the signal.
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n
1) it was impressive. I see what the hype is about.
2) it hallucinated.
www.qedscience.com
Overly long #SciPub🧵 1/n