Fabrice Senger
@senger.bsky.social
Mechanobiology / Multi-cellular assemblies
Reposted by Fabrice Senger
Optogenetic control of mechanotransduction based on light-induced homodimerization of talin url: journals.biologists.com/jcs/article-...
Optogenetic control of mechanotransduction based on light-induced homodimerization of talin
Integrin-based adhesion complexes serve as primary sites for actomyosin force transmission to the extracellular matrix, providing traction that drives cell mechanical responses including adhesion, mig...
journals.biologists.com
November 24, 2025 at 4:49 PM
Optogenetic control of mechanotransduction based on light-induced homodimerization of talin url: journals.biologists.com/jcs/article-...
Reposted by Fabrice Senger
In our new #Preprint, we pilot a revolutionary new idea: no supplemental data (it has 21 figures, though):
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
We have previously shown that the calcium sensing receptor (CaSR) activates different G proteins and second messengers in single cells, and that GPCR and G protein-mediated ERK activity can be highly ...
www.biorxiv.org
November 24, 2025 at 8:29 AM
In our new #Preprint, we pilot a revolutionary new idea: no supplemental data (it has 21 figures, though):
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR
www.biorxiv.org/content/10.1...
Pourquoi je vais à la mediatheque...
November 22, 2025 at 7:12 PM
Pourquoi je vais à la mediatheque...
Very interesting read
Lee, J., Abdeen, A. A., Wycislo, K. L., Fan, T. M., & Kilian, K. A. (2016). Interfacial geometry dictates cancer cell tumorigenicity. Nature materials, doi.org/10.1038/nmat... #EpithelialMechanics
November 21, 2025 at 12:33 PM
Very interesting read
Reposted by Fabrice Senger
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
Reposted by Fabrice Senger
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
November 21, 2025 at 9:29 AM
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
🤩
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 2:25 PM
🤩
Reposted by Fabrice Senger
Extremely thankful to @caixaresearch.bsky.social for supporting our vision, and to all the amazing collaborators who enable our research. It takes a vilage and this is a road we walk together. Now onwards to make those scopes go pew pew only when needed
Light from high-res microscopes can damage cells and limit the study of viral infection cycles.
With a #HealthResearch grant, @henriqueslab.bsky.social (@itqbnova.bsky.social) uses AI to adjust light in real time and boost our understanding of infectious diseases.
https://tinyurl.com/3y8zwyes
With a #HealthResearch grant, @henriqueslab.bsky.social (@itqbnova.bsky.social) uses AI to adjust light in real time and boost our understanding of infectious diseases.
https://tinyurl.com/3y8zwyes
November 20, 2025 at 11:17 AM
Extremely thankful to @caixaresearch.bsky.social for supporting our vision, and to all the amazing collaborators who enable our research. It takes a vilage and this is a road we walk together. Now onwards to make those scopes go pew pew only when needed
Reposted by Fabrice Senger
Our new paper is published in the Journal of Chemical Biology! 🏮 We share StayRose, a red version of StayGold 🏮 StayRose has an unnatural amino acid-based chromophore, and has the same immense photobleach-resistance as StayGold 💡
StayRose: A photostable StayGold derivative redshifted by genetic code expansion
Photobleaching of fluorescent proteins often limits the acquisition of high-quality
images in microscopy. StayGold, a novel dimeric GFP recently monomerized through sequence
engineering, addresses thi...
www.jbc.org
November 17, 2025 at 9:03 AM
Our new paper is published in the Journal of Chemical Biology! 🏮 We share StayRose, a red version of StayGold 🏮 StayRose has an unnatural amino acid-based chromophore, and has the same immense photobleach-resistance as StayGold 💡
Reposted by Fabrice Senger
quick test with SAM3 - impressed with how well it seems to track long protrusions? prompted for "cell", does not find anything when looking for "fibroblast" or "nucleus"
November 19, 2025 at 8:15 PM
quick test with SAM3 - impressed with how well it seems to track long protrusions? prompted for "cell", does not find anything when looking for "fibroblast" or "nucleus"
Une FSEP a Grenoble, a l'IAB ... Mecanique cellulaire, microfabrication, microfluidique ... Plus de détails bientôt ...Pour les collègues CNRS eventuellement interressés
November 19, 2025 at 4:29 PM
Une FSEP a Grenoble, a l'IAB ... Mecanique cellulaire, microfabrication, microfluidique ... Plus de détails bientôt ...Pour les collègues CNRS eventuellement interressés
Reposted by Fabrice Senger
Searching for physical principles of morphogenesis
In this #OpenAccess Spotlight, Nikolas Claussen, Fridtjof Brauns and @streichan.bsky.social highlight the ‘physics of development’, focusing on the interplay between quantitative experiments and mathematical theory
doi.org/10.1242/dev....
In this #OpenAccess Spotlight, Nikolas Claussen, Fridtjof Brauns and @streichan.bsky.social highlight the ‘physics of development’, focusing on the interplay between quantitative experiments and mathematical theory
doi.org/10.1242/dev....
November 19, 2025 at 10:28 AM
Searching for physical principles of morphogenesis
In this #OpenAccess Spotlight, Nikolas Claussen, Fridtjof Brauns and @streichan.bsky.social highlight the ‘physics of development’, focusing on the interplay between quantitative experiments and mathematical theory
doi.org/10.1242/dev....
In this #OpenAccess Spotlight, Nikolas Claussen, Fridtjof Brauns and @streichan.bsky.social highlight the ‘physics of development’, focusing on the interplay between quantitative experiments and mathematical theory
doi.org/10.1242/dev....
Reposted by Fabrice Senger
We have a multidisciplinary PhD position on offer, through a BBSRC funded doctoral training program, open to UK and International students at Bath Uni. Microfluidics, microscopy, mechanobiology and epigenetics!
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
SWBio DTP PhD Project: Mapping the epigenetic landscape in cells under compressive forces at University of Bath on FindAPhD.com
PhD Project - SWBio DTP PhD Project: Mapping the epigenetic landscape in cells under compressive forces at University of Bath, listed on FindAPhD.com
www.findaphd.com
November 19, 2025 at 5:29 AM
We have a multidisciplinary PhD position on offer, through a BBSRC funded doctoral training program, open to UK and International students at Bath Uni. Microfluidics, microscopy, mechanobiology and epigenetics!
www.findaphd.com/phds/project...
www.findaphd.com/phds/project...
Reposted by Fabrice Senger
After 3 broken trains, and 2h delay, I’m finally in Delft for the MicroNano conference. If you’re around, in the afternoon I’ll give a talk on “uncommon microfluidics” . Which, you know me, it is mostly 3D printing :)
November 19, 2025 at 10:56 AM
After 3 broken trains, and 2h delay, I’m finally in Delft for the MicroNano conference. If you’re around, in the afternoon I’ll give a talk on “uncommon microfluidics” . Which, you know me, it is mostly 3D printing :)
Reposted by Fabrice Senger
OK. First post on Bluesky…
November 19, 2025 at 11:40 AM
OK. First post on Bluesky…
Reposted by Fabrice Senger
How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
November 18, 2025 at 4:15 PM
How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
Reposted by Fabrice Senger
Gemini 3 leak shows solid gains on math, vision, and SimpleQA
Sonnet still ahead on SWE-bench though, while Gemini takes TerminalBench
Nice to see models getting better at different things
Sonnet still ahead on SWE-bench though, while Gemini takes TerminalBench
Nice to see models getting better at different things
November 18, 2025 at 2:41 PM
Gemini 3 leak shows solid gains on math, vision, and SimpleQA
Sonnet still ahead on SWE-bench though, while Gemini takes TerminalBench
Nice to see models getting better at different things
Sonnet still ahead on SWE-bench though, while Gemini takes TerminalBench
Nice to see models getting better at different things
Reposted by Fabrice Senger
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Python package managers: uv vs pixi?
When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I don’t hear much ab...
jacobtomlinson.dev
November 18, 2025 at 12:56 PM
For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing.
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow.
jacobtomlinson.dev/posts/2025/p...
Reposted by Fabrice Senger
Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration:
www.i2kconference.org/workshops
www.i2kconference.org/workshops
November 18, 2025 at 12:13 PM
Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration:
www.i2kconference.org/workshops
www.i2kconference.org/workshops
Reposted by Fabrice Senger
The first meeting was a blast and the second one promises to be even better - if you submit your abstract and join us!
Join us for the second edition of 'AI and biology'! 🤖🧬
Explore how AI transforms biological research – from foundation models for biology to generative modelling.
10 – 13 March 2026
EMBL Heidelberg and Virtual
Submit your abstract by 2 Dec: s.embl.org/ees26-02-bl
#EESAIBio #AI
Explore how AI transforms biological research – from foundation models for biology to generative modelling.
10 – 13 March 2026
EMBL Heidelberg and Virtual
Submit your abstract by 2 Dec: s.embl.org/ees26-02-bl
#EESAIBio #AI
November 18, 2025 at 12:43 PM
The first meeting was a blast and the second one promises to be even better - if you submit your abstract and join us!
Reposted by Fabrice Senger
📢Check out our latest #preprint list on FocalPlane
This list focusses on the latest research on bioimage analysis and data management. Let us know if there are any preprints that we should add to our list and send us recommendation for the next one!
focalplane.biologists.com/2025/11/14/m...
This list focusses on the latest research on bioimage analysis and data management. Let us know if there are any preprints that we should add to our list and send us recommendation for the next one!
focalplane.biologists.com/2025/11/14/m...
Microscopy preprints – bioimage analysis - FocalPlane
Microscopy preprints – bioimage analysis - News
focalplane.biologists.com
November 18, 2025 at 10:07 AM
📢Check out our latest #preprint list on FocalPlane
This list focusses on the latest research on bioimage analysis and data management. Let us know if there are any preprints that we should add to our list and send us recommendation for the next one!
focalplane.biologists.com/2025/11/14/m...
This list focusses on the latest research on bioimage analysis and data management. Let us know if there are any preprints that we should add to our list and send us recommendation for the next one!
focalplane.biologists.com/2025/11/14/m...
Reposted by Fabrice Senger
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
November 6, 2025 at 6:56 PM
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
Un univers fascinant
November 16, 2025 at 6:07 PM
Un univers fascinant
Reposted by Fabrice Senger
☕Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, enabling single-cell developmental stage inference.
👉https://rdcu.be/eP9HH
bit.ly/49VARB8
👉https://rdcu.be/eP9HH
bit.ly/49VARB8
TemporalVAE: atlas-assisted temporal mapping of time-series single-cell transcriptomes during embryogenesis - Nature Cell Biology
Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, e...
bit.ly
November 16, 2025 at 8:34 AM
☕Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, enabling single-cell developmental stage inference.
👉https://rdcu.be/eP9HH
bit.ly/49VARB8
👉https://rdcu.be/eP9HH
bit.ly/49VARB8
Reposted by Fabrice Senger
Microfluidic pumping with active nematics! Self-organized and self-sustained. No external pumps.
@pnas.org @ub.edu
www.pnas.org/doi/10.1073/...
#ActiveMatter #Microfluidics #SoftMatter
@pnas.org @ub.edu
www.pnas.org/doi/10.1073/...
#ActiveMatter #Microfluidics #SoftMatter
Active nematic pumps | PNAS
Microfluidics involves the manipulation of flows at the microscale, typically requiring
external power sources to generate pressure gradients. Alte...
www.pnas.org
November 12, 2025 at 7:20 PM
Microfluidic pumping with active nematics! Self-organized and self-sustained. No external pumps.
@pnas.org @ub.edu
www.pnas.org/doi/10.1073/...
#ActiveMatter #Microfluidics #SoftMatter
@pnas.org @ub.edu
www.pnas.org/doi/10.1073/...
#ActiveMatter #Microfluidics #SoftMatter