Fabrice Senger
@senger.bsky.social
Mechanobiology / Multi-cellular assemblies
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
Reposted by Fabrice Senger
Reposted by Fabrice Senger
@vicidominilab.bsky.social's lecture is online !
👉 “Photon-Resolved Microscopy : Image-Scanning Microscopy with SPAD Array Detector and Beyond”
👉 youtu.be/Pgn-8F87RUE
@iitalk.bsky.social
#SPADarray #BrightEyes_ERC #photonresolvedmicroscopy #imagescanningmicroscopy #Mifobio2025 #GDRImabio
👉 “Photon-Resolved Microscopy : Image-Scanning Microscopy with SPAD Array Detector and Beyond”
👉 youtu.be/Pgn-8F87RUE
@iitalk.bsky.social
#SPADarray #BrightEyes_ERC #photonresolvedmicroscopy #imagescanningmicroscopy #Mifobio2025 #GDRImabio
Giuseppe VICIDOMINI : Photon-Resolved Microscopy: Image-Scanning Microscopy with SPAD Array Det... ”
YouTube video by GDR Imabio - CNRS
youtu.be
October 30, 2025 at 8:25 PM
@vicidominilab.bsky.social's lecture is online !
👉 “Photon-Resolved Microscopy : Image-Scanning Microscopy with SPAD Array Detector and Beyond”
👉 youtu.be/Pgn-8F87RUE
@iitalk.bsky.social
#SPADarray #BrightEyes_ERC #photonresolvedmicroscopy #imagescanningmicroscopy #Mifobio2025 #GDRImabio
👉 “Photon-Resolved Microscopy : Image-Scanning Microscopy with SPAD Array Detector and Beyond”
👉 youtu.be/Pgn-8F87RUE
@iitalk.bsky.social
#SPADarray #BrightEyes_ERC #photonresolvedmicroscopy #imagescanningmicroscopy #Mifobio2025 #GDRImabio
something new (at leaast to me) every day, pickle, is cool
October 31, 2025 at 10:36 AM
something new (at leaast to me) every day, pickle, is cool
Reposted by Fabrice Senger
Wei OUYANG's lecture is online !
👉 Generative AI for Microscopy : From Automated Imaging to Virtual Cell Modeling”
👉 youtu.be/bIAfX3uewE4
#Kungliga_Tekniska_Högskolan
#KTH #SciLifeLab
@cnrs.fr @cnrsingenierie.bsky.social
@gdr-imabio-ysn.bsky.social
#Mifobio2025 #GDRImabio
👉 Generative AI for Microscopy : From Automated Imaging to Virtual Cell Modeling”
👉 youtu.be/bIAfX3uewE4
#Kungliga_Tekniska_Högskolan
#KTH #SciLifeLab
@cnrs.fr @cnrsingenierie.bsky.social
@gdr-imabio-ysn.bsky.social
#Mifobio2025 #GDRImabio
October 30, 2025 at 10:22 AM
Wei OUYANG's lecture is online !
👉 Generative AI for Microscopy : From Automated Imaging to Virtual Cell Modeling”
👉 youtu.be/bIAfX3uewE4
#Kungliga_Tekniska_Högskolan
#KTH #SciLifeLab
@cnrs.fr @cnrsingenierie.bsky.social
@gdr-imabio-ysn.bsky.social
#Mifobio2025 #GDRImabio
👉 Generative AI for Microscopy : From Automated Imaging to Virtual Cell Modeling”
👉 youtu.be/bIAfX3uewE4
#Kungliga_Tekniska_Högskolan
#KTH #SciLifeLab
@cnrs.fr @cnrsingenierie.bsky.social
@gdr-imabio-ysn.bsky.social
#Mifobio2025 #GDRImabio
Reposted by Fabrice Senger
Using endocytosis to switch between chemoattraction and chemorepulsion https://www.biorxiv.org/content/10.1101/2025.10.28.685129v1
October 30, 2025 at 10:30 AM
Using endocytosis to switch between chemoattraction and chemorepulsion https://www.biorxiv.org/content/10.1101/2025.10.28.685129v1
Reposted by Fabrice Senger
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
October 29, 2025 at 2:20 PM
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!