Image of a calcium calibration curve, calcium concentration traces of individual cells and lifetime images of cells
📣 New preprint alert! Co-authored by @spalaciosm.bsky.social and @andreacaldarola.bsky.social :
Quantitative imaging of calcium dynamics with a green fluorescent biosensor and fluorescence lifetime imaging
www.biorxiv.org/content/10.6...
We tracked a zebrafish tail tip for 30h of light-sheet imaging.
It didn’t exist at t=0.
LiLiTTool: CoTracker3 + object detection → real-time microscope steering.
3D, multi-ROI, open source.
www.biorxiv.org/content/10.6...
#bioimaging #lightsheet
thanks @jytinevez.bsky.social
Painted 100+ lung organoids for Easter, stained with live-cell Cell Tracker/ @spirochrome.com dyes, imaged at our @leicamicrosystems.bsky.social Viventis Deep light-sheet 🔬 at Charité (soon @Si-M - Der Simulierte Mensch) and visualized using inverted lookup tables designed by @christlet.bsky.social
And very well deserved recognition!
Félicitations @shamtlili.bsky.social!🥳 Nice to see some familiar images and faces in this video🙂
Join us this Friday in the Euro-BioImaging #VirtualPub!🔬
🧵 1/5 A new BioRxiv preprint reveals that membrane tension acts as a mechanical gate for lung cell fate during development! 🫁
Our Flipper-TR probe was key to assess live Cell Membrane Tension (CMT)
Here’s how Flipper-TR unlocked a hidden layer of lung development & fibrosis. 👇 #Mechanobiology
I am looking forward to present our recent works on volumetric light-sheet FLIM (www.nature.com/articles/s42...) and two-photon multiscale imaging & analysis (elifesciences.org/reviewed-pre...) of organoids in the Euro-BioImaging #VirtualPub on March 27th!
I’d like to thank @hfspo.bsky.social for continuous support with a long-term fellowship, providing the freedom to embark on such exciting projects.
This was a fantastic collaboration with @mundhegayatri.bsky.social, Claudio Collinet and @thomaslecuit.bsky.social at @ibdm.bsky.social during my postdoc time in Marseille. The paper is available in Nat. Comms., featured in the collection “Organizers and self-organization in developmental biology”.
New paper out! In this project, we focused on the question how tissue mechanics is spatially controlled during development. We show that the GPCR ligand Fog acts as a “mechanogen” during Drosophila gastrulation, driving a self-organized wave of tissue invagination:
www.nature.com/articles/s41...
To turn spatial data into a 3D object, check our protocol (open source, napari plug-in). @guignardlab.bsky.social @adrianobolondi.bsky.social @ibdm.bsky.social
For example, if you have spatial RNA-seq as sections, you can align them automatically to analyse directly in 3D.
bio-protocol.org/e5607
For good reasons. Some of my favourite SPIM acronyms were born back then!
Oh, I am very sorry. I thought we had cited and listed all previous SPIM-FLIM publications. We missed yours somehow (by no means intentionally of course!). Your implementation was frequency domain based then?
Thank you! This is fully volumetric time lapse FLIM data over a ca. 50 um depth range (1 plane every 2 um). In the end we only analysed Flipper-TR lifetimes in one 2d section per cell, but in principle one could analyse individual cells or junctions and their dynamics in 3D.
Thank you Amir!
Thank you Joachim! I think there are many cool applications that hopefully we and others will explore in the future. Could be also promising in combination with OPM-like systems.
Lastly, I want to thank the Human Frontier Science Program @hfspo.bsky.social for continuous support with a long-term postdoctoral fellowship.
I want to thank my postdoc mentor Pierre-François Lenne @pflenne.bsky.social for giving me the freedom to embark on this exciting project.
This project was a great collaboration with Johan Hummert and colleagues at @picoquant.bsky.social kindly providing equipment, PI Imaging Technologies in Lausanne where the detector was developed, co-workers in Marseille and in Bordeaux and Singapore that originally developed the soSPIM microscope.
Our implementation opens up new applications for fluorescence lifetime based sensing (e.g. of forces, metabolites, pH, protein-protein interactions) in 3D specimen at sub-cellular resolution using light-sheet microscopy.
Analysis code is available on GitHub: github.com/ValDunsing/s....
Finally, by sub-sampling our data, we show that sub-100ms acquisition times can still provide robust lifetime estimates.
We also achieved time-lapse 3D imaging of membrane tension in live organoids. This revealed illumination-induced lifetime changes of Flipper-TR requiring further investigation. Strikingly though, we could detect subtle changes in individual cells and junctions tracked over time with 1s frame times.
This allowed us to perform 3D FLIM and volumetric lifetime-multiplexed imaging on dense multicellular aggregates (embryonic organoids).
We benchmarked soSPIM-FLIM with both static and scanning light-sheet illumination, making our implementation transferable to many light-sheet configurations.
We achieved excellent quantitative agreement to confocal FLIM at orders of magnitude shorter acquisition times, down to 100ms per image.
New paper out! Combining single-objective light-sheet microscopy and time-resolved SPAD array detection, we massively accelerate fluorescence lifetime imaging (FLIM) compared to confocal FLIM, making FLIM applicable to 3D specimen such as organoids and embryos.
www.nature.com/articles/s42...
Thanks! You are very welcome to visit! It has BIMSB-like stairs, just wider, and microscopes will be on an upper floor and not in the basement :)
Thank you, Helge! You are welcome to visit once the doors are opened.
My research activities will continue and exciting projects are ahead.
Personally, I seriously doubted a future in academia and its compatibility with family life after just missing out on a DFG Emmy Noether Grant at the final Interview stage in June, when our twins were just 5 months old. The long-term perspective of the new position brought back a lot of motivation.
