Valentin Dunsing-Eichenauer

elifesciences.orgA quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scalesThe Tapenade pipeline enables single-cell, whole-mount 3D quantification in dense multilayer organoids, linking spatial gene co-expression and nuclear deformation to emerging tissue-scale…

#FluorescenceFriday: Given the recently grown interest in ciliary beating, here is a movie of beating cilia in a human airway model that I captured last week with lattice light-sheet microscopy. No AI „processing“, this is the raw data! Frame rate is ca. 170fps, displayed here at 25fps.

Valentin Dunsing-Eichenauer reposted

eLife

@elife.bsky.social

2 July

A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales elifesciences.org/articles/107...

epithelial mechanics fan club

6 July

Already out for a while as the final version: Our @elife.bsky.social paper presenting an experimental and computational pipeline for whole mount deep imaging and multi-scale analysis of organoid systems: elifesciences.org/articles/107... A great collaboration during my postdoc in Marseille.

Biomedical Picture of the Day BPoD@bpodaily.bsky.social

User-friendly pipeline Tapenade quantifies spatial patterns of gene expression & nuclear morphology in 3D cell assembly '...oids' 📹 @alicegros.bsky.social, @jules-vanaret.bsky.social, @dunsingvalentin.bsky.social et al @centuri-ls.bsky.social in @elife.bsky.social ➡️ bpod.org.uk/archive/2026...

Valentin Dunsing-Eichenauer reposted

@epimechfc.bsky.social

12 Apr

How does an orbiting spherical tissue suddenly break symmetry and sprout invasive strands? We can predict this behavior from the initial morphology! Hi, I’m @jiwon-kim.bsky.social from @ianywonglab.bsky.social.

@joachimgoedhart.bsky.social

22 Apr

Today we celebrated the opening of Si-M (The Simulated Human), a new joint institute by Charité and TU Berlin. Si-M combines expertise in biology and medicine with engineering and data science to advance human model systems for biomedical research and translation into diagnostics and therapy.

Technische Universität Berlin@tuberlin.bsky.social

Starkes Zeichen für die #Medizin der Zukunft: Neuer Campus für Bio- & Medizintechnologie feierlich eröffnet 🔬 Mit dem Forschungszentrum „Der Simulierte Mensch“ (Si-M) stärken #TUBerlin & @berlinualliance.bsky.social -Partnerin #CharitéBerlin ihre Zusammenarbeit. 🤝 #BMFTR #SENWGP

Valentin Dunsing-Eichenauer reposted

Joachim Goedhart

13 Apr

📣 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...

Valentin Dunsing-Eichenauer reposted

clementhelsens.bsky.social

@clementhelsens.bsky.social

11 Apr

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

7 Apr

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

youtube.comMédaille de bronze 2025 : Sham Tlili, décrypter les lois physiques de la formation des tissusYouTube video by CNRS

7 Apr

Félicitations @shamtlili.bsky.social!🥳 Nice to see some familiar images and faces in this video🙂

IBDM, Institut de Biologie du Développement de Marseille@ibdm.bsky.social

🎥 Our researcher @shamtlili.bsky.social explores the physical laws governing tissue formation in this video, following the CNRS Bronze Medal she received last year 🏅 www.youtube.com/watch?v=-22F...

7 Apr

And very well deserved recognition!

25 Mar

Join us this Friday in the Euro-BioImaging #VirtualPub!🔬

eurobioimaging.bsky.social@eurobioimaging.bsky.social

#VirtualPub We welcome Valentin Dunsing-Eichenauer, Charité Universitätsmedizin Berlin, on "Functional & deep imaging of #organoids via light-sheet #FLIM and two-photon microscopy." 🗓️ Fri, March 27 @ 13:00 CET Register ⤵️ www.eurobioimaging.eu/events/funct...

Valentin Dunsing-Eichenauer reposted

Spirochrome

@spirochrome.com

10 Mar

🧵 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

4 Mar

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!

eurobioimaging.bsky.social@eurobioimaging.bsky.social

📣 We're delighted to share the latest calendar for the #EuroBioImaging #VirtualPub! Lots of exciting talks in the coming weeks - many from our Node colleagues. We hope you can join for these great lectures on 🕐 Fridays @ 1 pm CET. Register🔽 www.eurobioimaging.eu/our-events/v...

nature.comSpatial patterning of contractility by a self-organized mechanogen activity gradient underlies Drosophila gastrulation - Nature CommunicationsDuring morphogenesis patterned contractility drives tissue shape changes. Here they show that GPCR signaling and integrin activation give rise to a dynamically translocating gradient of contractility ...

24 Feb

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...

24 Feb

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”.

@miquelsendra.bsky.social

24 Feb

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.

Valentin Dunsing-Eichenauer reposted

miquelsendra.bsky.social

6 Feb

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

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...

I want to thank my postdoc mentor Pierre-François Lenne @pflenne.bsky.social for giving me the freedom to embark on this exciting project.

Lastly, I want to thank the Human Frontier Science Program @hfspo.bsky.social for continuous support with a long-term postdoctoral fellowship.

github.comGitHub - ValDunsing/soSPIM-FLIM: Python code associated to "Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy" by Dunsing-Eichenauer,...Python code associated to "Fast volumetric fluorescence lifetime imaging of multicellular systems using single-objective light-sheet microscopy" by Dunsing-Eichenauer, Hummert et al., bio...

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....

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.

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.

Finally, by sub-sampling our data, we show that sub-100ms acquisition times can still provide robust lifetime estimates.

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.

This allowed us to perform 3D FLIM and volumetric lifetime-multiplexed imaging on dense multicellular aggregates (embryonic organoids).

Very happy to share that starting in January, I will take on a new position as microscopic imaging facility leader and researcher at Der Simulierte Mensch (Si-M), a new joint institute by Charité and TUBerlin, which aims at advancing human model systems (e.g. organoids) for biomedical research.

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.

My research activities will continue and exciting projects are ahead.

jbc.orgStayRose: a photostable StayGold derivative red-shifted by genetic code expansionPhotobleaching of fluorescent proteins often limits the acquisition of high-quality images in microscopy. StayGold, a novel dimeric green fluorescent protein recently monomerised through sequence engi...

I look forward to contribute my expertise in quantitative optical microscopy and biophysics to the interdisciplinary scope of Si-M to make an impact for the biomedicine of the future.

Valentin Dunsing-Eichenauer reposted

Falk Schneider

@faldalf.bsky.social

22 Oct 2025

mStayRose is published in JBC 🥳🎉 Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable: www.jbc.org/article/S002...