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

A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales

The 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…

elifesciences.org

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.

A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales

The 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 organization...

elifesciences.org

Biomedical Picture of the Day BPoD@bpodaily.bsky.social · 2mo ago

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...

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.

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 · 4mo ago

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

📣 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

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 · 4mo ago

🎥 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...

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

eurobioimaging.bsky.social@eurobioimaging.bsky.social · 4mo ago

#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...

🧵 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!

eurobioimaging.bsky.social@eurobioimaging.bsky.social · 5mo ago

📣 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...

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...

Spatial patterning of contractility by a self-organized mechanogen activity gradient underlies Drosophila gastrulation - Nature Communications

During 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 ...

nature.com

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...

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.

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...

StayRose: a photostable StayGold derivative red-shifted by genetic code expansion

Photobleaching 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...

jbc.org

It has been great two days of scientific exchange at @picoquant.bsky.social 30th Single Molecule Workshop in Berlin #WS30. Looking forward to present a poster on in vivo applications of FCS tomorrow and a talk on fast, volumetric light-sheet FLIM in organoids on Friday!

Latest paper elifesciences.org/articles/107... closes an important cycle in our efforts to study regeneration: week-long recordings allow us to observe the behaviour of cells during the entire course of regeneration in a crustacean leg – bright objects in movie are fluorescent nuclei of cells. 1/6

🥇Sham Tlili has been awarded the CNRS 2025 Bronze Medal! She studies how physical forces shape living tissues by using mouse stem cell models known as gastruloids. A unique blend of physics & biology. 🔗 Read more: www.ibdm.univ-amu.fr/sham-tlili-w...

Sham Tlili, winner of the CNRS 2025 bronze medal - IBDM | Institut de Biologie du Développement de Marseille

A distinction that rewards a promising and already fruitful scientific career.

ibdm.univ-amu.fr

A computational framework links transcriptomic analyses with mechanical signatures to study the interplay between cell mechanical forces and gene expression. www.nature.com/articles/s41...

🔬🎤 As pre-announced a few days ago... please let us proudly present to you: 𝑴𝒊𝒄𝒓𝒐𝕊𝒑𝒍𝒊𝒕 - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. 🔬 doi.org/10.1101/2025... Like ❤️, repost 🔂, and most importantly... please send feedback ✉️ our way! 🙏

Florian Jug@florianjug.bsky.social · last yr.

Immagine you could image two cellular structures in the same fluorescent channel and still reliably get them separated afterwards… What would you do with this? Now… what would you do if that also worked with 4 structures at once? 👇 #MicroSplit #preview🧵

Thrilled to share our latest review paper, "Advanced Fluorescence Lifetime-Enhanced Multiplexed Nanoscopy of Cells", co-authored with @samratb.bsky.social, now published in Methods in Microscopy! 🚀✨ Check it out here: www.degruyter.com/document/doi... #FLIM #SMLM #FLPAINT #FLSMLM #MIETPAINT

Hello bsky :). Application still opened for an exciting @centuri-ls.bsky.social PhD project with C. Collinet combining AI and stochastic modeling to understand how living embryos rearrange their own shape! Project & application details here: centuri-livingsystems.org/application-... DL Jan 27th.

Delighted to share our last preprint!!! 🎉🎉🎉 biorxiv.org/content/10.1101/2024.12.11.627621v1 We share the first synthetic gene circuit guiding the self-organization of mammalian tissues in elongating structures by dynamically tuning growth, viscosity and adhesion.

How does nano-scale plasma membrane structure underpin tissue development? Let’s find out! First opportunity to do a PhD with me, co-supervised by Darius Koester, at Warwick. Fully funded studentship by #MIBTP and University of Warwick. 🔬✨🐟📸 More info here: www.findaphd.com/phds/project...

Discover the winners of the FBI Image Contest 2024🔬 🥇Place: Vanessa Weichselberger (IBDM-Université Aix-Marseille) 🥈Place: Dalia El Arawi (IBDM) 🥉Place: Frédéric Fercoq (Musée National d'Histoire Naturelle-Unité MCAM) 🏆 Congratulations to them! 👏 A big thank you to all the participants!

Happy to have the Srinivas lab on Bluesky! Even our embryos are starting to feel a little festive in the Srinivas lab! We are excited to share our new bioRχiv pre-print – investigating the role of calcium in the early embryo www.biorxiv.org/content/10.1...

Any more FFS/FCS Folks on bluesky? Where are you? Time to correlate. Please let me know who is on here and needs to be added. go.bsky.app/4BbiZyW

📣Exciting meeting ahead! Join us at Shaping Life 3 in beautiful Cassis next June! www.atoutcom.com/shaping-life/ @justinmcrocker.bsky.social @guignardlab.bsky.social @bulutkarslioglu.bsky.social @dudinlab.bsky.social @flowerwhatelse.bsky.social @laghalab.bsky.social @sfbd.bsky.social