I'll be speaking at the Open Bioimaging Practices meetup tomorrow - join us if you're curious about (3D) multiplexed protein image analysis! 🔬

Joel Lüthi@joelluethi.bsky.social · last wk.

Do you want to learn about multiplexed image analysis using OME-Zarr? Tomorrow, @rhornb.bsky.social , @nrepina.bsky.social & Flurin Sturzenegger will share their learnings about building workflows around multiplexed image analysis, see www.biovisioncenter.uzh.ch/en/events/Up...

Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵

From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence

Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...

doi.org

Excited to share that our **3D-4i multiplexed imaging method** is now out in @natcomms.nature.com 🎉 🔗 www.nature.com/articles/s41... Huge thanks to the reviewers and editor for their constructive feedback and smooth handling of the work!

Shayan Shamipour@shamipourshayan.bsky.social · last yr.

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!

Excited for the first work of my PhD to see the light of day! This was a fantastic collaboration with my co-author @shamipourshayan.bsky.social and many others who contributed! ❤️

Shayan Shamipour@shamipourshayan.bsky.social · 4mo ago

🚀Excited to share our latest efforts in bringing highly multiplexed whole-mount imaging to intact multicellular systems! Shield-4i: an integrated platform to study multi-scale information flow in 3D embryos and embryo-like systems. Kudos to @rhornb.bsky.social for this major milestone in the lab!🚀

Once upon a time I just admired nudis and sea slugs. But it was not enough. Now apparently I'm creating an R package to celebrate their colour palettes? 😅 First up, my Sydney fave, Hypselodoris bennetti. #rstats #nudibranch #dataviz 🦑🐙🧪 #marinelife #invertebrates

We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10🧵) www.biorxiv.org/content/10.6...

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

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!

See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A 🧵...

How can cells self-organize rapidly into complex patterns during development? Let’s explore a powerful and underappreciated mechanism: Directed Cell Migration (DCM). Preprint @biorxivpreprint.bsky.social : doi.org/10.1101/2025... 👇Thread 🧵(1/11)

📣 Symposium 2050 at the University of Zurich Join us for this event exploring emerging directions in life sciences, presented by a diverse group of leading experts. Free and open to all! More info/register: ema.uzh.ch/RTTHF

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀 Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich. 🔗 Read the preprint: osf.io/preprints/bi... 🧵 (1/15)

We present a simple yet comprehensive model integrating multiple mechanical forces to guide lung development. These principles operate during both development and disease, providing a dynamic framework to understand and predict lung remodeling processes. 👇Thread 🧵(9/9)

Big parts of my PhD work is now out on bioRxiv!! We look at how biophysical parameters shape the fractal lung during development and disease. Go check it out: www.biorxiv.org/content/10.1...

The emergence of the fractal bronchial tree

The fractal design of the bronchial tree, as described by the Hess-Murray law, facilitates energy-efficient lung ventilation, yet its developmental origins remain unclear. Here, we quantify the rearra...

biorxiv.org

Dagmar Iber & CoBi@iberd.bsky.social · 2y ago

How does an #embryo build an energy-efficient #fractal #lung in time for the first breath at birth? 🫁 Discover the mechanical forces shaping the bronchial tree in our latest preprint: #LungDevelopment #Mechanobiology doi.org/10.1101/2025... 👇Thread 🧵(1/9)

How does an #embryo build an energy-efficient #fractal #lung in time for the first breath at birth? 🫁 Discover the mechanical forces shaping the bronchial tree in our latest preprint: #LungDevelopment #Mechanobiology doi.org/10.1101/2025... 👇Thread 🧵(1/9)