Lucien Hinderling

Leclech, C., Cardillo, G., Roellinger, B., Zhang, X., Frederick, J., Mamchaoui, K., Coirault, C., & Barakat, A. I. (2025). Micro-Scale Topography Triggers Dynamic 3D Nuclear Deformations. Advanced science, 12(11), e2410052. #EpithelialMechanics
doi.org/10.1002/advs...

A cochlea imaged in light-sheet microscopy (right) with staining for spiral ganglion neurons (red) and inner hair cells (blue). You will develop AI-based methods to analyze these structures, for example via segmentation of the individual cells (right) that will support gene therapy development for hearing loss and a better overall understanding of the anatomy of hearing.

Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx

Part of sfb1690.uni-goettingen.de to study hearing, vision, and more.

Plus, you can create pretty pictures as the one below :).

Very happy that MuViT, our (CVPR 2026!) work on learning across spatial scales in microscopy w transformers, is out! Check Martin's thread for a nice walkthrough :)
Big thanks to my advisors @maweigert.bsky.social @gioelelamanno.bsky.social!
🖥️: github.com/weigertlab/muvit
📜: arxiv.org/abs/2602.24222

Excited to share our new paper (CVPR 2026 🚀): "MuViT: Multi-Resolution Vision Transformers for Learning Across Scales in Microscopy" which enables local predictions to use global context.
Great work led by @albertdm.bsky.social & another fun collab w @gioelelamanno.bsky.social! @scadsai.bsky.social

👏👏👏

mail to smwgadmin@eurobioimaging.eu :)

Go Lucien!! Love to see it

Feel welcome to add your smart microscopy project! smartmicroscopy.github.io/implementati... (mail/dm or PR on github). We also have a monthly online meeting on all things smart microscopy, all labs & companies welcome!

PAPER OUT ✨ How can we make smart microscopy more interoperable? What are the technical and cultural challenges? 30+ people from academia and industry propose a roadmap: doi.org/10.1515/mim-... Also a review of applications and repo of implementations. Join the discussion! smartmicroscopy.github.io

Our article on how to use micropatterned presynapses-on-glass is out in its final form in the latest issue of the Journal of Neuroscience @sfnjournals.bsky.social: www.jneurosci.org/content/46/8...
The cover went to the special section on social neuroscience, so here's our #notthecover attempt

Get in touch if you want to be paid to work with us this summer. We are particularly interested in hearing from scientists who are interested in software development!

GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile

Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package:

- fully bootstrapped Java setup (just pip install)
- lazy, repeatably-indexable Array object
- fully spec-compliant OME-Zarr group obj.
- xarray/dask exports

github.com/imaging-form...
v0.0.rc1 on PyPI

In this Virtual Pub recording, Lucien Hinderling of the University of Bern gives a talk on "Smart microscopy for automation of optogenetic targeting." Learn more about the Virtual Pub:… Smart microscopy for automation of optogenetic targeting

🎥 Don't miss this recording of the #VirtualPub with @lhinderling.bsky.social PertzLab on Smart Microscopy workflows - for automation of optogenetic targeting & beyond.
Great talk 👏 🔽
youtu.be/YpGmMzrFJ80

Apply to join us this July for a crash course on Python & bioimage analysis tailored specifically for beginners! Applications due May 18th 🔬💻 #BoBiAC2026 bobiac.github.io

And save >80% on the cost by pooling 6 or more plasmids into a single sample using our free SAVEMONEY algorithm!

elifesciences.org/articles/88794

colab.research.google.com/github/Masaa...

Inducing novel endosymbioses by implanting bacteria in fungi - Nature A study presents an approach to establish and track a new endosymbiotic partnership by implanting bacteria in a non-host fungus and shows that stable inheritance of the implanted bacteria is possible ...

Vorholt Lab re-created endosymbiosis in the lab: injected bacteria into a fungus and evolved a heritable partnership.

Evolution, fast-forwarded.

doi.org/10.1038/s415...

I'll never get tired of lazily browsing elastix-coregistered #WSI data in @napari.org using the upcoming @openmicroscopy.org ome-zarr @zarr.dev format version that allows to specify and read transformations directly from the image data itself.

Data source: rodare.hzdr.de/record/3131

Enhance your timeline on #InternationalDayOfWomenAndGirlsInScience by following our two(!) Starter Packs of outstanding Group Leaders and Senior Scientists from the #zebrafish community! 🐟 🧪

#WomenInScience Volume 1: go.bsky.app/4BegEjv
#WomenInScience Volume 2: go.bsky.app/VoebYrt

Hello epithelial mechanics fans!! I’m Juanma @juanmagararc.bsky.social 👋 I work on cell mechanics (see celldynamicslab.com) and use Flipper-TR FLIM to probe membrane biophysics in cells.

Join me on this tour about Flipper: what it measures, strengths, advice, cool case studies, and cute drawings!

I witnessed the Flipper-TR development from day 1. I remember how I told myself "it can't work" when I first saw the concept. Until it actually worked beautifully! It took a decade, but now Flipper-TR is a widely used tool and an inspiring tale.
Congrats to the many who contributed to this journey!🧪

1/ 🚀🧪🤖 Big update for #Omega — the LLM-powered autonomous agent for bioimage analysis in @napari.org ! Custom LLM endpoints, layer actions, plugin extensibility, agentic widget maker, modernized UI, & 30+ fixes. Here's what's new in version *2026.2.8.2*:

Announcing two new Python tools for OME-Zarr (and TIFF) I'm happy to announce a couple tools that we've been building in the OME-Zarr/OME-TIFF ecosystem 1. ome-writers A unified, common interface for writing directly to OME-Zarr or OME-TIFF as it is acqui...

forum.image.sc/t/announcing...

COS7 cells labeled for actin (gray), microtubules (orange) and clathrin (blue). The two middle cells are dividing, with a reorganisation of microtubules into a spindle and denser clathrin assemblies. Image taken with an Apotome microscope.

Busy #cellfie 🧪

Electrifying story from @ritamateus.bsky.social lab. @mpi-cbg.de @poldresden.bsky.social

An mTurquoise2-Based Glucose Biosensor Glucose is an important substrate for organisms to acquire energy needed for cellular growth. Despite the importance of this metabolite, single-cell information at a fast time-scale about the dynamics...

Great to see this officially out: An mTurquoise2-Based Glucose Biosensor - works in yeast & mammalian cells and is compatible with FLIM: pubs.acs.org/doi/10.1021/...

Little reminder about this paper out there, it's a great reference for anyone working on Flipper-TR experiments! By @chloeroffay.bsky.social @rouxlab.bsky.social

Mammalian cells labeled with lysotracker are perfect for teaching live cell imaging.
Minimal preparation, always works, and, as a bonus, results in nice data for #FluorescenceFriday

How do cells orchestrate themselves to achieve a directional movement as a group?

Hi, I’m @sayukihirano.bsky.social. In this thread, I’ll highlight key mechanisms of how cells communicate with each other to perform directional collective migration.

Curious if anyone has applied #MCP in materials physics or other scientific fields. Concrete use cases, prototypes, or lessons learned are very welcome. Looking to connect with fellow scientists and exchange experiences in this area.
#OpenScience #MaterialsPhysics #Physics #Langchain

working on microscope control for cell biology! happy to chat