Olivier Pertz

Had the Kapitein lab in Bern for a retreat about smart microscopy for optogenetics - a lot of science, walking up the hill to look at our beautiful mountains and even a Jazz concert.
Outcome: new ideas, tired brains, and the beginning of something awesome.
Can’t wait for round 2 in Utrecht

I did not know you had such ambitions in life …

Coevolution of cooperative lifestyles and reduced cancer prevalence in mammals While cooperative mammals evolve reducing cancer prevalence, oncogenes can be maintained by selection in competitive species.

Why do whales and elephants have much lower rates of cancer than expected?
"Species with a lower cancer prevalence and mortality
risk are those with a higher presence of cooperative and caring habits, while the opposite is found....:"
www.science.org/doi/10.1126/...

Universal consensus 3D segmentation of cells from 2D segmented stacks - Nature Methods u-Segment3D is a universal framework that translates and enhances 2D instance segmentations to a 3D consensus instance segmentation without training data. It performs well across diverse datasets, inc...

A game changer in our hands... www.nature.com/articles/s41...

This Wednesday @bgraedel.bsky.social defended his PhD — crowning an extraordinary scientific journey.
He showed how live-cell imaging and computational modeling can reveal and perturb cytoskeletal dynamics at micrometer and second-level scales.
Thanks Benjamin — a wild, inspiring ride! 🚀

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!

Fibroblast Growth Factor Signalling in Development, Health & Disease Conference | Fusion Conferences Receptor Tyrosine Kinases (RTKs) are cell-surface receptors that, upon ligand binding, regulate cell-to-cell communication during embryonic development and in adult life. Among RTKs, the twenty-two Fi...

Excited to join the Fusion Conference on Fibroblast Growth Factor Signalling this May in Malta 🇲🇹!
I’ll be discussing how FGF–MAP kinase signaling unfolds at the single-cell level — bridging molecules to cell decisions 🔬✨
#FGF #MAPK #conference www.fusion-conferences.com/conference/195

Went to see Yayoi Kusama’s mind-bending art at the Beyeler Foundation in Basel. As a biologist, I tried to enjoy the art… but my brain kept yelling "nuclei!", “organoid!”, and “endocytosis!”. Here are some of my favorite accidental biology sightings. 🧬🎨🧫

screenshots of some of the sample implementations

Screenshot of smartmicroscopy.github.io/implementations.html, showing an overview of collected implementation examples

Want to get started with smart microscopy? 🧠🔬
Check out our online repository with implementations from labs and industry -- lots of practical tips and links to sample code! smartmicroscopy.github.io/implementati...

More details in the ✨updated preprint!✨
www.biorxiv.org/content/10.1...

Cell and developmental biologists; This is well worth a read: Maik and Roberto synthesize work over decades to propose a provocative model of who mesenchymal cells migrate and shape tissues 🧪 Go for the cool Figures, stay for the deep insights

Its raining #Ichthyos ... Hallelujah!

#Lattice #LightSheet #Ichthyosporeans #Creolimax #Cellularization #ProtistsOnSky

so happy to have Katie as a colleague !

Catherine Peichel Interview with Katie Peichel, who studies the evolutionary genetics of sticklebacks at the University of Bern, Switzerland.

Nice interview to Katie Peichel @currentbiology.bsky.social

I completely agree with her claims for more funding for curiosity-driven research, basic Science... Science.

www.cell.com/current-biol...

looks like an ingenious combination of technologies to study out of equilibrium developmental processes ... Congrats !

Assistant Professor with tenure-track for Quantitative Cell Biology (80-100%) - Bern, Switzerland job with University of Bern, Institute of Cell Biology | 12840798 Assistant Professor with tenure-track for Quantitative Cell Biology (80-100%) at the University of Bern, Switzerland.

⚡️ Don’t forget that we’re looking for a Tenure-track Assistant Professor in Quantitative Cell Biology @ UniBern!

🔬 Bridge experiments + theory
📈 Tackle processes across scales
💡 Join our vibrant research community

Deadline Oct 17 👉 shorturl.at/1Y1WP

Summer break prevented me from properly advertising this serie of reviews on the function of cell death during development that I edited. There is still a lot to dig in regarding regulation of apoptosis in vivo ad I hope we managed to illustrate this well
www.sciencedirect.com/special-issu...

2 weeks ago we were some of the first to see 'Cancer Revolution: Science, Innovation & Hope,' the astounding new exhibition from Breakthrough Cancer Research. Read more about this free interactive display & our involvement in the project along w/ @precisiononcire.bsky.social

ucd.ie/sbi/news/new...

“New paper out 🎉 We built a system to automate optogenetic cell control across scales. For the demo, we made the cells spell my name — because if you can’t use science to feed your ego, what’s the point? 😎🧫✨”

Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out! www.biorxiv.org/content/10.1...

Congrats @lhinderling.bsky.social and team

So many people involved! Special thanks to @hannah-superres.bsky.social, Alfredo Rates, @olivierpertz.bsky.social, @nilsnorlin.bsky.social, Aliaksandr Halavatyi & Rafael Camacho. Link again to the paper: www.biorxiv.org/content/10.1...

Not only acquisition settings can be changed, but also perturbation: Popular is automated targeting of photomanipulation:

For example event-driven acquisition: rare events (here mitoses) are detected in a low-res overview scan, the microscope switches objective to automatically image only the mitotic cells in high-res. 🔎

Figure legend: Categories and capabilities of smart microscopy systems integrating real-time image analysis and feedback control. Top: Smart microscopy workflows can be classified based on the driving logic behind decision-making: Event-driven (reacting to rare biological events), Outcome-driven (using feedback-control to steer biological systems toward a desired state), Quality-driven (optimizing signal quality or imaging metrics), and Information-driven (guided by models that predict which measurements/perturbations will yield the most informative data). Middle: Central feedback loop between the microscope and an image analysis system, which continuously exchanges images and commands to guide acquisition dynamically. Bottom: Key control actions enabled by smart microscopy: adjusting imaging modality (e.g. switching from brightfield to fluorescence, adjusting sampling rate), repositioning the field of view (e.g. tracking, drift correction), optimizing acquisition settings (e.g. adaptive optics), and performing photomanipulation (e.g. FRAP, ablation, optogenetics).

🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:

Teach your microscope how to print: low-cost and rapid-iteration microfabrication for biology The application of traditional microfabrication techniques to biological research is hindered by their reliance on clean rooms, expensive or toxic materials, and slow iteration cycles. We present an a...

In the latest issue of Lab on a Chip:
Teach your microscope how to print: low-cost and rapid-iteration microfabrication for biology.
#OpenAccess from Olivier Pertz, Lucien Hinderling et al @olivierpertz.bsky.social @lhinderling.bsky.social‬.
Read now: pubs.rsc.org/en/content/a...

Adapted from Fig. 1 from Kadiyala et al 2025.

Introducing five concepts from dynamical systems to decode developmental regulatory mechanisms, have a read! @perez-carrasco.bsky.social‬ @roederlab.bsky.social @mpipz.bsky.social This effort started in a morphogenesis meeting @kitp-ucsb.bsky.social‬ in 2023. journals.biologists.com/dev/article/...

@lwellberg.bsky.social @josjonkers.bsky.social @olivierpertz.bsky.social @juliosaezrod.bsky.social
please share with your followers - thank you!

Thanks for having me !

first data from the new LLSM in PertzLab @olivierpertz.bsky.social! i always thought nuclei were spherical but they are pancakes???? so much more to see in 3d, but data volume produced is insane, we will have to rethink our analysis pipelines. tips welcome! here shown in @napari.org

Loved the preprint, congrats on the paper!