Josiah Passmore

JCS snapshot - Tracking coordinated cellular dynamics in time-lapse microscopy with ARCOS.px

@macdobry.bsky.social presents the key findings from their recent JCS paper with @bgraedel.bsky.social and colleagues @olivierpertz.bsky.social.

journals.biologists.com/jcs/article/...

Laboratory Engineer (Senior), in Advanced Imaging, 1.5.2026-31.12.2028

🚨 Job Alert! 🚨

We have an opening at our Microscopy Core Facility in Turku 🇫🇮.
If you love imaging 🔬 and helping scientists succeed, we want you! 👇

abo.rekrytointi.com/paikat/index...

#Microscopy #ScienceJobs #CoreFacility #Imaging
@turkubioscience.bsky.social

YouTube video by Pertz Lab Smart microscopy, computer vision, and controlling cells with light -- my PhD thesis in 3 minutes

Won best thesis award with this video! 4 years of research and play in 3 minutes :')
youtu.be/so0fPlK1-LM

Uni Bern: PhD Position in Statistics with a focus on Statistical Machine Learning for Self-Driving Microscopy

🔬📊 PhD (100%) – Statistics & ML for self-driving microscopy

Joint PhD with David Ginsbourger (Stats) & Pertz Lab (Cell Biology).
Gaussian Processes, Bayesian design, active learning on live-cell experiments.

ohws.prospective.ch/public/v1/jo...

#PhD #Statistics #MachineLearning #Bayesian

Cells can sense the geometry of their environment, from tiny subcellular features to whole-tissue patterns. How can we engineer environments to systematically probe these responses?

🧵 I'm @lhinderling.bsky.social from @olivierpertz.bsky.social lab, let’s do a short tour on microfabrication!

We’re excited to announce the opening of the Geneva Expansion Microscopy Facility (GenExM)!

GenExM is a full-service U-ExM platform (U-ExM, Cryo-ExM, iU-ExM), delivering nanoscale imaging.

Led by Dr. Olivier Mercey, GenExM welcomes academic & industrial collaborations.

👉 www.unige.ch/genexm/

BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...

Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...

🚨Our collaboration with @centriolelab.bsky.social & @gautamdey.bsky.social is out today in @cp-cell.bsky.social
We show that #Expansion #Microscopy is a broad-spectrum modality for Euks, enabling 3D phenotypic maps rooted to phylogeny.
#ProtistsOnSky #SciComm #SciSky

www.cell.com/cell/fulltex...

E11 Bio is excited to unveil PRISM technology for mapping brain wiring with simple light microscopes. Today, brain mapping in humans and other mammals is bottlenecked by accurate neuron tracing. PRISM uses molecular ID codes and AI to help neurons trace themselves.

Read more: e11.bio/blog/prism

Now out on bioRxiv. 🥳My research on #cytokinesis, averaging thousands of #ExM images🔬, creating a dynamic atlas of cytokinesis 🦠⏳. Here's an animated sneak peek of what we found. Better resolution on bioRxiv😄 #PSFoftheGIF

Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy.
Four years of very hard work from our very talented Emma van Grinsven. www.biorxiv.org/content/10.1... (1/N)

Excited to share my postdoc work from the Eggeling lab in Jena (@leibnizipht.bsky.social, #FSUJena, #KTHuniversity) on bringing smart microscopy to super-resolution MINFLUX: event-triggered MINFLUX microscopy.

Collective cell motion has many forms, but rotation is the coolest of them all.

I'm @onenimesa.bsky.social , and in this short🧵, I'll highlight some instances of global tissue rotation like this one from @BauschLab

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...

🚨Scaling multiplexed imaging 📈 We are excited to share Pathology-oriented multiPlexing (PathoPlex). Now out in @nature.com: www.nature.com/articles/s41...

🧵Walk-through thread below ⬇️

Expansion microscopy image, and accompanying sketch, of S. arctica nucleus with labelled microtubules and nuclear pore complexes.

9/ The observed patterns matched our model, and their parameters place these systems near the predicted optimal filtering regime -- These NPCs may act as efficient spatial thresholding filters! #Microscopy #QuantBio #Microtubules #UExM

🎀✨Recording now available ✨🎀

youtu.be/jtDunWK8g1o?...

In the context of our @reviewcommons.org revision process, I'm happy to announce Microscopy Nodes v2.2.0!
This packs lots of new fun features, including new color management 🌈, clearer transparency handling 🫥, custom default settings 🔧 and more!
Preprint at doi.org/10.1101/2025...

I’m excited to announce that my paper describing non-canonical mitotic mechanisms in the early mouse embryo is out in @science.org ! (link at end of 🧵)

Light-microscopy-based connectomic reconstruction of mammalian brain tissue - Nature A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling quantification of c...

Thanks to expansion microscopy, clever labeling, and modern segmentation approaches, doing connectomics with #light #microscopy has become feasible - huge congratulations Mojtaba & the Danzl lab at @istaresearch.bsky.social !
www.nature.com/articles/s41...

Interphase cell morphology defines the mode, symmetry, and outcome of mitosis During tissue formation, dynamic cell shape changes drive morphogenesis while asymmetric divisions create cellular diversity. We found that the shifts in cell morphology that shape tissues could conco...

My first post on Bluesky! Very excited to share our work just published in @science.org. We find that “Interphase cell morphology defines the mode, symmetry, and outcome of mitosis” - in angiogenesis and other tissues! www.science.org/doi/abs/10.1... www.science.org/doi/abs/10.1...

Investigating Local Negative Feedback of Rac Activity by Mathematical Models and Cell Motility Simulations For polarization and directed migration, cells use a combination of local positive feedback and long-range inhibition. We have previously used mathematical models to show the ability of this core…

If you're curious about how cells make decisions in complex environments, and how mathematical models can capture such behaviour, our preprint is now live!
Check it out here: www.biorxiv.org/content/10.1...

🚀🔬🦠 Releasing 🤖Cellpose-SAM🤖, a cellular segmentation algorithm with superhuman generalization 🦸‍♀️. Try it now on 🤗 huggingface.co/spaces/mouse...

paper: www.biorxiv.org/content/10.1...
w/ @computingnature.bsky.social 1/n

We may not have really squared the circle — but we came close! 😉 In our @NaturePhysics paper w/ @fakhrilab.bsky.social, light-triggered membrane excitability enables programmable shapes — a step toward engineering living matter.
🔗 www.nature.com/articles/s41...
#biophysics #syntheticcell #softmatter

1/14 “Epithelial” & “Mesenchymal” aren’t binary categories—they form a spectrum, or better yet, a multidimensional space. This becomes especially clear in collective cell migration, which often depends on a finely tuned degree of “mesenchymal-ness”.

#cellbio #devbio #cellmigration

Happy to officially introduce FilaBuster - a strategy for rapid, light-mediated intermediate filament disassembly. Compatible with multiple IF types, modular in design, and precise enough to induce localized filament disassembly in live cells.

www.biorxiv.org/content/10.1...

Our latest preprint www.biorxiv.org/content/10.1..., describes Willi Stepp’s project to make smart microscopy even gentler by doing event detection in phase contrast. We developed neural networks to detect mito-LD and mito-lysosome contacts, as well as mitochondrial pre-fission constrictions.

Fluorescence microscopy of an MRC5 cell highlighting the microtubule and actin cytoskeleton. Stained with: 🔵 DAPI – Nucleus (blue) 🟠 Tyrosinated tubulin – Dynamic microtubules (orange) 🔷 Acetylated tubulin – Stable microtubules (cyan) ⚪ Phalloidin – Actin filaments (grey)

An MRC5 cell labelled for microtubules and actin. #FluorescenceFriday

Join the biocontrol seminar tomorrow to hear about the fun things we are doing with controlling cells!

Polarity reversal of stable microtubules during neuronal development Neurons critically depend on long-distance transport orchestrated by motor proteins walking over their highly asymmetric microtubule cytoskeleton. These microtubules are organized uniformly in axons w...

My main PhD paper is on bioRxiv! 🥳 We used motor-PAINT, expansion microscopy, and live-cell imaging of StableMARK to map out how the microtubule cytoskeleton reorganizes during neuronal development.
www.biorxiv.org/content/10.1...