Josiah Passmore
@jpassmore.bsky.social
370 followers 550 following 25 posts
Making cells run in circles, and gels with squares in them. Automated optogenetics, Smart microsopy, Expansion microscopy, GelMap. Postdoc @ Utrecht University | visualise.bio.
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jpassmore.bsky.social
Advances in microscopy mean we can now do more than just observe biology—we can control it. But how far can we really push this in mammalian cells with all their (beautiful but annoying) heterogeneity? 🧪🔬(🧵)
HT1080 cells with various morphologies. DAPI (blue) Phalloidin (grey) GM130 (green).
Reposted by Josiah Passmore
andrewcpayne.bsky.social
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
Reposted by Josiah Passmore
nadjahuempf.bsky.social
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
Reposted by Josiah Passmore
ekatrukha.bsky.social
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)
Reposted by Josiah Passmore
jonatanalvelid.bsky.social
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.
Demonstrative schematics and example timeline of event-triggered MINFLUX microscopy.
Reposted by Josiah Passmore
epimechfc.bsky.social
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
Reposted by Josiah Passmore
lhinderling.bsky.social
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...
Reposted by Josiah Passmore
maltekuehl.com
🚨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 ⬇️
Reposted by Josiah Passmore
jennaelliott.bsky.social
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
Expansion microscopy image, and accompanying sketch, of S. arctica nucleus with labelled microtubules and nuclear pore complexes.
Reposted by Josiah Passmore
Reposted by Josiah Passmore
aafkegros.bsky.social
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...
Reposted by Josiah Passmore
loxstoplox.bsky.social
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 🧵)
Reposted by Josiah Passmore
marius10p.bsky.social
🚀🔬🦠 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
Reposted by Josiah Passmore
physicsoflifelmu.bsky.social
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
Reposted by Josiah Passmore
epimechfc.bsky.social
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
Reposted by Josiah Passmore
aaandmoore.bsky.social
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...
Reposted by Josiah Passmore
sulianamanley.bsky.social
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.
jpassmore.bsky.social
An MRC5 cell labelled for microtubules and actin. #FluorescenceFriday
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)
jpassmore.bsky.social
Join the biocontrol seminar tomorrow to hear about the fun things we are doing with controlling cells!
Reposted by Josiah Passmore
ryotaiino.bsky.social
On-Demand Photoactivation of DNA-Based Motor Motion
pubs.acs.org/doi/10.1021/...
On-Demand Photoactivation of DNA-Based Motor Motion
A major challenge in the field of synthetic motors relates to mimicking the precise, on-demand motion of biological motor proteins, which mediates processes such as cargo transport, cell locomotion, and cell division. To address this challenge, we developed a system to control the motion of DNA-based synthetic motors using light. DNA motors are composed of a central chassis particle modified with DNA “legs” that hybridize to RNA “fuel”, and move upon enzymatic consumption of RNA. We first concealed RNA fuel sites using photocleavable oligonucleotides that block DNA leg binding. Upon UV activation, the RNA blocking strands dissociate, exposing the RNA fuel and initiating active, directional motion. We also created a “brake” system using photocleavable DNA stalling strands, anchoring the motors until UV light removes the “brake” while simultaneously “fueling” the motors, initiating spatiotemporally controlled stop → go motion. Additionally, we modified the “brake” system to activate the motors via a chemical input, while an optical input is required to fuel the motors. This dual-input approach, functioning as an “AND” gate, demonstrates the potential for DNA motors to perform light-triggered computational tasks. Our work provides a proof of concept for enhancing the complexity and functionality of synthetic motors.
pubs.acs.org
Reposted by Josiah Passmore
aafkegros.bsky.social
Now out in PLOS CB: Spherical Texture extraction! doi.org/10.1371/jour...

This method quantifies the intensity distribution in microscopy objects, and is implemented parameter-free in @ilastik-team.bsky.social object classification!

We show applications in cells, C. elegans and Drosophila! 😁
Reposted by Josiah Passmore
aafkegros.bsky.social
Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...
FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023