Fantastic look into sub-cellular patterning and functional organization of ciliary arrays in Paramecium! This is a great platform for decoding the mechanistic details that organize these sub-cellular layouts as well-- congrats @guille-rochelle.bsky.social and @daphnelaan.bsky.social !!

Density. Crowding. Tomato. Tomato 🍅 @gabepopkin.bsky.social kin.bsky.social @quantamagazine.bsky.social Thx for covering the debate! We promise we're all friends 🥰 @liamholt.bsky.social & @gwgl.bsky.social Nothing would have been possible without @gucklab.bsky.social @vasilyzaburdaev.bsky.social

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

This is work that we presented at last year's #Cosyne workshop on #GNN s sites.google.com/bu.edu/gnnwo.... Better late than never. You can reproduce everything with the associated notebooks. I think it's a good start to learn how to use GNNs to infer something about NNs. arxiv.org/abs/2602.13325

🔬🧠 Releasing the 1.0 version of #Suite2p and THE PAPER w/ @marius10p.bsky.social! Now with GPU acceleration. Want to use Suite2p but don’t have 100,000 neuron recordings? We show you how to get those with a standard 2p microscope #neuroscience #imaging #neuroAI www.biorxiv.org/content/10.6...

Two weeks of struggling with Java's Swing and async/multi-thread processes. Asking LLM for help, it rolls out the plan and the final "what NOT TO DO". Well, yes, I know it, it is exactly my current implementation.

Proud and excited to share our work with the community! Helen @helenfoster.bsky.social Foster et al. study how #cilia axonemes are built. 👀 Don't miss the gorgeous and insightful movies by @margotriggi.bsky.social, they really show our discoveries in full action! www.biorxiv.org/content/10.6...

New preprint alert! We developed an automated framework to optimize tracking pipelines for bacteria, along with a nice integration of tools for bacteria imaging, in the recently released TrackMate 8 (Fiji plugin). www.biorxiv.org/content/10.6... 👇🧵

Never wrote for a specific journal, never used a template. We just write the best manuscript with what we have, then preprint, then see where it could fit best and submit as is, adapting the format at later stages if journal and reviewers are interested (revision stage). Why should we do it sooner?

There was so much to unpack with this data, we teamed up with the marvellous @margotriggi.bsky.social to help explain what we think is going on. (Please also check out our model of central apparatus assembly here: www.biorxiv.org/content/10.6...)

The recording of my talk at BINA lattice light-sheet meeting is online www.youtube.com/watch?v=MWtk...

If you're into epic space operas, here are a couple of my scifi novels discoveries from the last year: "House of Suns" by Alastair Reynolds and Commonwealth Saga by Peter Hamilton.

The peer reviewed and updated version of this work is now online (although not quite the fully formatted version). We had an existential crisis about kinesin-1 regulation while developing this work, but we are super proud of everything we put into this project. www.cell.com/iscience/ful...

#SAM3 is getting a lot of attention, but how well does it work in specialized domains? On microscopy data, it performs surprisingly well without any fine-tuning — just careful hyperparameter tuning. In fact, it reaches the same level of agreement as two human annotators. #Preprint (under review)

In this week’s Fourier Optics course we shall be looking at diffraction from 2D apertures, with arrays of identical structures. A quiz to test your understanding of the array theorem. Can you match the apertures to their Fraunhofer diffraction patterns? 🧪 #physics ⚛️ #optics 💡 #iTeachPhysics 🎢

Really excited to share our new paper in @nature.com! We uncovered how a physical instability of the cytoplasm coupled with the cell cycle drives cytoplasmic partitioning in early embryos #zebrafish #drosophila. Read more in this🧵 www.nature.com/articles/s41... 🤩 @poldresden.bsky.social @mpi-cbg.de

#TubulinTuesday!

One of the perks of living in San Francisco is free visits to the Photonics West trade show. Sharing my notes for those missing out: nicost.github.io/microscope-t...

Released a new version of #BigTrace with some improvements (32-bit file support, shaded volume rendering). + I was able to fix a bug in spatial pose interpolation. The previous implementation (taken from BDV, left) was giving strange detours. In comparison, the new simpler one (right) seems ok.

🚨 We are hiring TWO postdocs to join the Cell Migration Lab (cellmig.org) 🇫🇮 as part of the new Centre of Excellence in Immune–Endothelial Interfaces (IMMENs). Join us to decode immune regulation & develop next-gen imaging tools! 🧪🔬 Details in thread 🧵👇 #ScienceSky #Postdoc #AcademicJobs Please RT🫶

Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....

🚨 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

We spend way too much time manually analyzing #microtubules 🔬 Together with Mario, Justus, Dominik, Felix & Erik we used synthetic data and foundation models to build a fully automated segmentation pipeline.
 #microscopy, #imageanalysis & #AI Check out our preprint: www.biorxiv.org/content/10.6...

Nice summary, very close to what I am doing

I finally got around to writing the discussion section of our lab's basic training course on live cell #microscopy. I explain the tradeoffs involved in designing an imaging experiment and the art of thinking of the experiment as an optimization problem. leb-epfl.github.io/basic_traini...

🚨The Neurocyto lab is branching out in our latest preprint! We used tubulin microinjection to directly visualize microtubule turnover in developing hippocampal neurons, demonstrating the presence of in-lattice repair and a selective stabilization in the nascent axon. Check below, or read on 🧵 1/9

Tried the vertex normals averaging for the smooth shading of meshes. (Is this what you were talking about @herrsaalfeld.bsky.social?) Nice explanation video here www.youtube.com/watch?v=PMgj... #BigVolumeBrowser

Direct labeling of microtubule turnover reveals in-lattice repair and stabilization patterns in developing neurons https://www.biorxiv.org/content/10.64898/2026.01.11.698892v1

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

Delighted to share the latest paper from the lab "Fast label-free live imaging with FlowVision reveals key principles of cancer cell arrest on endothelial monolayers" Amazing work driven by @follainga.bsky.social with contributions from many. link.springer.com/article/10.1...

Our paper describing the development of ShapeSpaceExplorer is now out: journals.plos.org/ploscompbiol... The software and documentation is available here: github.com/cmcb-warwick... Explainer thread below.

A thorough review of deep-learning approaches (I prefer that to "AI") for enhancing super-resolution microscopy by @orangeroad2017.bsky.social, Yang Zhang and colleagues in @natmethods.nature.com: doi.org/10.1038/s415...

If you have time tomorrow, join my online talk about LLS/single molecule/microtubules and 3D data at @bioimagingna.bsky.social user group (18:00 CET for Europe). I hope I manage to fit 25 movies into 20 cohesive slides and connection will be ok.

Introducing Cyclically Multiplexed Expansion Microscopy (Cy-ExM): a workflow for 3D nanoscale, high-plex imaging in whole cells. Cryo-preserved ultrastructure + iterative labeling + expansion microscopy → 20 targets in one dataset with ~70 nm lateral resolution. www.biorxiv.org/content/10.6...

Last project of the year: self blinking JF635 + lattice light sheet + #BigVolumeBrowser to deskew both volume and localization data (and render) @zeiss-microscopy.bsky.social

Bored over the holidays? Give our new preprint on how #microtubule lattice alteration by taxols can regulate #RhoA #signalling via GEF-H1 a read! Perhaps a new mechanism of action for taxol #chemotherapeutics during interphase. www.biorxiv.org/content/10.6... Happy holidays ✨🎄

Pfffffff. Chains of transformations are hard. It took me two releases to get the live deskew slider right and looking ok (hopefully) #bigvolumebrowser

We also tried it recently and indeed, it blinks nicely without any smelly buffers or extra stuff added. Makes SMLM sample preparation a breeze. I hope soon new additional colors will be discovered, apart from the far red.

One of the difficulties in developing code for microscopes is to get access to the equipment. So, wouldn't it be nice to have emulators? Turns out that AI is really good at converting documentation into an emulator: nicost.github.io/microscope-t...

Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff: Paper: doi.org/10.1242/jcs.... Code: github.com/pertzlab/arc... Plugin: github.com/pertzlab/arc...

Vaults. They are cell biology's greatest puzzle! This preprint from Martin Beck's lab shows them docked on ER membranes with a ribosome inside. What on earth is going on there?? #CellBiology #WTFology www.biorxiv.org/content/10.6...

🚨Amazing news for a cloudy Monday!🌩️😎 I'm extremely happy to share that our last adventure is finally out!🚀🎉Phototoxicity fitness time trial (#PhotoFiTT) - a quantitative framework for assessing phototoxicity in live-cell microscopy experiments 🔬❤️‍🔥⚡️ doi.org/10.1038/s414...

#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you. www.biorxiv.org/content/10.6...

Wait, Mastodon wasn't published yet???????? @jytinevez.bsky.social @paveltomancak.bsky.social

Hmmm, maybe instead of confident and reassuring instructions in the beginning of the "dealing with large data" wiki page I should put PREPARE FOR A LONG STRUGGLE announcement.

New release of #BigVolumeBrowser. Many things were added: UI improvement (thanks to @kwolbachia.bsky.social feedback), pyramidization for BioFormats dataset, bug fixes. Now there is an isosurface rendering mode (1/4)

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/

The new version of TrackMate, the v8.1 has just been released. It builds upon the recent v8, linked below, and offers two main improvements 👇

Here is a presentation by Samuel Panze on ManVR3D (Manfred), PhD student extraordinaire in the unit of Ulrik Gunther, and that built an eye tracker, VR based tool for tracking cells. ManVR3D uses Mastodon as the tracking backbone 🎉 youtu.be/02WpqQypVig?...

Back in 2016, I spent some time centrifuging chambers containing a kinesin/microtubule -based active gel so that all the material ended up on one side of the chamber. Then recorded how long it took to expand.