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.

Just look at those microtubules go! Happy to see our paper out in JCS ✨

Pinpointing single molecules with a technique called motor-PAINT to analyse microtubule filament orientation & polarity at super resolution in developing neurons 📹 @mkiwanski.bsky.social et al Kapitein lab @utrechtuniversity.bsky.social in @jcellsci.bsky.social ➡️ bpod.org.uk/archive/2025...

We mapped the whole human fallopian tube in 3D and at single-cell resolution via our CODA workflow. More about this work here: biorxiv.org/content/10.1...

Ultrack on the cover of Nature Methods! Thanks @alexandredizeux.bsky.social for helping us with the beautiful cover art! 😍

Cells can form patterns within themselves just like embryos do. How? Connie Yan's new preprint shows how the anterior-posterior cytoskeleton pattern in Stentor is dictated by regionalized scaffolding proteins www.biorxiv.org/content/10.1...

Do you have 2D-to-3D image registration challenges? Let me know about them here forum.image.sc/t/toward-bet...

So called microtubule organizing centers (MTOCs) are not "organizing centers". They don't control their position (network center), nor MT orientation, length and shape (network shape). The actual organizers are MTs, molecular motors and regulators of MT +ends. MTOCs nucleate MTs. Let's rename MTOCs.

ahah IT WORKS look it's a C² dual quaternion B-spline!! this is interpolating *poses* in dual quaternion form, coupling position and rotation, instead of treating them independently (this is a really neat thing!!)

In our new #Preprint, we pilot a revolutionary new idea: no supplemental data (it has 21 figures, though): Multiplexed imaging of G-proteins and ERK activity upon activation of CaSR www.biorxiv.org/content/10.1...

Trying "surface" render mode for volumetric (segmentation here) data for #BigVolumeBrowser (not released yet).

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...

Python notebook from a two year old paper: Oh, no, I cannot run, there is a slight mismatch of a logging library. ImageJ plugin from 2001 running on Quantum Java 51 in 2078: Your 100 petabyte temporal hologram was successfully thresholded.

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:

Turns out, there are fully opened LIDAR point scans of the whole Netherlands surface available geotiles.nl With up to 25 cm. It was hard not to load our building and around it into #bigvolumebrowser (22 M points + Fire LUT for height)

Felix Zhou's u-Segment3D is out: www.nature.com/articles/s41... It leverages 2D cell segmentations from orthoviews to generate a ‘consensus’ 3D segmentation. It does a great job on segmenting densely packed samples, and we have used the algorithm in many applications.

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

I am beyond excited to share that my postdoc project @szndohrn.bsky.social and the @arnonelab.bsky.social is now available in #ScienceAdvances @science.org. www.science.org/doi/10.1126/...

HL60 cells take on so many fun shapes as they migrate! This #InsightFromImaging data features cells prepared by Leanna and imaged on the @aicjanelia.bsky.social LLSM by @cmhobson.bsky.social

"Neurons are highly polarized cells"

I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way. quantixed.org/2025/11/04/a...

We are planning the build of a light sheet setup and are considering a Powell lens to generate the sheet. I've not been able to find a discussion of the pros and cons in literature, so if you ever used a Powell lens or have considered using one in your setup, I would love to hear your opinion. THX!

Exciting day for the lab: our 1rst paper is officially out in @currentbiology.bsky.social 🥳 Wonderful collaboration wt @gautamdey.bsky.social showing how Cryo-ExM achieves consistent immunostaining in diverse diatoms, from the lab and the natural environment 1/n #ProtistsOnSky tinyurl.com/2zxaund7

🚨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...

How a trick from flow cytometry can help colocalization visualization for microscopy forum.image.sc/t/cytofluoro...

Tracking has always been at the ❤️ of the scientific method, from planetary motion to single particles. Weiqing’s thesis intro on tracking was so beautiful we turned it into a perspective in JCP who then selected it as a #Scilight. Take a look! 😊 www.aip.org/scilights/tr...

Internet people, please help me to decide on the logo for #bigvolumebrowser, a multi-volume 3D viewer plugin for Fiji I'm working on. Please vote by replying with a number or liking one that was already mentioned. My favorites are 6, 7, 8 and 10 so far.

PAPER OUT ✨ What if you could use your microscope as a 3D printer? Prototype microfluidics in-house, <5$ in material costs per chip. From idea to experiment within a day. Now published in Lab-on-a-Chip (open-access): doi.org/10.1039/D5LC...