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

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...

🔬📊 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

🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint Preprint updated: arxiv.org/abs/2508.00836

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...

How does Ras signalling affect actin? Some answers in a new review from Joe Tyler & I @mcb-sheffield.bsky.social authors.elsevier.com/a/1m8v-3PA3s... We discuss how Ras proteins coordinate local and global changes to the actin cytoskeleton and contribute to cytoskeletal plasticity in cancer.

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...

I was invited by @focalplane.bsky.social to write a short description about it: focalplane.biologists.com/2025/12/12/a...

ICYMI, our #preprint list is now up on FocalPlane, highlighting the latest research using #microscopy to answer questions in #biology. As always, send us any recommendations for preprints that we've missed: focalplane.biologists.com/2025/12/12/m...

🚨 PhD Position Available 🚨 I’m recruiting a PhD student to join my lab at the Multiscale Imaging Centre (MIC), Münster, Germany. www.bischofflab.com/jobs Fully funded ✅ #Cellbio #Morphogenesis #Microscopy #Drosophila #PhD (Details Below) Original Posting: stellen.uni-muenster.de/jobposting/d...

Wondering how to control the environment of cells? Check out this insightful #EpithelialMechanics thread by @lhinderling.bsky.social 👇

#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...

So how are these structures made? Early experiments used natural materials, even spider webs! 🕸️ bsky.app/profile/epim...

Want even smaller features? We recently published a method to convert your microscope into a microfabrication station, printing features from μm to cm scale for less than $5 in materials per design. Thread: bsky.app/profile/lhin... Paper: bsky.app/profile/epim...

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!

#LivingArchitectures We put cells and cytoskeleton filaments on the architecture of the musée d'Orsay. www.musee-orsay.fr/fr/agenda/ev... Scientists of the #CytoMorphoLab adapted their protocols to illustrate the questions that keep them awake at night. -> Two shows on the 24th and 25th of January.

Have you ever wondered what you would find if you could keep your eyes on a bee for more than a few meters? Us, too! preprint (with videos!) + thread 🧵 Precise, individualized foraging flights in honey #bees 🐝 revealed by multicopter drone-based tracking www.biorxiv.org/content/10.6... 1/9

Do you enjoy exploring embeddings interactively as much as I do? Check out _embeddoor_! I recently vibe-coded it while watching too many Harry Potter movies 😃 Feedback welcome as more features will certainly come! github.com/haesleinhuep...

I'll be there :)

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

Lock-in-SIM, a new approach to reject background and minimize artefacts in structured illumination microscopy (SIM): www.nature.com/articles/s41... Glad to see @esoubies.bsky.social's FlexSIM is the best opponent in side-by-side comparisons!

🚀 New preprint out! We introduce SMOLM-LFM: a simple, ratiometric, light-field–based method for 6D single-molecule orientation + localization, no polarization optics, no complex PSFs. Fast.Robust.Large DoF. A work done at @henriqueslab.bsky.social. In colaboration with the great L. AlemanCastaneda

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

📢Check out our latest #preprint list on FocalPlane This list focusses on the latest research on bioimage analysis and data management. Let us know if there are any preprints that we should add to our list and send us recommendation for the next one! focalplane.biologists.com/2025/11/14/m...

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...

We are happy to share our latest work, 4Pi-SIMFLUX, which combines structured illumination with interferometric detection to achieve near-isotropic 3D localization precision of 2–3 nm and resolve sub-10 nm structural features across whole mammalian cells. www.nature.com/articles/s41... rdcu.be/eQVxt

Excited to share a new preprint! Wireless devices use FM modulation to transmit multiplexed noise-resistant data. Led by @born2raisecell.bsky.social, we create a biochemical analogue of this paradigm using genetically encoded oscillators (GEOs) for single-cell FM streaming tinyurl.com/nbs8rw42 🧵

quick test with SAM3 - impressed with how well it seems to track long protrusions? prompted for "cell", does not find anything when looking for "fibroblast" or "nucleus"

The new open source syringe pump control boards arrived. Exciting!

The first meeting was a blast and the second one promises to be even better - if you submit your abstract and join us!

Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration: www.i2kconference.org/workshops

🚨New paper! 🚨 @jasminealqassar.bsky.social led this work on the silk glands of the pantry moth. These two long tubes inside the caterpillar continuously make a ton of silk How does this special organ work? www.cell.com/iscience/ful... @cp-iscience.bsky.social 🧵THREAD🧵

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵

New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇 www.biorxiv.org/content/10.1...

Dish soap. Seriously. 😆

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.

Check out this sneaky lamin A knockdown cell (pink dot) swimming against the tide (migration into gap) & slithering between its sisters. It also slides over another nucleus that deforms underneath it. MCF10A cells, #Spirochrome SPY650-DNA, 20 min time-lapse, taken on a #Zeiss #CellDiscoverer7.

Hi Fans of Feedback Microscopy, what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org? Btw, it works as well in Fiji&ImageJ :-) Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.

Intestinal villus cells extrude living, following a calcium pulse. Unlike from extruding apoptotic cells, Ca2+ messaging stops at the first neighbors! #FluorescenceFriday Part of our TrepatLab preprint: www.biorxiv.org/content/10.1... Video by @ronjahoutekamer.bsky.social @gloerichlab.bsky.social

A bit delayed, but excited to still share our latest paper, showing that intercellular forces transduced by E-cadherin activate EGFR-ERK signaling in epithelia by inducing EGFR ligand shedding! Mechanical and biochemical signals can act together within a single, linear cascade! tinyurl.com/mr9mj9j2

We've now discovered some neat cell culture dishes that feature a 50 micron thick film of a proprietary polymer with refractive index even closer to water than FEP. They work just as well as our homemade FEP assembly and are available in multiwell plate format too! www.sarstedt.com/en/products/...

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!

What a gem from @dudinlab.bsky.social @gautamdey.bsky.social @centriolelab.bsky.social in Cell! Expansion microscopy atlas of >200 eukaryotes comparing cytoskeletal architectures revealing structures not seen before. Stunning visualisation! Exactly the kind of transformative cell biology we need.

🚨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...

microfabricated stamps, fresh off the printer :)

www.nature.com/articles/s41... Emiliani Lab

Low-Cost 3D Printed Optics for Super-Resolution Multifocal Structured Illumination Microscopy https://www.biorxiv.org/content/10.1101/2025.10.09.680962v1

Un-frigging-believable. I have waited for something like this for so long!

Hi Fans of Smart Microscopy, Are you ready to automate your next large scale microscopy experiment and work smarter, not harder? Join us for the Smart Microscopy workshop organized by EPFL Bio-Imaging Platform (Lausanne) and @zeiss-microscopy.bsky.social www.zeiss.ch/mikroskopie/...