Nico Stuurman

@patrickzager.bsky.social acquired this lovely 3D timelapse of live neutrophil membrane protrusions on the snoutscope at the UCSF Center for Advanced Light Microscopy. Shown are three orthogonal maximum intensity projections.

I had beers with an old friend the other night - we’re both programmers (working in science) in this age range and we were both talking about how giddy Claude code made us feel.

5 laptops stacked on a table

How many laptops does a married couple need?

No, but if I get one, there will be😄

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...

‘Remote controlled’ proteins illuminate living cells The discovery that some fluorescent proteins are sensitive to magnets could lead to the development of switchable drugs and biosensors.

Researchers have engineered magnetically controlled fluorescent proteins that can be remotely dimmed and brightened in cells and living animals

go.nature.com/3NUSY12

Deep Learning for Microscopy Image Analysis Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,

🚨 Alarm!!! 🚨
AI/ML course for microscopy image analysis!!! 🧐
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!?

20 students, ~14 TAs and lecturers
🗓️ June 4-18 2026

✍️ Jan 15 2026 ✍️

🔁 pls!!

www.janelia.org/you-janelia/...

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...

All the best with your new lab at the Whitehead Ron! We miss you at UCSF! wi.mit.edu/news/whitehe...

Here's a six-month time-lapse of me building the single objective light sheet fluorescence microscope at the UCSF Center for Advanced Light Microscopy!

Also pictured is @nicostuurman.bsky.social and @kahsage.bsky.social.

#snouty

Seattle’s Allen Institute launches ‘moonshot’ to create new approach to cell biology research A 75-person team at Seattle's Allen Institute is embarking on a 10-year project called CellScapes to devise a mathematical language to capture cell behavior.

www.geekwire.com/2025/seattle...

Some Micro-Manager device adapters are not included in the installer. That can cause problems when the device API changes. When the device adapter vendor does not release a new version you can try the following work-around: nicost.github.io/microscope-t...

Top: the global biomass distribution of the mammalian class, represented by a Voronoi diagram. The area of each cell is proportional to the biomass contribution of each group. The global mammalian biomass distribution is dominated by humans and domesticated mammals, including livestock and pets (illustrated at the species level in SI Appendix). Bottom: enlarged view of the biomass of wild terrestrial (Left, grouped by order) and marine mammals (Right, grouped by family, or few families).

Here's one of the incredible dataviz images that Ron Milo just showed at #EMBOclimateResilience, from the excellent Greenspan et al PNAS paper www.pnas.org/doi/epub/10....

Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.

Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...

Just had the pleasure to experiment with a camera targeting the astronomy market, but offering great value for microscopy. Cooled, low noise (<1.5 e read-noise), high QE cameras that work with Micro-Manager can be bought for ~$1k: nicost.github.io/microscope-t...

Mechanism of giant magnetic field effect in fluorescence of mScarlet3, a red fluorescent protein Several fluorescent proteins, when expressed in E. coli, are sensitive to weak magnetic fields1. We found that mScarlet3 fluorescence in E. coli reversibly decreased by 21% in the presence of a 60 mT ...

How do tiny magnetic fields affect biochemistry? Overflowing with pride over Katherine Xiang's study on a giant magnetic field effect in a red fluorescent protein, www.biorxiv.org/content/10.1...

PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

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...

Fig. 1 Photostable and fluorescence properties of mScarlet3-S2. a, b, Photostability of red emitting mScarlet variants expressed in live U-2 OS cells under continuous WF illumination at 1.9 W/cm2

A highly photostable monomeric red fluorescent protein
www.researchsquare.com/article/rs-5...

Progress on the quest for a red mStayGold!
Just out: mScarlet3-S2, a new photostable red FP derived from mScarlet3: www.researchsquare.com/article/rs-5...

We made a photoswitchable HaloTag (psHaloTag), which can reversibly turn-on fluorogenic dyes upon illumination 💡. Congrats to Franzi, Bego and all co-authors, check out our preprint below 👇
www.biorxiv.org/content/10.1...

HT1080 cells with various morphologies. DAPI (blue) Phalloidin (grey) GM130 (green).

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? 🧪🔬(🧵)

New report highlights the scientific impact of open source software Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing

“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯

www.statnews.com/sponsor/2024...

We designed MS2 and PP7 binding coat proteins that are degraded in cells except when bound by their hairpin RNAs.

You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...

Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment Author Summary Single amino acid repeats are common in eukaryotic proteins. Some of them are associated with developmental and neurodegenerative disorders in humans, suggesting that they play importan...

If I can add to the his-tag data: at least 6 consecutive his-residues target proteins to nuclear speckles: journals.plos.org/plosgenetics... So this could drive condensation in nuclear speckles.

Hi #biabob users,
there comes a new edit mode with the new 0.24.0 release: If you ask %%bob to modify code, it will update the current notebook cell. This should make AI-assisted iterative code modifications much smoother. 🤓
github.com/haesleinhuep...
[video shortened; Bob needs ~10 sec to respond]

Am I crazy or is there another one? PFC A2AR KO column, control right side is identical to bTBI 24h left side (slightly displaced upwards).

Yes, that is how it resolved (needed lots of counterintuitive mouse movements). Would love to ask those Dell engineers what they were thinking;)