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Nico Stuurman

@nicostuurman.bsky.social
910 followers 81 following 12 posts
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Reposted by Nico Stuurman
Mark Pownall @mpownall.bsky.social · 15/09/2026
❗Postdoc positions available! We have multiple fully funded openings in the lab - please reach out if you’re interested. I’ll be at CSHL Epigenetics and Chromatin this week, so come find me if you’d like to learn more about the lab or potential projects
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Reposted by Nico Stuurman
Johannes Hohlbein @hohlbeinlab.bsky.social · 05/09/2026
(LinkedIn cross post) 0.12.0 of #webSMLM released. Work mainly by @kjamartens.bsky.social introduced live streaming and real time analysis from frames recorded in MicroManager or Python. hohlbeinlab.github.io/webSMLM/webS...
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Reposted by Nico Stuurman
Egon Willigh☮gen 🟥 @egonw.mastodon.social.ap.brid.gy · 13/07/2026
please, digital sovereignty is not about the country where the product comes from, it comes for rights we normally associate with open source Don't make the mistake to switch to yet another closed source product with vendor lock-in
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Reposted by Nico Stuurman
Kari Herrington @kahsage.bsky.social · 19/06/2026
I'm super excited my art is gracing the cover of Nature cell biology! Thanks @henrydebelly.bsky.social for letting me draw the cover for you and congratulations on your paper! www.nature.com/articles/s41...
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Reposted by Nico Stuurman
Journal of Cell Biology @jcb.org · 19/06/2026
SynSeg: A synthetic data-driven approach for robust subcellular structure segmentation. A new tool from Zhengyang Guo, Guangshuo Ou and colleagues: rupress.org/jcb/article/... 📕 Part of our #Microtubules collection: rupress.org/jcb/collecti... #EESMicrotubules
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Nico Stuurman @nicostuurman.bsky.social · 26/05/2026
Because @tanner-fadero.bsky.social asked for it and I had tokens to spare, I built an orthogonal viewer for @micro-manager.bsky.social today.
Screenshot of a viewer showing xy, xz, and yz planes of a 3D dataset.
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Reposted by Nico Stuurman
Carl T. Bergstrom @carlbergstrom.com · 22/05/2026
“Units of the NIH are privately directing grantees to request permission in advance for any co-authorship with a scholar affiliated with a foreign institution, even if all the work was done in the United States.” Grantees also told to remove papers with foreign authors from progress reports.
science.org
U.S. researchers face new restrictions on publishing with foreign collaborators
NIH, NASA grantees are confused and concerned amid agencies’ piecemeal communication
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Nico Stuurman @nicostuurman.bsky.social · 21/05/2026
I'll be writing a few posts about new features in Micro-Manager. If you are interested in those, please follow @micro-manager.bsky.social.
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Reposted by Nico Stuurman
David Gaboriau @dgaboriau.bsky.social · 07/05/2026
Random thanks to the image.sc forum, for such a treasure trove of information on bioimage analysis. It's always a great read!
image.sc
Image.sc Forum
Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).
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Reposted by Nico Stuurman
Julia Lazzari-Dean @jlazzaridean.bsky.social · 05/05/2026
We’re hiring a scientist to work on microscopy at Calico! If you’re excited about developing and applying cutting edge microscopy to a variety of biological questions, we’d love to hear from you. Find more information and apply here: www.calicolabs.com/careers/?gh_...
calicolabs.com
Careers - Calico
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 30/04/2026
After 9 years, I am finally finishing the story about normalized cross-correlation (and reviving my blog). The new blog post about deep technical details on the most used image registration technique. I know y'all have been waiting. katpyxa.info/feedbacks/?p...
katpyxa.info
Calculating normalized cross-correlation (part 3) – //><=~!=//
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Jonas Wietek @jwietek.bsky.social · 24/04/2026
Finally online @natmethods.nature.com www.nature.com/articles/s41... This was a fun collaboration with @finkryan.bsky.social @massecklab.bsky.social @tpatriarchi.bsky.social @martinfuhrmann.bsky.social @campbell-lab.bsky.social @jangrundemann.bsky.social 🧪🧠🔬🧬
nature.com
PinkyCaMP: an mScarlet-based calcium sensor with enhanced brightness, photostability and multiplexing capabilities - Nature Methods
PinkyCaMP is a red genetically encoded calcium indicator with improved brightness and photostability. Derived from mScarlet, it does not exhibit photoswitching upon blue light illumination and is ther...
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Reposted by Nico Stuurman
Falk Schneider @faldalf.bsky.social · 06/04/2026
Mirror mirror on the wall who is the brightest of them all? Brightness is a key parameter for choosing fluorescent reporters in bioimaging. As tricky to assess, we present a pipeline to compare chemigenetic labels and FPs in tissue culture and #zebrafish embryos. www.biorxiv.org/content/10.6...
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Joachim Goedhart @joachimgoedhart.bsky.social · 09/04/2026
HiCaRI: A StayGold-based calcium ion indicator by Robert E. Campbell and team: www.biorxiv.org/content/10.6...
Overview of HiCaRI design and engineering
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Reposted by Nico Stuurman
Kai Johnsson @kjohnsson.bsky.social · 26/03/2026
A high-affinity split-HaloTag for live-cell protein labeling. And much more. www.nature.com/articles/s41...
nature.com
A high-affinity split-HaloTag for live-cell protein labeling
Nature Communications - Lin and colleagues present high-affinity split-HaloTag pairs for protein tagging and multiplexed labelling. This versatile system allows protein visualisation with diverse...
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Nico Stuurman @nicostuurman.bsky.social · 11/03/2026
The previous ScienceScoop by Joe DeRisi was amazing. I am very much looking forward to this one. If you are in the are, come see. It is open to everyone.
https://ucsfsciensecoop.eventbrite.com Announcement for public lecture by David Julius, March 25 6pm, Byers Auditorium Genentech Hall, 600 16th Street, San Francisco
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Reposted by Nico Stuurman
Tanner Fadero @tanner-fadero.bsky.social · 10/03/2026
@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.
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Reposted by Nico Stuurman
Kurt Thorn @kurtthorn.bsky.social · 09/03/2026
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.
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Nico Stuurman @nicostuurman.bsky.social · 21/02/2026
How many laptops does a married couple need?
5 laptops stacked on a table
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Nico Stuurman @nicostuurman.bsky.social · 26/01/2026
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...
nicost.github.io
Photonics West 2026 impressions
The Photonics West conference includes a gigantic tradeshow spanning 2 halls of the Moscone Center and some of the space in between. I visited on two consecutive afternoon, trying to at least walk by ...
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Reposted by Nico Stuurman
Nature @nature.com · 21/01/2026
Researchers have engineered magnetically controlled fluorescent proteins that can be remotely dimmed and brightened in cells and living animals go.nature.com/3NUSY12
go.nature.com
‘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.
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Reposted by Nico Stuurman
Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 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/...
janelia.org
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.,
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Nico Stuurman @nicostuurman.bsky.social · 21/12/2025
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...
nicost.github.io
Firmware Emulators
title: “Firmware Emulators for Microscope Devices” author: Nico Stuurman date: 2025-12-21 —
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Nico Stuurman @nicostuurman.bsky.social · 04/12/2025
All the best with your new lab at the Whitehead Ron! We miss you at UCSF! wi.mit.edu/news/whitehe...
wi.mit.edu
Whitehead Institute welcomes Ron Vale as its newest Member | Whitehead Institute
Ron Vale, a world-renowned cell biologist who is an expert on motor proteins and cell transport systems, joins Whitehead Institute this December as a Member.
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Reposted by Nico Stuurman
Tanner Fadero @tanner-fadero.bsky.social · 20/08/2025
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
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Wallace Marshall @wallaceucsf.bsky.social · 18/05/2025
www.geekwire.com/2025/seattle...
geekwire.com
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.
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Reposted by Nico Stuurman
micro-manager.bsky.social @micro-manager.bsky.social · 10/05/2025
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...
nicost.github.io
Using a Decompiler to change the MM Device Interface Version
Some companies (like Cairn and Mightex, but there are others) wrote device adapters for their equipment but did not share the source code with the Micro-Manager team. Therefore, you need to ask these ...
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Reposted by Nico Stuurman
Roli Roberts @roliroberts.bsky.social · 15/04/2025
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....
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).
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Rita Strack @ritastrack.bsky.social · 10/04/2025
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.
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QI@CSHL @qiatcshl.bsky.social · 29/03/2025
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...
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Reposted by Nico Stuurman
micro-manager.bsky.social @micro-manager.bsky.social · 29/03/2025
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...
nicost.github.io
PlayerOne cooled CMOS camera
The Sony STARVIS and STARVIS2 image sensors are back-illuminated, have high QE and low readnoise (where STARVIS2 increases full well depth over STARVIS). Even though these sensors are marketed towards...
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Reposted by Nico Stuurman
adamezracohen.bsky.social @adamezracohen.bsky.social · 28/02/2025
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...
biorxiv.org
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 ...
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Lucien Hinderling @lhinderling.bsky.social · 23/02/2025
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...
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Aafke Gros @aafkegros.bsky.social · 15/01/2025
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
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Joachim Goedhart @joachimgoedhart.bsky.social · 06/01/2025
A highly photostable monomeric red fluorescent protein www.researchsquare.com/article/rs-5...
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
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Christophe 🔬 Leterrier @christlet.bsky.social · 25/12/2024
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...
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Claire Deo @clairedeo.bsky.social · 07/01/2025
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...
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Josiah Passmore @jpassmore.bsky.social · 17/12/2024
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).
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Robert Aboukhalil @robert.bio · 04/12/2024
“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...
statnews.com
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
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John Ngo @johntngo.bsky.social · 30/11/2024
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...
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Tanja Bhuiyan @tanjabhuiyan.bsky.social · 25/11/2024
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.
journals.plos.org
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...
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Robert Haase @haesleinhuepf.bsky.social · 24/11/2024
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]
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Nico Stuurman @nicostuurman.bsky.social · 31/10/2024
New Dell laptop decided to install Windows sideways. Rotating it will flip the screen, but impossible to get it back to normal orientation. Hope this will straighten out.
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Heather Brown-Harding @microscopyed.bsky.social · 09/10/2024
Check out "ONE" Microscopy, which can achieve protein level resolution with a light microscope! I've been trying to combine Magnify + STED to visualize protein complexes. Looks like they were able to do it with X10 + SRFF ;-)
nature.com
One-step nanoscale expansion microscopy reveals individual protein shapes - Nature Biotechnology
Combining expansion microscopy with super-resolution radial fluctuations captures the morphology of single proteins.
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