Teun Huijben

... Poster (#B415) on Monday, 2:30 pm, about my PhD work: calibration-free molecular counting from a single DNA-PAINT intensity trace 🧬🧪🔬

#bps2026 #SanFrancisco

What a luxury to travel to #bps2026 by bike this year 🚲, locally in SF! I will be presenting the work from the Royer lab (@biohub.org) on Monday, 1:30 pm, in the Biophysics 101 session 🐠🔬. Followed by a poster ...

Join us for the AI Applications in Biology Symposium at @biohub.org! A full day of talks on ML for structural biology, imaging, single-molecule & multimodal/omics data

🗓️ Feb. 20, 2026 (1 day before BPS)
📍San Francisco
🔗 shorturl.at/uQerL

Attend in-person or virtual. Submit abstracts by Jan. 20!

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

Apparently, 🐟 cells are not at all different from herds of 🦓! Great use of #inTRACKtive on very different types of data. Thanks Niko, for trying it out and getting it working already 'during’ my talk 😮

Second speaker is @teunhuijben.bsky.social from @loicaroyer.bsky.social group at @czbiohub.bsky.social #CBIAS2025
Tracking is hard because segmentation is hard, especially in whole zebra fish embryos: Ultrack can help github.com/royerlab/ult...

Our very own @teunhuijben.bsky.social from the @loicaroyer.bsky.social lab at the Biohub gave a brilliant overview of their journey to improve tracking and visualisation (and our lives in general 😝) at #CBIAS2025 👩🏻‍💻🔬👩🏻‍🔬 #tracking #interdisciplinary #bioimageanalysis

Happy to be in London for #CBIAS2025! Looking forward to two days of image analysis, and presenting #inTRACKtive and #Ultrack tomorrow 🔬😊

Had a great time in Janelia this summer developing #geff with this amazing group of cell tracking enthousiasts and software engineers! #geff is a file format for tracking data allowing universal cross-tool communication for a wealth of tracking tools, amongst others our #ultrack and #inTRACKtive 🚀

🍾What a day 🥳 Two papers of the Royer lab in Nature Methods today, including #inTRACKtive! Check out Loïc's thread below for the details ⬇️

Over the next days, I will share the exciting new features we have added since the original preprint. Stay tuned!

Saying goodbye to beautiful @hhmijanelia.bsky.social, after an intense two weeks trackhathon. Organized by legends Caroline Malin-Mayor and Morgan Schwartz in the @janfunkey.bsky.social.

It has been awesome and productive. Thank you!!

Janelia research campus - Virginia

Enjoying two weeks of cell tracking tools, file formats, and collaboration, all at the beautiful Janelia Research Campus. What a place! 🤩🔬🧪 @hhmijanelia.bsky.social

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...

Little Nanobiology reunion in San Diego. Great to see multiple professors/alumni at the Cell Bio conference! 🙌

@tudelft.bsky.social #nanobiology #ASCB24 #CellBio2024

Sunny San Diego view

Happy to be in sunny☀️San Diego for ASCB Cell Bio! Tomorrow I will present #Ultrack and #inTRACKtive (poster B513) at 11:15 am. Swing by the CZI+@czbiohub.bsky.social
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬

#CellBio2024 #ASCB24 #celltracking

Join us next Friday at UC San Diego for a day full of microscopy 💡🔬, mass spec, and AI! Shout out to @manorlaboratory.bsky.social for putting this together! I will present our recent work on cell tracking algorithms and visualization with #Ultrack and #inTRACKtive🧪

#CellBio2024

Hi Eric, could you add me to the Science 🧪 feed? I am employed at the Chan Zuckerberg Biohub in San Francisco working at the interface of developmental biology, microscopy, and machine learning.

Google Scholar: scholar.google.com/citations?us...

Orcid: orcid.org/0000-0002-89...

Congrats on the paper! Also, it’s time to bring Sjoerd Stallinga over to the BlueSky-verse ;)

We modified our STED🔬to make it more efficient ('smart') to acquire high-resolution data of small and rare objects in a 3D cell volume. This enabled collecting a large amount of data in a fully automated fashion. With that, we visualized the ulra-structure a small nuclear body, the paraspeckle👇🏻(1/3)

Point-spread function deformations unlock 3D localization microscopy on spherical nanoparticles

10/ Thanks to all co-authors: Sarojini Mahajan, Masih Fahim, Peter Zijlstra, Rodolphe Marie and Kim I. Mortensen🙌. And of course our #Horizon2020 #MSCActions SuperCol ITN network! 🥳

In addition to the metal nanoparticles (gold 🟠), Masih Fahim’s work showed that the same holds for dielectric (polystyrene ⚪️) particles, allowing us to reconstruct the distribution of single DNA molecules on the nanoparticle surface 🧬

9/ In addition to the metal nanoparticles (gold 🟠), Masih Fahim’s work showed that the same holds for dielectric (polystyrene ⚪️) particles, allowing us to reconstruct the distribution of single DNA molecules on the nanoparticle surface 🧬

8/ In this way, we can map out the full surface. We show that the surface functionalization is patchy and heterogeneous between particles. This will allow studying the surface functionalization at the single-particle level to design and produce the nanoparticles of the future.

Fitting the experimental images with our new analytical PSF model, we obtain the coordinates of the emitters relative to the nanoparticle surface. Allowing us to map the position of the DNA strands that engaged in DNA-PAINT, with <5nm precision!

7/ Fitting the experimental images with our new analytical PSF model, we obtain the coordinates of the emitters relative to the nanoparticle surface. Allowing us to map the position of the DNA strands that engaged in DNA-PAINT, with <5nm precision!

Zoo of exotic PSF shapes resulting from DNA-PAINT on gold spherical nanoparticles

6/ To showcase the fitting approach, we perform DNA-PAINT on DNA-coated 100nm gold nanoparticles, resulting in a zoo of exotic PSFs!

We developed the first-ever analytical PSF model for a fluorophore near a spherical nanoparticle, of any size, material, and composition. Our model is 4 orders of magnitude faster than numerical calculations, allowing us to use it directly to fit experimental data.

5/ We developed the first-ever analytical PSF model for a fluorophore near a spherical nanoparticle, of any size, material, and composition. Our model is 4 orders of magnitude faster than numerical calculations, allowing us to use it directly to fit experimental data.

4/ The PSF doesn’t always deform in the same way, but the PSF shape depends on the fluorophore’s position relative to the nanoparticle. This means that the PSF shape encodes information about the fluorophore’s position, which we can use to our advantage during localization.

A single (freely rotating) fluorophore creates a symmetric PSF, which we conventionally fit with a 2D Gaussian. However, the presence of a nanoparticle deforms the PSF, resulting in significant biases when simply fitted with a Gaussian.

3/ A single (freely rotating) fluorophore creates a symmetric PSF, which we conventionally fit with a 2D Gaussian. However, the presence of a nanoparticle deforms the PSF, resulting in significant biases when simply fitted with a Gaussian.

Nanoparticles are important for biosensing, drug delivery, and cancer therapy.

2/ Nanoparticles are important for biosensing, drug delivery, and cancer therapy. The functionality of the nanoparticle crucially depends on the distribution and number of functional groups on their surface, which can ideally be studied with localization microscopy🔬

PSFs are just Gaussians, right??

Not when your fluorophore💡is close to a nanoparticle 🟠!
Excited to share our recent ACS Nano paper 🥳 in which we present a novel PSF-fitting approach for localization microscopy near nanoparticles.

pubs.acs.org/doi/full/10....

Main findings below in🧵[1/10]

We show that the surface functionalization is patchy and heterogeneous between particles.

8/ In this way, we can map out the full surface. We show that the surface functionalization is patchy and heterogeneous between particles. This will allow studying the surface functionalization at the single-particle level to design and produce the nanoparticles of the future.