Teun Huijben
Scientist/PostDoc with Loïc Royer at Biohub, San Francisco 🔬 image analysis | localization microscopy | machine learning, 🇳🇱 by bike 🚲
📍San Francisco
- 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! 😍
- Our November issue is now live! 🎉 www.nature.com/nmeth/volume... On the cover, cell tracking in a developing zebrafish embryo visualized using Ultrack. Cover by Alexandre Dizieux, Jordão Bragantini, Loic Royer, Merlin Lange, CZ Biohub. Paper here: www.nature.com/articles/s41...
- 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 😮
- Great track visualisation tool by @teunhuijben.bsky.social and colleagues. Over lunch we discovered that inTRACKtive can handle herds of zebras almost as well as groups of migrating cells.
- Reposted by Teun HuijbenSecond 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...
- Reposted by Teun HuijbenOur 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 🔬😊
- And we’re off. #CBIAS2025 6th Edition, first outside of the Crick but impressed by the localities at @wellcomecollection.bsky.social @david-j-barry.bsky.social welcoming the community
- 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 🚀
- #geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/
- 🍾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!
- 🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...
- Reposted by Teun HuijbenSaying 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!!
- Enjoying two weeks of cell tracking tools, file formats, and collaboration, all at the beautiful Janelia Research Campus. What a place! 🤩🔬🧪 @hhmijanelia.bsky.social
- Reposted by Teun HuijbenMicroscopy 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
- Nanobiology Rocks! #ASCB2024
- 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
- Re-upping this - please register if you're in San Diego this Friday and want to hear about the latest advances in cryoEM/cryoET, mass spec, live imaging, and AI! tinyurl.com/ASCBSANDBOX
- Reposted by Teun HuijbenWe 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)
- 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]
- 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🔬
- 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.
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View full thread10/ 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! 🥳
- Reposted by Teun HuijbenIndeed! Hello everyone!
- 🚀Thrilled to announce #inTRACKtive: a web-based tool for exploring massive cell-tracking datasets, no software installation required! Open your browser and dive into terabytes of developmental biology data 🐭🪰🪱🪲🐠 Preprint: biorxiv.org/content/10.1... Repository: github.com/royerlab/inT... 🧵1/n
- 2/ 💻 The size and complexity of microscopy datasets, spanning terabytes and thousands of cells, require expertise and resources, which limits accessibility. We present #inTRACKtive: a user-friendly web-based client-side solution for visualizing and interacting with large cell tracking datasets.
- 3/ ⭐️ #inTRACKtive enables researchers to visualize, analyze, and share cell-tracking datasets – in real-time, in your browser, without downloading any file. You can select specific groups of cells and trace their lineages interactively through time, perfect for virtual fate-mapping experiments! 💻📊
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View full thread16/ Disclaimer: Loïc Royer and I originally posted this thread on the Bird app
