Teun Huijben
@teunhuijben.bsky.social
Scientist/PostDoc with Loïc Royer at Biohub, San Francisco 🔬 image analysis | localization microscopy | machine learning, 🇳🇱 by bike 🚲
📍San Francisco
📍San Francisco
Enjoying two weeks of cell tracking tools, file formats, and collaboration, all at the beautiful Janelia Research Campus. What a place! 🤩🔬🧪 @hhmijanelia.bsky.social
July 21, 2025 at 3:44 PM
Enjoying two weeks of cell tracking tools, file formats, and collaboration, all at the beautiful Janelia Research Campus. What a place! 🤩🔬🧪 @hhmijanelia.bsky.social
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
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
December 15, 2024 at 2:33 AM
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
booth (#119) for live demos of these tools + #napari & #zebrahub 🐠 Looking forward to connect!🤩🧪🔬
#CellBio2024 #ASCB24 #celltracking
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! 🥳
November 26, 2024 at 5:58 PM
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! 🥳
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 🧬
November 26, 2024 at 5:58 PM
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.
November 26, 2024 at 5:58 PM
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.
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!
November 26, 2024 at 5:58 PM
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!
6/ To showcase the fitting approach, we perform DNA-PAINT on DNA-coated 100nm gold nanoparticles, resulting in a zoo of exotic PSFs!
November 26, 2024 at 5:58 PM
6/ To showcase the fitting approach, we perform DNA-PAINT on DNA-coated 100nm gold nanoparticles, resulting in a zoo of exotic PSFs!
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.
November 26, 2024 at 5:58 PM
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.
November 26, 2024 at 5:58 PM
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.
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.
November 26, 2024 at 5:58 PM
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.
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🔬
November 26, 2024 at 5:58 PM
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]
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]
November 26, 2024 at 5:58 PM
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]
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]
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.
November 26, 2024 at 5:39 PM
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.
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!
November 26, 2024 at 5:39 PM
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!
6/ To showcase the fitting approach, we perform DNA-PAINT on DNA-coated 100nm gold nanoparticles, resulting in a zoo of exotic PSFs!
November 26, 2024 at 5:39 PM
6/ To showcase the fitting approach, we perform DNA-PAINT on DNA-coated 100nm gold nanoparticles, resulting in a zoo of exotic PSFs!
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.
November 26, 2024 at 5:39 PM
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 manner, 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.
November 26, 2024 at 5:39 PM
4/ The PSF doesn’t always deform in the same manner, 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.
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 fitted with a Gaussian.
November 26, 2024 at 5:39 PM
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 fitted with a Gaussian.
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🔬
November 26, 2024 at 5:39 PM
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🔬
11/ 🙌 All credits to the amazing team that made #inTRACKtive and the virtual embryo zoo happen: Ashley Anderson, Andrew Sweet, Erin Hoops, Connor Larsen, Kyle Awayan, Jordão Bragantini, Chi-Li Chiu, and Loïc Royer
November 13, 2024 at 7:53 PM
11/ 🙌 All credits to the amazing team that made #inTRACKtive and the virtual embryo zoo happen: Ashley Anderson, Andrew Sweet, Erin Hoops, Connor Larsen, Kyle Awayan, Jordão Bragantini, Chi-Li Chiu, and Loïc Royer
10/ 🛜 The #inTRACKtive platform is open source (github.com/royerlab/inT...) and has multiple use cases: (i) to explore the Virtual Embryo Zoo, (ii) to visualize your own cell tracking data, 2D or 3D, and (iii) to host your own customizable instance of the viewer.
November 13, 2024 at 7:53 PM
10/ 🛜 The #inTRACKtive platform is open source (github.com/royerlab/inT...) and has multiple use cases: (i) to explore the Virtual Embryo Zoo, (ii) to visualize your own cell tracking data, 2D or 3D, and (iii) to host your own customizable instance of the viewer.
9/ 🔗 With #inTRACKtive, your exact viewing configuration - cells, zoom level, selections, and more - can be shared via a simple hyperlink. Collaboration has never been easier! 👩🔬
November 13, 2024 at 7:53 PM
9/ 🔗 With #inTRACKtive, your exact viewing configuration - cells, zoom level, selections, and more - can be shared via a simple hyperlink. Collaboration has never been easier! 👩🔬
8/ 📱 #inTRACKtive works in any browser, including on tablets and smartphones, offering flexibility in how users interact with the data. A larger screen and keyboard are recommended to utilize the full UI functionalities.
November 13, 2024 at 7:53 PM
8/ 📱 #inTRACKtive works in any browser, including on tablets and smartphones, offering flexibility in how users interact with the data. A larger screen and keyboard are recommended to utilize the full UI functionalities.
7/ 🤖 The #inTRACKtive platform is optimized for interaction with large-scale datasets. The key innovation is using a specialized cell tracking format based on #Zarr, which enables asynchronous, lazy data loading. We provide scripts to convert tracking data into the required Zarr format.
November 13, 2024 at 7:53 PM
7/ 🤖 The #inTRACKtive platform is optimized for interaction with large-scale datasets. The key innovation is using a specialized cell tracking format based on #Zarr, which enables asynchronous, lazy data loading. We provide scripts to convert tracking data into the required Zarr format.
6/ 🏆 Within the Virtual Embryo Zoo, users can visualize the tracked datasets with #inTRACKtive, download the complete tracking data (ready to visualize in #napari) and see details of the datasets.
November 13, 2024 at 7:53 PM
6/ 🏆 Within the Virtual Embryo Zoo, users can visualize the tracked datasets with #inTRACKtive, download the complete tracking data (ready to visualize in #napari) and see details of the datasets.