Joachim Goedhart
@joachimgoedhart.bsky.social
Scientist + Teacher UvA/Amsterdam | Cells | Molecules | Microscopy | Fluorescent Proteins | Biosensors | Lifetime imaging | Open Science | dataViz | R | web apps
Homepage: https://joachimgoedhart.github.io/
DataViz Apps: https://huygens.science.uva.nl
Homepage: https://joachimgoedhart.github.io/
DataViz Apps: https://huygens.science.uva.nl
Revealing acute consequences of rapid degradation of synaptic fusion proteins at individual synapses using Auxin-Inducible Degron 2 technology
www.nature.com/articles/s42...
www.nature.com/articles/s42...
November 22, 2025 at 7:59 PM
Revealing acute consequences of rapid degradation of synaptic fusion proteins at individual synapses using Auxin-Inducible Degron 2 technology
www.nature.com/articles/s42...
www.nature.com/articles/s42...
Uploading >30 files to change our preprint into a VOR for @elife.bsky.social
What could possibly go wrong?
What could possibly go wrong?
November 19, 2025 at 1:58 PM
Uploading >30 files to change our preprint into a VOR for @elife.bsky.social
What could possibly go wrong?
What could possibly go wrong?
Hilarious, here's a variant for rotated x-axis labels
November 14, 2025 at 10:39 AM
Hilarious, here's a variant for rotated x-axis labels
Independent validation of the SnxA biosensor as a sensitive reporter of PI(3,5)P₂ dynamics by Gerald R Hammond and team: www.biorxiv.org/content/10.1...
November 12, 2025 at 6:57 PM
Independent validation of the SnxA biosensor as a sensitive reporter of PI(3,5)P₂ dynamics by Gerald R Hammond and team: www.biorxiv.org/content/10.1...
Emerging trends of fluorescence lifetime imaging microscopy (FLIM): advances, challenges, and prospects
www.biophysics-reports.org/article/doi/...
www.biophysics-reports.org/article/doi/...
November 3, 2025 at 11:24 AM
Emerging trends of fluorescence lifetime imaging microscopy (FLIM): advances, challenges, and prospects
www.biophysics-reports.org/article/doi/...
www.biophysics-reports.org/article/doi/...
HaloTrace: A spatiotemporally precise fluorescent readout of blood-brain barrier permeability in mice by Chenghua Gu and team: www.biorxiv.org/content/10.1...
November 1, 2025 at 2:01 PM
HaloTrace: A spatiotemporally precise fluorescent readout of blood-brain barrier permeability in mice by Chenghua Gu and team: www.biorxiv.org/content/10.1...
A most surprising world map came by this night - it was correctly categorized by Pub quiz team member @andreacaldarola.bsky.social
October 28, 2025 at 10:11 PM
A most surprising world map came by this night - it was correctly categorized by Pub quiz team member @andreacaldarola.bsky.social
Periodic reminder that the fluorescent compound in mammalian cell culture media, such as DMEM, is riboflavin (not phenol red)
October 14, 2025 at 7:51 PM
Periodic reminder that the fluorescent compound in mammalian cell culture media, such as DMEM, is riboflavin (not phenol red)
Visualizing PINK1 Activity Dynamics in Single Cells with a Phase Separation-Based Kinase Activity Reporter by @schmittwitt.bsky.social and team: www.biorxiv.org/content/10.1...
October 10, 2025 at 11:55 AM
Visualizing PINK1 Activity Dynamics in Single Cells with a Phase Separation-Based Kinase Activity Reporter by @schmittwitt.bsky.social and team: www.biorxiv.org/content/10.1...
FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single-cell fluorescence lifetime data by Rupsa Datta and team: www.biorxiv.org/content/10.1...
October 9, 2025 at 10:40 AM
FLIM Playground: An interactive, end-to-end graphical user interface for analyzing single-cell fluorescence lifetime data by Rupsa Datta and team: www.biorxiv.org/content/10.1...
Brilliant talk by Petra Schwille at #NWOBiophysics2025 on her work on synthetic cells - which she summarized as “a lot of playing around and a bit of progress“
October 6, 2025 at 6:42 PM
Brilliant talk by Petra Schwille at #NWOBiophysics2025 on her work on synthetic cells - which she summarized as “a lot of playing around and a bit of progress“
Identification of optimal fluorophores for use in the Drosophila embryo by Timothy E Saunders and team: www.biorxiv.org/content/10.1...
September 30, 2025 at 2:43 PM
Identification of optimal fluorophores for use in the Drosophila embryo by Timothy E Saunders and team: www.biorxiv.org/content/10.1...
From my experience (which is anecdotal and qualitative, I realize that), one needs really high S/N for proper unmixing.
Even under these conditions the structures do not look crisp and free from crosstalk ⬇️ (cropped from figure 4)
Even under these conditions the structures do not look crisp and free from crosstalk ⬇️ (cropped from figure 4)
September 30, 2025 at 8:21 AM
From my experience (which is anecdotal and qualitative, I realize that), one needs really high S/N for proper unmixing.
Even under these conditions the structures do not look crisp and free from crosstalk ⬇️ (cropped from figure 4)
Even under these conditions the structures do not look crisp and free from crosstalk ⬇️ (cropped from figure 4)
Since the simultaneous visualisation of 2 - 4 fluorescent proteins is usually enough, using spectral variants is the easier way to go. There are numerous spectral variants with high brightness and good photostability that allow this.
September 29, 2025 at 5:51 PM
Since the simultaneous visualisation of 2 - 4 fluorescent proteins is usually enough, using spectral variants is the easier way to go. There are numerous spectral variants with high brightness and good photostability that allow this.
So was it really necessary to generate a library of new variants? Probably not. Yet, it is nice that the authors took the effort, as the more FPs the better! The engineering of a mTurquoise2 variant with a QY of 100% is definitely interesting!
September 29, 2025 at 5:51 PM
So was it really necessary to generate a library of new variants? Probably not. Yet, it is nice that the authors took the effort, as the more FPs the better! The engineering of a mTurquoise2 variant with a QY of 100% is definitely interesting!
Since lifetime information was key in the engineering of mScarlets, we have also tested mScarlet variants for lifetime unmixing. For fun, we plated several RFPs to generate an image with lifetime contrast (courtesy of Daphne Bindels).
September 29, 2025 at 5:51 PM
Since lifetime information was key in the engineering of mScarlets, we have also tested mScarlet variants for lifetime unmixing. For fun, we plated several RFPs to generate an image with lifetime contrast (courtesy of Daphne Bindels).
The quality of the unmixed data in the paper by Xin Zhang are much better than what was achieved with our home-build system, but that's due to the strongly improved (commercially available) hardware. This is is mainly driven by microscope companies (especially Leica).
September 29, 2025 at 5:51 PM
The quality of the unmixed data in the paper by Xin Zhang are much better than what was achieved with our home-build system, but that's due to the strongly improved (commercially available) hardware. This is is mainly driven by microscope companies (especially Leica).
Did it work? Yes! We also included an error analysis to present the S/N ratio for the unmixed images.
Were the images impressive? Not really! This is a limitation of the hardware, which limits the resolution. Here's an example for 3 CFP variants that were unmixed (co-expressed with a YFP and RFP).
Were the images impressive? Not really! This is a limitation of the hardware, which limits the resolution. Here's an example for 3 CFP variants that were unmixed (co-expressed with a YFP and RFP).
September 29, 2025 at 5:51 PM
Did it work? Yes! We also included an error analysis to present the S/N ratio for the unmixed images.
Were the images impressive? Not really! This is a limitation of the hardware, which limits the resolution. Here's an example for 3 CFP variants that were unmixed (co-expressed with a YFP and RFP).
Were the images impressive? Not really! This is a limitation of the hardware, which limits the resolution. Here's an example for 3 CFP variants that were unmixed (co-expressed with a YFP and RFP).
But is is new?
Discrimination of FPs on basis of their lifetime was first reported in 1999 by Rainer Pepperkok et al: doi.org/10.1016/S096...
They also solved the equations for unmixing three species that were acquired in the same spectral channel:
Discrimination of FPs on basis of their lifetime was first reported in 1999 by Rainer Pepperkok et al: doi.org/10.1016/S096...
They also solved the equations for unmixing three species that were acquired in the same spectral channel:
September 29, 2025 at 5:51 PM
But is is new?
Discrimination of FPs on basis of their lifetime was first reported in 1999 by Rainer Pepperkok et al: doi.org/10.1016/S096...
They also solved the equations for unmixing three species that were acquired in the same spectral channel:
Discrimination of FPs on basis of their lifetime was first reported in 1999 by Rainer Pepperkok et al: doi.org/10.1016/S096...
They also solved the equations for unmixing three species that were acquired in the same spectral channel:
The authors have generated a library that they name tr-FPs for time-resolved Fluorescent Proteins. The tr-FPs are designed to have different lifetimes, which enable discrimination by fluorescence lifetime imaging microscopy (FLIM). They certainly did a lot of experiments, that’s impressive.
September 29, 2025 at 5:51 PM
The authors have generated a library that they name tr-FPs for time-resolved Fluorescent Proteins. The tr-FPs are designed to have different lifetimes, which enable discrimination by fluorescence lifetime imaging microscopy (FLIM). They certainly did a lot of experiments, that’s impressive.
Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM by Juan Manuel Garcia-Arcos and team: www.biorxiv.org/content/10.1...
September 26, 2025 at 1:29 PM
Fluorescence lifetime estimation: a practical approach using Flipper-TR FLIM by Juan Manuel Garcia-Arcos and team: www.biorxiv.org/content/10.1...
Genetically Encoded Death Indicator (GEDI): a live cell biosensor protocol for high-resolution screening of therapy-resistant cancer cells by Jessica S Blackburn and team: www.biorxiv.org/content/10.1...
September 26, 2025 at 1:24 PM
Genetically Encoded Death Indicator (GEDI): a live cell biosensor protocol for high-resolution screening of therapy-resistant cancer cells by Jessica S Blackburn and team: www.biorxiv.org/content/10.1...
Logic-gating the HaloTag system with Conditional-Halo-ligator 'CHalo' reagents by Oliver Thorn-Seshold and team: www.biorxiv.org/content/10.1...
September 24, 2025 at 12:54 PM
Logic-gating the HaloTag system with Conditional-Halo-ligator 'CHalo' reagents by Oliver Thorn-Seshold and team: www.biorxiv.org/content/10.1...
By reading your emails!
September 24, 2025 at 8:42 AM
By reading your emails!