Shuyu Li
@shuyuli.bsky.social
Reposted by Shuyu Li
Method of the Year 2025: In her feature, @vivienm.bsky.social asks scientists about their strategies and decision-making as they scale EM-based approaches for larger brains.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Method of the Year: EM connectomics - Nature Methods
Using electron microscopy, scientists mapped a Caenorhabditis elegans nervous system and Drosophila brain at single-neuron resolution. Connectomics work on bigger brains takes new methods strategies.
www.nature.com
December 8, 2025 at 10:26 PM
Method of the Year 2025: In her feature, @vivienm.bsky.social asks scientists about their strategies and decision-making as they scale EM-based approaches for larger brains.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Shuyu Li
Electron microscopy is @nature.com's Method of the Year! 🧠🔬🏆
@natmethods.nature.com shares why MICrONS and FlyWire are proof that #ElectronMicroscopy is helping us see the brain and its incredible complexity at a new level: https://www.nature.com/articles/s41592-025-02988-6
🧠📈 #studyBRAIN
@natmethods.nature.com shares why MICrONS and FlyWire are proof that #ElectronMicroscopy is helping us see the brain and its incredible complexity at a new level: https://www.nature.com/articles/s41592-025-02988-6
🧠📈 #studyBRAIN
December 9, 2025 at 8:14 PM
Electron microscopy is @nature.com's Method of the Year! 🧠🔬🏆
@natmethods.nature.com shares why MICrONS and FlyWire are proof that #ElectronMicroscopy is helping us see the brain and its incredible complexity at a new level: https://www.nature.com/articles/s41592-025-02988-6
🧠📈 #studyBRAIN
@natmethods.nature.com shares why MICrONS and FlyWire are proof that #ElectronMicroscopy is helping us see the brain and its incredible complexity at a new level: https://www.nature.com/articles/s41592-025-02988-6
🧠📈 #studyBRAIN
Reposted by Shuyu Li
Read yet another review today that ascribes GECIs' larger SNR vs GEVIs to their being evolved earlier (suggesting the GECIs are better optimized). This assumption is understandable but incorrect. GEVIs' photonic response per molecule per AP have been as good as GECIs since ASAP3.
December 6, 2025 at 12:36 AM
Read yet another review today that ascribes GECIs' larger SNR vs GEVIs to their being evolved earlier (suggesting the GECIs are better optimized). This assumption is understandable but incorrect. GEVIs' photonic response per molecule per AP have been as good as GECIs since ASAP3.
Reposted by Shuyu Li
Introducing mScarlet3-S2: a highly photostable and bright red fluorescent protein.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
December 4, 2025 at 8:19 PM
Introducing mScarlet3-S2: a highly photostable and bright red fluorescent protein.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Shuyu Li
Thanks to @nature.com for featuring our work in this piece on genetically-encoded sensors.
The article does a great job highlighting their importance for both basic research and translational impact, such as in our lab's research on serotonin.
www.nature.com/articles/d41...
The article does a great job highlighting their importance for both basic research and translational impact, such as in our lab's research on serotonin.
www.nature.com/articles/d41...
How genetically encoded sensors have lit up neuroscience
Tools that track specific molecules in neurons have enabled researchers to probe previously unexplored aspects of neurobiology — although important caveats remain.
www.nature.com
November 21, 2025 at 5:56 PM
Thanks to @nature.com for featuring our work in this piece on genetically-encoded sensors.
The article does a great job highlighting their importance for both basic research and translational impact, such as in our lab's research on serotonin.
www.nature.com/articles/d41...
The article does a great job highlighting their importance for both basic research and translational impact, such as in our lab's research on serotonin.
www.nature.com/articles/d41...
Reposted by Shuyu Li
Thankful for this blog piece by @ptrrupprecht.bsky.social on the Dirigo project. Glad you liked the posts!
gcamp6f.com/2025/11/14/d...
gcamp6f.com/2025/11/14/d...
Dirigo: a future Python alternative to Scanimage?
Over the last 20 years, many microscopes that are capable of resonant scanning two-photon microscopy have converged on using ScanImage, a powerful software package with many strengths but also two …
gcamp6f.com
November 21, 2025 at 4:24 PM
Thankful for this blog piece by @ptrrupprecht.bsky.social on the Dirigo project. Glad you liked the posts!
gcamp6f.com/2025/11/14/d...
gcamp6f.com/2025/11/14/d...
Reposted by Shuyu Li
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Shuyu Li
Happy to share our new preprint on the red-shifted channelrhodopsin ChR024, recently discovered by Inoue Lab (biorxiv.org/content/10.1...
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
September 18, 2025 at 3:28 AM
Happy to share our new preprint on the red-shifted channelrhodopsin ChR024, recently discovered by Inoue Lab (biorxiv.org/content/10.1...
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
), highlighting its long-wavelength absorption and ion conductance:
biorxiv.org/content/10.1...
Many thanks to our wonderful lab members and collaborators!
Reposted by Shuyu Li
Really cool stuff! Engineered excitatory opsins responding to 15nW light
WAChRs are excitatory opsins sensitive to indoor lighting www.biorxiv.org/content/10.1...
September 18, 2025 at 4:23 AM
Really cool stuff! Engineered excitatory opsins responding to 15nW light
Reposted by Shuyu Li
🌹🔬🤩
Our new paper is published in the Journal of Chemical Biology! 🏮 We share StayRose, a red version of StayGold 🏮 StayRose has an unnatural amino acid-based chromophore, and has the same immense photobleach-resistance as StayGold 💡
StayRose: A photostable StayGold derivative redshifted by genetic code expansion
Photobleaching of fluorescent proteins often limits the acquisition of high-quality
images in microscopy. StayGold, a novel dimeric GFP recently monomerized through sequence
engineering, addresses thi...
www.jbc.org
November 17, 2025 at 9:37 AM
🌹🔬🤩
Reposted by Shuyu Li
This work is now out @pnas.org. Result of fantastic collaborations with @so-lets-kilab70.bsky.social and Jason vevea @St Jude. Look out for two cool fluorescent ligands.
November 16, 2025 at 5:11 AM
This work is now out @pnas.org. Result of fantastic collaborations with @so-lets-kilab70.bsky.social and Jason vevea @St Jude. Look out for two cool fluorescent ligands.
Reposted by Shuyu Li
New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 13, 2025 at 4:20 PM
New preprint 🥳! We made photoclickable HaloTag ligands to precisely control protein labeling on living cells. With it, we can do some cool multicolor stuff. Huge congrats to Franzi and all co-authors! Check it out 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Shuyu Li
Have you ever wanted to make your own climate warming stripes plot? It's super easy with #rstats! (code here gist.github.com/andrewheiss/... )
November 7, 2025 at 10:14 PM
Have you ever wanted to make your own climate warming stripes plot? It's super easy with #rstats! (code here gist.github.com/andrewheiss/... )
Reposted by Shuyu Li
🚨Curious how synthetic fluorophores simplify microscopy? Our review covers applications such as super-resolution microscopy and biosensing. 🎉👩🔬Congrats to my first PhD student, Agnese Nicoli, for the fearless deep dive! 🔬 ⚗️
D-CHAB @ethz.ch
www.nature.com/articles/s41...
D-CHAB @ethz.ch
www.nature.com/articles/s41...
Synthetic fluorophores for live-cell fluorescence microscopy and biosensing - Nature Chemical Biology
Performing live-cell microscopy experiments with high spatial and temporal resolution requires fluorophores with highly optimized properties. This Review examines the progress in developing synthetic ...
www.nature.com
November 5, 2025 at 9:29 PM
🚨Curious how synthetic fluorophores simplify microscopy? Our review covers applications such as super-resolution microscopy and biosensing. 🎉👩🔬Congrats to my first PhD student, Agnese Nicoli, for the fearless deep dive! 🔬 ⚗️
D-CHAB @ethz.ch
www.nature.com/articles/s41...
D-CHAB @ethz.ch
www.nature.com/articles/s41...
Reposted by Shuyu Li
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
November 4, 2025 at 10:40 PM
My new ImageJ / Fiji toolkit is out 🔥! The goal is to make image handling & visualization easy, with an intuitive interface! Install it on Fiji with the "Image Viewer" update site
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
#microscopy #ImageJ #FluorescenceFriday #microscopyMonday
imagej.net/plugins/imag...
Reposted by Shuyu Li
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/...
Reposted by Shuyu Li
A Sensitive Soma-localized Red Fluorescent Calcium Indicator for Multi-Modality Imaging of Neuronal Populations In Vivo. It works well with wide-field imaging, two-photon microscopy, and fiber photometry biorxiv.org/content/10.1...
February 4, 2025 at 3:49 AM
A Sensitive Soma-localized Red Fluorescent Calcium Indicator for Multi-Modality Imaging of Neuronal Populations In Vivo. It works well with wide-field imaging, two-photon microscopy, and fiber photometry biorxiv.org/content/10.1...
Reposted by Shuyu Li
Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....
A Photoswitchable HaloTag for Spatiotemporal Control of Fluorescence in Living Cells
Photoswitchable fluorophores are critical for advanced bioimaging. Here, we develop a photoswitchable self-labeling HaloTag that can reversibly modulate the emission of a bound fluorogenic dye via a ....
onlinelibrary.wiley.com
October 25, 2025 at 8:56 AM
Our photoswitchable HaloTag is out in Angewandte Chemie @angewandtechemie.bsky.social ! We now also show that this system can be used to control emitter density in SMLM. Congrats to Franzi, Bego, and our amazing collaborators. Check it out: onlinelibrary.wiley.com/doi/full/10....
Reposted by Shuyu Li
Very cool collaborative work between multiple groups across three institutions. Shoutout to @rhodamine110.bsky.social and his crew along with longtime @the.3i.social community @so-lets-kilab70.bsky.social for deploying 3i's #latticelightsheet for some particularly elegant chromatin microscopy. 🔥🔬🧠🧬🥽
October 28, 2025 at 5:51 PM
Very cool collaborative work between multiple groups across three institutions. Shoutout to @rhodamine110.bsky.social and his crew along with longtime @the.3i.social community @so-lets-kilab70.bsky.social for deploying 3i's #latticelightsheet for some particularly elegant chromatin microscopy. 🔥🔬🧠🧬🥽
Reposted by Shuyu Li
Now online @nature.com!
Want to change the consequences of receptor activation?
Small molecules binding the GPCR-transducer interface change G protein subtype preference in predictable ways, enabling rational drug design 💥
So many new possibilities! 🧪🧠🟦
www.nature.com/articles/s41...
🧵👇
Want to change the consequences of receptor activation?
Small molecules binding the GPCR-transducer interface change G protein subtype preference in predictable ways, enabling rational drug design 💥
So many new possibilities! 🧪🧠🟦
www.nature.com/articles/s41...
🧵👇
Designing allosteric modulators to change GPCR G protein subtype selectivity - Nature
Studies of the G-protein-coupled receptor NTSR1 show that the G protein selectivity of this receptor can be modified by small molecules, enabling the design of drugs that work by switching receptor su...
www.nature.com
October 27, 2025 at 8:50 PM
Now online @nature.com!
Want to change the consequences of receptor activation?
Small molecules binding the GPCR-transducer interface change G protein subtype preference in predictable ways, enabling rational drug design 💥
So many new possibilities! 🧪🧠🟦
www.nature.com/articles/s41...
🧵👇
Want to change the consequences of receptor activation?
Small molecules binding the GPCR-transducer interface change G protein subtype preference in predictable ways, enabling rational drug design 💥
So many new possibilities! 🧪🧠🟦
www.nature.com/articles/s41...
🧵👇
Reposted by Shuyu Li
mStayRose is published in JBC 🥳🎉
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
StayRose: a photostable StayGold derivative red-shifted by genetic code expansion
Photobleaching of fluorescent proteins often limits the acquisition of high-quality
images in microscopy. StayGold, a novel dimeric green fluorescent protein recently
monomerised through sequence engi...
www.jbc.org
October 22, 2025 at 4:58 PM
mStayRose is published in JBC 🥳🎉
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
Congratulations @wsctt.bsky.social @sporemohan.bsky.social and team for the monumental effort to make a non-natural amino acid incorporating fluorescent protein accessible. It's based on mStayGold, bright, and photostable:
www.jbc.org/article/S002...
Reposted by Shuyu Li
My initial assessment of this paper ⬇️ was brief, so let’s have a better look at it:
🧵
🧵
Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains.
Is it impressive? Yes
Is it new? No
Should you use it? Probably not.
www.cell.com/cell/fulltex...
Is it impressive? Yes
Is it new? No
Should you use it? Probably not.
www.cell.com/cell/fulltex...
Time-resolved fluorescent proteins expand fluorescent microscopy in temporal and spectral domains
A family of rationally designed time-resolved fluorescent proteins with controllable
lifetimes across the visible spectrum enables simultaneous multiplexed live imaging,
super-resolution microscopy, a...
www.cell.com
September 29, 2025 at 5:51 PM
My initial assessment of this paper ⬇️ was brief, so let’s have a better look at it:
🧵
🧵
Reposted by Shuyu Li
Now out in JACS. pubs.acs.org/doi/full/10....
Grateful to thoughtful reviewers who found some errors in our model and encouraged us to make a better one! A renaissance in magnetobiology is coming...
Grateful to thoughtful reviewers who found some errors in our model and encouraged us to make a better one! A renaissance in magnetobiology is coming...
May 15, 2025 at 4:04 PM
Now out in JACS. pubs.acs.org/doi/full/10....
Grateful to thoughtful reviewers who found some errors in our model and encouraged us to make a better one! A renaissance in magnetobiology is coming...
Grateful to thoughtful reviewers who found some errors in our model and encouraged us to make a better one! A renaissance in magnetobiology is coming...
Reposted by Shuyu Li
There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...
December 16, 2024 at 9:25 AM
There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...