Nico Stuurman
@nicostuurman.bsky.social
Reposted by Nico Stuurman
Here's a six-month time-lapse of me building the single objective light sheet fluorescence microscope at the UCSF Center for Advanced Light Microscopy!
Also pictured is @nicostuurman.bsky.social and @kahsage.bsky.social.
#snouty
Also pictured is @nicostuurman.bsky.social and @kahsage.bsky.social.
#snouty
August 20, 2025 at 6:57 PM
Here's a six-month time-lapse of me building the single objective light sheet fluorescence microscope at the UCSF Center for Advanced Light Microscopy!
Also pictured is @nicostuurman.bsky.social and @kahsage.bsky.social.
#snouty
Also pictured is @nicostuurman.bsky.social and @kahsage.bsky.social.
#snouty
Reposted by Nico Stuurman
Reposted by Nico Stuurman
Some Micro-Manager device adapters are not included in the installer. That can cause problems when the device API changes. When the device adapter vendor does not release a new version you can try the following work-around: nicost.github.io/microscope-t...
Using a Decompiler to change the MM Device Interface Version
Some companies (like Cairn and Mightex, but there are others) wrote device adapters for their equipment but did not share the source code with the Micro-Manager team. Therefore, you need to ask these ...
nicost.github.io
May 10, 2025 at 4:04 PM
Some Micro-Manager device adapters are not included in the installer. That can cause problems when the device API changes. When the device adapter vendor does not release a new version you can try the following work-around: nicost.github.io/microscope-t...
Reposted by Nico Stuurman
Here's one of the incredible dataviz images that Ron Milo just showed at #EMBOclimateResilience, from the excellent Greenspan et al PNAS paper www.pnas.org/doi/epub/10....
April 15, 2025 at 9:16 AM
Here's one of the incredible dataviz images that Ron Milo just showed at #EMBOclimateResilience, from the excellent Greenspan et al PNAS paper www.pnas.org/doi/epub/10....
Reposted by Nico Stuurman
Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.
April 10, 2025 at 1:38 PM
Your yearly reminder to acknowledge the core facilities you use and their staff scientists in your papers. These scientists are a crucial part of the scientific ecosystem and to continue to exist they need tangible credit for their work. Plus their associated expertise adds credibility to your work.
Reposted by Nico Stuurman
Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...
March 29, 2025 at 2:42 PM
Our openSPIM is officially up and running to image the latest catch of the day! Fueled by pymmcore-plus & pymmcore-gui! 💪⚡🔬 pymmcore-plus.github.io/pymmcore-plus/ github.com/pymmcore-plu...
Reposted by Nico Stuurman
Just had the pleasure to experiment with a camera targeting the astronomy market, but offering great value for microscopy. Cooled, low noise (<1.5 e read-noise), high QE cameras that work with Micro-Manager can be bought for ~$1k: nicost.github.io/microscope-t...
PlayerOne cooled CMOS camera
The Sony STARVIS and STARVIS2 image sensors are back-illuminated, have high QE and low readnoise (where STARVIS2 increases full well depth over STARVIS). Even though these sensors are marketed towards...
nicost.github.io
March 29, 2025 at 12:56 AM
Just had the pleasure to experiment with a camera targeting the astronomy market, but offering great value for microscopy. Cooled, low noise (<1.5 e read-noise), high QE cameras that work with Micro-Manager can be bought for ~$1k: nicost.github.io/microscope-t...
Reposted by Nico Stuurman
How do tiny magnetic fields affect biochemistry? Overflowing with pride over Katherine Xiang's study on a giant magnetic field effect in a red fluorescent protein, www.biorxiv.org/content/10.1...
Mechanism of giant magnetic field effect in fluorescence of mScarlet3, a red fluorescent protein
Several fluorescent proteins, when expressed in E. coli, are sensitive to weak magnetic fields1. We found that mScarlet3 fluorescence in E. coli reversibly decreased by 21% in the presence of a 60 mT ...
www.biorxiv.org
February 28, 2025 at 4:00 PM
How do tiny magnetic fields affect biochemistry? Overflowing with pride over Katherine Xiang's study on a giant magnetic field effect in a red fluorescent protein, www.biorxiv.org/content/10.1...
Reposted by Nico Stuurman
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
February 23, 2025 at 2:06 PM
PREPRINT OUT ✨ "hack" your microscope to work as a 3D printer! print micrometer sized features at cm scale. a method for easy and cheap microfabrication, with a focus on biological applications. THREAD ↓
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nico Stuurman
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...
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...
January 15, 2025 at 1:39 PM
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...
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...
Reposted by Nico Stuurman
A highly photostable monomeric red fluorescent protein
www.researchsquare.com/article/rs-5...
www.researchsquare.com/article/rs-5...
January 6, 2025 at 9:03 AM
A highly photostable monomeric red fluorescent protein
www.researchsquare.com/article/rs-5...
www.researchsquare.com/article/rs-5...
Reposted by Nico Stuurman
Progress on the quest for a red mStayGold!
Just out: mScarlet3-S2, a new photostable red FP derived from mScarlet3: www.researchsquare.com/article/rs-5...
Just out: mScarlet3-S2, a new photostable red FP derived from mScarlet3: www.researchsquare.com/article/rs-5...
December 25, 2024 at 8:45 AM
Progress on the quest for a red mStayGold!
Just out: mScarlet3-S2, a new photostable red FP derived from mScarlet3: www.researchsquare.com/article/rs-5...
Just out: mScarlet3-S2, a new photostable red FP derived from mScarlet3: www.researchsquare.com/article/rs-5...
Reposted by Nico Stuurman
We made a photoswitchable HaloTag (psHaloTag), which can reversibly turn-on fluorogenic dyes upon illumination 💡. Congrats to Franzi, Bego and all co-authors, check out our preprint below 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
January 7, 2025 at 8:45 AM
We made a photoswitchable HaloTag (psHaloTag), which can reversibly turn-on fluorogenic dyes upon illumination 💡. Congrats to Franzi, Bego and all co-authors, check out our preprint below 👇
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nico Stuurman
Advances in microscopy mean we can now do more than just observe biology—we can control it. But how far can we really push this in mammalian cells with all their (beautiful but annoying) heterogeneity? 🧪🔬(🧵)
December 17, 2024 at 5:47 PM
Advances in microscopy mean we can now do more than just observe biology—we can control it. But how far can we really push this in mammalian cells with all their (beautiful but annoying) heterogeneity? 🧪🔬(🧵)
Reposted by Nico Stuurman
“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯
www.statnews.com/sponsor/2024...
www.statnews.com/sponsor/2024...
New report highlights the scientific impact of open source software
Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing
www.statnews.com
December 4, 2024 at 12:08 AM
“We don’t value software, data, and methods in the same way we value papers, even though those resources empower millions of scientists” 💯
www.statnews.com/sponsor/2024...
www.statnews.com/sponsor/2024...
Reposted by Nico Stuurman
We designed MS2 and PP7 binding coat proteins that are degraded in cells except when bound by their hairpin RNAs.
You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...
You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...
November 30, 2024 at 8:48 PM
We designed MS2 and PP7 binding coat proteins that are degraded in cells except when bound by their hairpin RNAs.
You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...
You can check out our pre-print here: tinyurl.com/27p7hyt9,
and listen to a Google AI-generated podcast on it here: notebooklm.google.com/notebook/d71...
Reposted by Nico Stuurman
If I can add to the his-tag data: at least 6 consecutive his-residues target proteins to nuclear speckles: journals.plos.org/plosgenetics... So this could drive condensation in nuclear speckles.
Genome-Wide Analysis of Histidine Repeats Reveals Their Role in the Localization of Human Proteins to the Nuclear Speckles Compartment
Author Summary Single amino acid repeats are common in eukaryotic proteins. Some of them are associated with developmental and neurodegenerative disorders in humans, suggesting that they play importan...
journals.plos.org
November 25, 2024 at 4:58 PM
If I can add to the his-tag data: at least 6 consecutive his-residues target proteins to nuclear speckles: journals.plos.org/plosgenetics... So this could drive condensation in nuclear speckles.
Reposted by Nico Stuurman
Hi #biabob users,
there comes a new edit mode with the new 0.24.0 release: If you ask %%bob to modify code, it will update the current notebook cell. This should make AI-assisted iterative code modifications much smoother. 🤓
github.com/haesleinhuep...
[video shortened; Bob needs ~10 sec to respond]
there comes a new edit mode with the new 0.24.0 release: If you ask %%bob to modify code, it will update the current notebook cell. This should make AI-assisted iterative code modifications much smoother. 🤓
github.com/haesleinhuep...
[video shortened; Bob needs ~10 sec to respond]
November 24, 2024 at 4:48 PM
Hi #biabob users,
there comes a new edit mode with the new 0.24.0 release: If you ask %%bob to modify code, it will update the current notebook cell. This should make AI-assisted iterative code modifications much smoother. 🤓
github.com/haesleinhuep...
[video shortened; Bob needs ~10 sec to respond]
there comes a new edit mode with the new 0.24.0 release: If you ask %%bob to modify code, it will update the current notebook cell. This should make AI-assisted iterative code modifications much smoother. 🤓
github.com/haesleinhuep...
[video shortened; Bob needs ~10 sec to respond]
New Dell laptop decided to install Windows sideways. Rotating it will flip the screen, but impossible to get it back to normal orientation. Hope this will straighten out.
October 31, 2024 at 10:08 PM
New Dell laptop decided to install Windows sideways. Rotating it will flip the screen, but impossible to get it back to normal orientation. Hope this will straighten out.
Reposted by Nico Stuurman
Check out "ONE" Microscopy, which can achieve protein level resolution with a light microscope!
I've been trying to combine Magnify + STED to visualize protein complexes. Looks like they were able to do it with X10 + SRFF ;-)
I've been trying to combine Magnify + STED to visualize protein complexes. Looks like they were able to do it with X10 + SRFF ;-)
One-step nanoscale expansion microscopy reveals individual protein shapes - Nature Biotechnology
Combining expansion microscopy with super-resolution radial fluctuations captures the morphology of single proteins.
www.nature.com
October 9, 2024 at 3:06 PM
Check out "ONE" Microscopy, which can achieve protein level resolution with a light microscope!
I've been trying to combine Magnify + STED to visualize protein complexes. Looks like they were able to do it with X10 + SRFF ;-)
I've been trying to combine Magnify + STED to visualize protein complexes. Looks like they were able to do it with X10 + SRFF ;-)