Light-microscopy-based connectomic reconstruction of mammalian brain tissue rdcu.be/ek8GG Wow! 😍
Light-microscopy-based connectomic reconstruction of mammalian brain tissue
Nature - A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling...
rdcu.be
May 8, 2025 at 8:02 AM
Light-microscopy-based connectomic reconstruction of mammalian brain tissue rdcu.be/ek8GG Wow! 😍
Nature research paper: Light-microscopy-based connectomic reconstruction of mammalian brain tissue
https://go.nature.com/3YCLkuZ
https://go.nature.com/3YCLkuZ
Light-microscopy-based connectomic reconstruction of mammalian brain tissue - Nature
A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling quantification of cellular properties and multimodal analysis of brain tissue.
go.nature.com
May 9, 2025 at 4:16 PM
Nature research paper: Light-microscopy-based connectomic reconstruction of mammalian brain tissue
https://go.nature.com/3YCLkuZ
https://go.nature.com/3YCLkuZ
Thanks to expansion microscopy, clever labeling, and modern segmentation approaches, doing connectomics with #light #microscopy has become feasible - huge congratulations Mojtaba & the Danzl lab at @istaresearch.bsky.social !
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Light-microscopy-based connectomic reconstruction of mammalian brain tissue - Nature
A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling quantification of c...
www.nature.com
May 8, 2025 at 2:52 AM
Thanks to expansion microscopy, clever labeling, and modern segmentation approaches, doing connectomics with #light #microscopy has become feasible - huge congratulations Mojtaba & the Danzl lab at @istaresearch.bsky.social !
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Brightness demixing: a method for simultaneously detecting different fluorophores in single-molecule localization microscopy based on brightness. @slfort.bsky.social @laurent-le.bsky.social @ismolab.bsky.social @instlangevin.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Brightness demixing for simultaneous multi-target imaging in 3D single-molecule localization microscopy - Nature Methods
Brightness demixing is a method for simultaneously detecting different fluorophores in single-molecule localization microscopy based on their brightness rather than their spectral properties. As this ...
www.nature.com
June 11, 2026 at 5:50 PM
Brightness demixing: a method for simultaneously detecting different fluorophores in single-molecule localization microscopy based on brightness. @slfort.bsky.social @laurent-le.bsky.social @ismolab.bsky.social @instlangevin.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Microfluidics combined with electron microscopy for rapid and high-throughput mapping of antibody–viral glycoprotein complexes
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Microfluidics combined with electron microscopy for rapid and high-throughput mapping of antibody–viral glycoprotein complexes - Nature Biomedical Engineering
A microfluidics- and electron-microscopy-based method enables the characterization of polyclonal antibody responses to infection and vaccination.
www.nature.com
July 13, 2025 at 4:02 PM
Microfluidics combined with electron microscopy for rapid and high-throughput mapping of antibody–viral glycoprotein complexes
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Automated #microscopy meets #supercomputing in the web-based platform Distiller, now available through the @molecularfoundry.lbl.gov User Program.
A New Age of Electron Microscopy: Magnifying Possibilities with Automation
Automated electron microscopy meets supercomputing in the web-based platform Distiller
newscenter.lbl.gov
April 7, 2025 at 3:10 PM
Automated #microscopy meets #supercomputing in the web-based platform Distiller, now available through the @molecularfoundry.lbl.gov User Program.
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking.
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
December 8, 2025 at 9:48 AM
Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking.
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems.
Preprint: www.biorxiv.org/content/10.6...
[1/6]
New era for brain mapping, latest from Johann Danzl lab in @nature.com. Light-microscopy connectomics is at single-synapse resolution. Engineered hydrogel embedding + expansion, deep learning-based segmentation, and molecularly resolved reconstructions: axons, spines, connectivity, all visible.
May 7, 2025 at 6:49 PM
New era for brain mapping, latest from Johann Danzl lab in @nature.com. Light-microscopy connectomics is at single-synapse resolution. Engineered hydrogel embedding + expansion, deep learning-based segmentation, and molecularly resolved reconstructions: axons, spines, connectivity, all visible.
🔬⚙️💻 Excited to share #OptiCell3D, our new image-based framework for inferring cell mechanical properties with high precision from 3D microscopy.
www.biorxiv.org/content/10.6...
#ComputationalBiology #CellBiology #Biophysics #OpenSource
www.biorxiv.org/content/10.6...
#ComputationalBiology #CellBiology #Biophysics #OpenSource
May 28, 2026 at 5:40 AM
🔬⚙️💻 Excited to share #OptiCell3D, our new image-based framework for inferring cell mechanical properties with high precision from 3D microscopy.
www.biorxiv.org/content/10.6...
#ComputationalBiology #CellBiology #Biophysics #OpenSource
www.biorxiv.org/content/10.6...
#ComputationalBiology #CellBiology #Biophysics #OpenSource
My #BioimageTooloftheDay is the awesome 3Dscript that I use to make video of 3D/4D microscopy data www.nature.com/articles/s41...
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax - Nature Methods
Nature Methods - 3Dscript: animating 3D/4D microscopy data using a natural-language-based syntax
www.nature.com
November 16, 2024 at 8:42 AM
My #BioimageTooloftheDay is the awesome 3Dscript that I use to make video of 3D/4D microscopy data www.nature.com/articles/s41...
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
The best thing is that ChatGTP (probably other LLM) synergies beautifully with 3Dscript, making it ever easier to use. Voice to 3D video animation 😁
The next paper describes Segment Anything for Microscopy (μSAM), which is based on the Segment Anything vision foundation model and extended to be used for bioimage analysis in light and electron microscopy. www.nature.com/articles/s41...
February 12, 2025 at 2:39 PM
The next paper describes Segment Anything for Microscopy (μSAM), which is based on the Segment Anything vision foundation model and extended to be used for bioimage analysis in light and electron microscopy. www.nature.com/articles/s41...
PRISM: A Plasmid-based Reporter for Intracellular Spectral Microscopy by Jonathon Nixon-Abell and team: www.biorxiv.org/content/10.6...
September 3, 2026 at 10:40 AM
PRISM: A Plasmid-based Reporter for Intracellular Spectral Microscopy by Jonathon Nixon-Abell and team: www.biorxiv.org/content/10.6...
Brain tissue artificially expanded to show how neurons wire together @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/d41...
Light-microscopy-based connectomic reconstruction of mammalian brain tissue - Nature
A technique called LICONN (light-microscopy-based connectomics) allows mapping of brain tissue at synapse level and simultaneous measurement of molecular information, thus enabling quantification of c...
www.nature.com
May 8, 2025 at 7:21 PM
Brain tissue artificially expanded to show how neurons wire together @nature.com
www.nature.com/articles/s41...
www.nature.com/articles/d41...
www.nature.com/articles/s41...
www.nature.com/articles/d41...
Cleaning out the AC vents in the microscopy lab. A #MicroscopistsNightmares based on a true story from before my time in the lab.
December 3, 2024 at 8:36 AM
Cleaning out the AC vents in the microscopy lab. A #MicroscopistsNightmares based on a true story from before my time in the lab.
Segment Anything for Microscopy (μSAM) is based on Segment Anything, the vision transformer model for image segmentation, and offers generalist models for light and electron microscopy segmentation tasks.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
February 12, 2025 at 3:57 PM
Segment Anything for Microscopy (μSAM) is based on Segment Anything, the vision transformer model for image segmentation, and offers generalist models for light and electron microscopy segmentation tasks.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
I was looking forward to this one! An open source software for fast reconstruction of 3D structured illumination microscopy (SIM) from Xi Peng's lab : www.cell.com/the-innovati...
Matlab-based, code here: github.com/Cao-ruijie/F...
Matlab-based, code here: github.com/Cao-ruijie/F...
January 13, 2025 at 12:10 PM
I was looking forward to this one! An open source software for fast reconstruction of 3D structured illumination microscopy (SIM) from Xi Peng's lab : www.cell.com/the-innovati...
Matlab-based, code here: github.com/Cao-ruijie/F...
Matlab-based, code here: github.com/Cao-ruijie/F...
Ever wanted to do a genome-scale CRISPR screen for a microscopy phenotype? Pooled CRISPR screens are amazing, but hard to combine with imaging... Excited to share our latest work in Dev Cell on a technology platform for imaging screens and applications to primary cilia: www.cell.com/developmenta...
A microscopy-based CRISPR screening platform enables organellar functional genomics and illuminates ciliary biology
Sun et al. develop a microscopy-based CRISPR screening platform that combines ease
of implementation with flexible analysis of live-cell or antibody-based markers. Screens
in human cells using a serie...
www.cell.com
November 20, 2025 at 5:06 PM
Ever wanted to do a genome-scale CRISPR screen for a microscopy phenotype? Pooled CRISPR screens are amazing, but hard to combine with imaging... Excited to share our latest work in Dev Cell on a technology platform for imaging screens and applications to primary cilia: www.cell.com/developmenta...
“Cultures”, a set of 10 Petri dish sized gelatine prints based on microscopy, some pulled from old magazine ads, with added hand-painting and drawing, and bacterial DNA, that I made today. 1 of 3 #SciArt
May 28, 2025 at 9:42 PM
“Cultures”, a set of 10 Petri dish sized gelatine prints based on microscopy, some pulled from old magazine ads, with added hand-painting and drawing, and bacterial DNA, that I made today. 1 of 3 #SciArt
New blogpost outlining our work with @athenaakrami.bsky.social at @sainsburywellcome.bsky.social to build light-microscopy based atlases of the rat brain.
brainglobe.info/blog/swc-fem...
brainglobe.info/blog/swc-fem...
February 2, 2026 at 4:59 PM
New blogpost outlining our work with @athenaakrami.bsky.social at @sainsburywellcome.bsky.social to build light-microscopy based atlases of the rat brain.
brainglobe.info/blog/swc-fem...
brainglobe.info/blog/swc-fem...
Nature Methods has chosen electron microscopy (EM)-based connectomics as its Method of the Year 2025. #methods 🧪
Method of the Year 2025: electron microscopy-based connectomics
Nature Methods - A large network of interconnected neurons serves as the basis of brain function and of behavior. Methodological advances have enabled the reconstruction of large-scale and even...
go.nature.com
December 29, 2025 at 5:34 PM
Nature Methods has chosen electron microscopy (EM)-based connectomics as its Method of the Year 2025. #methods 🧪
Hello world 🌐, what's the best web-based open-source volume viewer for microscopy out there 🥽? Preferably browser-based. Help out Nuno on his quest =)!!
Does anyone know of a nice web viewer for biological image data that is preferably open source or something close to it? Asking for a friend 👀
May 9, 2025 at 3:23 PM
Hello world 🌐, what's the best web-based open-source volume viewer for microscopy out there 🥽? Preferably browser-based. Help out Nuno on his quest =)!!
🔬API-first feature extraction for image-based profiling workflows
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
July 8, 2025 at 7:22 PM
🔬API-first feature extraction for image-based profiling workflows
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.
1/6
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
August 21, 2025 at 2:22 PM
🔬🧠 Our paper on smart microscopy & the issue of interoperability! www.biorxiv.org/content/10.1... LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
A quick re-intro: we are interested in the mechanisms of collective cell behaviour, particularly cell movement. We use fly embryos, quantitative microscopy, image analysis and computer-based modelling. One of the systems where we study collective cell movement is the wound healing response.
November 11, 2024 at 3:02 PM
A quick re-intro: we are interested in the mechanisms of collective cell behaviour, particularly cell movement. We use fly embryos, quantitative microscopy, image analysis and computer-based modelling. One of the systems where we study collective cell movement is the wound healing response.
We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
December 19, 2024 at 10:10 PM
We developed a microscopy-based technique🔬 to measure attachment of viruses #phages to host cells. 🦠
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky
The paper was posted online today:
www.pnas.org/doi/10.1073/...
#phagesky #microsky