#lightsheet — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #lightsheet, aggregated by home.social.
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🧠📐 Kaltenecker et al present #MouseMapper, that combines whole-body tissue clearing, #lightsheet #imaging and foundation-model-based #DeepLearning to quantify nerves, immune cells & 31 organs/tissues across entire #mouse bodies.
Applied to diet-induced #obesity, it revealed reduced nerve density, infraorbital trigeminal nerve defects, impaired whisker sensing, & body-wide inflammatory CD68⁺ immune-cell clustering.
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🧠📐 Kaltenecker et al present #MouseMapper, that combines whole-body tissue clearing, #lightsheet #imaging and foundation-model-based #DeepLearning to quantify nerves, immune cells & 31 organs/tissues across entire #mouse bodies.
Applied to diet-induced #obesity, it revealed reduced nerve density, infraorbital trigeminal nerve defects, impaired whisker sensing, & body-wide inflammatory CD68⁺ immune-cell clustering.
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This week I had the pleasure of attending the #MesoSPIM Symposium in Zürich, Switzerland - and what an experience it's been! Top-notch presentations, great posters and great chats with my fellow #lightsheet #microscopy and #tissueclearing nerds. You know it's a good conference when you come back with a full notebook and a head fizzing with ideas on what to do next.
I could make the night train journey there thanks to @Co_Biologists's DMM Conference Travel Grant - much appreciated! -
This week I had the pleasure of attending the #MesoSPIM Symposium in Zürich, Switzerland - and what an experience it's been! Top-notch presentations, great posters and great chats with my fellow #lightsheet #microscopy and #tissueclearing nerds. You know it's a good conference when you come back with a full notebook and a head fizzing with ideas on what to do next.
I could make the night train journey there thanks to @Co_Biologists's DMM Conference Travel Grant - much appreciated! -
Last week to apply to the Light-Sheet Image Analysis Workshop.
A five-day practical course on the processing and analysis of light-sheet microscopy imaging data. It will take place in Santiago, Chile, from January 5–9, 2026.
Deadline: August 8.
Learn more and apply here: https://lightsheetchile.cl/light-sheet-image-analysis-workshop-2026-2/
#Microscopy #Lightsheet #ImageProcessing #ImageAnalysis #LatinAmerica #GlobalSouth
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Light-Sheet Image Analysis Workshop 2026
The Light-Sheet Image Analysis Workshop is a five-day intensive course that will take place in Santiago, Chile, from January 5–9, 2026, designed for students and researchers who wish to gain foundational skills in the processing and analysis of light-sheet microscopy imaging data.
The application deadline has been extended until August 8, 2025! The workshop is free to attend and travel fellowships are available. Learn more and apply here:
https://lightsheetchile.cl/light-sheet-image-analysis-workshop-2026-2/
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URL: https://brunovellutini.com/posts/light-sheet-image-analysis-workshop-2026/ -
New publication from Kwanghun Chung lab at MIT improves on their SWITCH approach and eFLASH stochastic electrotransport to improve antibody labeling by gradually shifting the microenvironment. Looks interesting, I wonder how well it can be adapted to other labeling protocols.
Uniform volumetric single-cell processing for organ-scale molecular phenotyping
Yun et al., Nature Biotechnology 2025
https://doi.org/10.1038/s41587-024-02533-4#neuroscience #tissueclearing #lightsheet #microscopy #fluorescenceFriday
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New publication from Kwanghun Chung lab at MIT improves on their SWITCH approach and eFLASH stochastic electrotransport to improve antibody labeling by gradually shifting the microenvironment. Looks interesting, I wonder how well it can be adapted to other labeling protocols.
Uniform volumetric single-cell processing for organ-scale molecular phenotyping
Yun et al., Nature Biotechnology 2025
https://doi.org/10.1038/s41587-024-02533-4#neuroscience #tissueclearing #lightsheet #microscopy #fluorescenceFriday
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Whole-mouse imaging the hard way: Clearing, then slicing + block-face imaging with beam-scan / sensor scan-line synchronization and continuous stage movement in an oblique imaging setup (ViSOR).
This time, they scaled it up to whole-mouse and used pre-cleared mouse bodies (ARCHmap-blockface-ViSOR):High-speed mapping of whole-mouse peripheral nerves at subcellular resolution
Shi et al., preprint at biorxiv 2025
https://doi.org/10.1101/2025.01.22.632569 -
Whole-mouse imaging the hard way: Clearing, then slicing + block-face imaging with beam-scan / sensor scan-line synchronization and continuous stage movement in an oblique imaging setup (ViSOR).
This time, they scaled it up to whole-mouse and used pre-cleared mouse bodies (ARCHmap-blockface-ViSOR):High-speed mapping of whole-mouse peripheral nerves at subcellular resolution
Shi et al., preprint at biorxiv 2025
https://doi.org/10.1101/2025.01.22.632569 -
New deep-learning cell detection pipeline for light-sheet mouse brain image stacks, with an interesting cell-coordinate clustering statistics approach:
A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy
Attarpour et al., Nature Methods 2025
https://doi.org/10.1038/s41592-024-02583-1Code: https://github.com/AICONSlab/MIRACL
Documentation: https://miracl.readthedocs.io/
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New deep-learning cell detection pipeline for light-sheet mouse brain image stacks, with an interesting cell-coordinate clustering statistics approach:
A deep learning pipeline for three-dimensional brain-wide mapping of local neuronal ensembles in teravoxel light-sheet microscopy
Attarpour et al., Nature Methods 2025
https://doi.org/10.1038/s41592-024-02583-1Code: https://github.com/AICONSlab/MIRACL
Documentation: https://miracl.readthedocs.io/
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Cool custom-built #lightsheet #microscopes: Turns out you can build a tiny light-sheet projector by whipping an optical fiber back and forth in front of a GRIN lens. The entire assembly is hand-made (coils, magnet, casing) and fits into an 18G needle. This looks like it could be super useful for imaging deep in vivo, e.g. low in a cortex.
Light-sheet microscopy enabled by a miniaturized plane illuminator
Kim et al., Biomed Optics Express 2024
https://opg.optica.org/boe/fulltext.cfm?uri=boe-16-1-115&id=565214 -
Cool custom-built #lightsheet #microscopes: Turns out you can build a tiny light-sheet projector by whipping an optical fiber back and forth in front of a GRIN lens. The entire assembly is hand-made (coils, magnet, casing) and fits into an 18G needle. This looks like it could be super useful for imaging deep in vivo, e.g. low in a cortex.
Light-sheet microscopy enabled by a miniaturized plane illuminator
Kim et al., Biomed Optics Express 2024
https://opg.optica.org/boe/fulltext.cfm?uri=boe-16-1-115&id=565214 -
The birth of fruit fly's central nervous system imaged with multicolor #adaptive #lightsheet microscopy. The microscope self-aligns to a signal that appears during imaging. www.nature.com/articles/nbt...
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Continuing to go through my trove of cool videos... here is a classic from my work with Philipp Keller's team at @hhmijanelia.bsky.social A developing fly embryo imaged with a SiMView #lightsheet microscope augmented with our Autopilot self-alignment system. www.nature.com/articles/nbt... 🧪🔬🪰💻
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Wow, TRISCO (née TRIC-DISCO) is out in Science! This cool approach allows imaging of mRNA transcripts throughout the cleared mouse brain. It uses a signal amplification step with in situ Hybridization Chain Reaction (isHCR) and combines it with DISCO-style solvent-based #tissueclearing to make the brain transparent.
Whole-brain spatial transcriptional analysis at cellular resolution
Kanatani et al., Science 2024
https://doi.org/10.1126/science.adn9947 -
Wow, TRISCO (née TRIC-DISCO) is out in Science! This cool approach allows imaging of mRNA transcripts throughout the cleared mouse brain. It uses a signal amplification step with in situ Hybridization Chain Reaction (isHCR) and combines it with DISCO-style solvent-based #tissueclearing to make the brain transparent.
Whole-brain spatial transcriptional analysis at cellular resolution
Kanatani et al., Science 2024
https://doi.org/10.1126/science.adn9947 -
In case anyone was following the recent Science paper about using Tartrazine for #tissueclearing, apparently there is at least one (competing) group that couldn't reproduce it and wrote a preprint about it:
Tartrazine cannot make live tissues transparent
https://doi.org/10.1101/2024.09.29.615648Discussion on Pubpeer, including the Tartrazine paper's author's response:
https://pubpeer.com/publications/81314BB3706B3D6ADAD49F301B2FA5 -
In case anyone was following the recent Science paper about using Tartrazine for #tissueclearing, apparently there is at least one (competing) group that couldn't reproduce it and wrote a preprint about it:
Tartrazine cannot make live tissues transparent
https://doi.org/10.1101/2024.09.29.615648Discussion on Pubpeer, including the Tartrazine paper's author's response:
https://pubpeer.com/publications/81314BB3706B3D6ADAD49F301B2FA5 -
New solvent-based #tissueclearing protocol claims reduced tissue distortion: Dehydration/delipidation with Hexanediol, tert-Butanol and N-butyldiethanolamine, and clearing with Benzyl Benzoate / PEGMA / N-butyldiethanolamine.
SOLID: minimizing tissue distortion for brain-wide profiling of diverse architectures
Zhu et al., Nature Comms 2024
https://doi.org/10.1038/s41467-024-52560-7 -
New solvent-based #tissueclearing protocol claims reduced tissue distortion: Dehydration/delipidation with Hexanediol, tert-Butanol and N-butyldiethanolamine, and clearing with Benzyl Benzoate / PEGMA / N-butyldiethanolamine.
SOLID: minimizing tissue distortion for brain-wide profiling of diverse architectures
Zhu et al., Nature Comms 2024
https://doi.org/10.1038/s41467-024-52560-7 -
Mitotic Waves video wins Small World in Motion
My video of mitotic waves won Nikon’s 2024 Small World in Motion video competition! I’m thrilled 🎉
https://www.youtube.com/watch?v=KhKlUu1SdZI
To learn more about the video, check out Nikon’s press release and their article for the series Masters of Microscopy.
There’s also a blog post that I wrote a couple of years ago with some biological information and technical details about how I created the video.
If you are wondering about the size of the embryo and how fast it really develops, there’s a version with a scale bar and time label on YouTube and available for download and re-use on Wikimedia Commons.
Thanks for your support :)
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URL: https://brunovellutini.com/posts/mitotic-small-world/#diptera #drosophilaMelanogaster #embryo #lightsheet #microscopy #scienceOutreach #video
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New #tissueclearing #preprint uses a custom mouse behaviour + deep-learning c-Fos analysis pipeline to compare several different Serotonin receptor agonists / antagonists in mice.
Concerted modulation of spontaneous behavior and time-integrated whole-brain neuronal activity by serotonin receptors
Friedmann et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.08.02.606282#lightsheet #microscopy #serotonin #neuroscience #preprint #brainmapping
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New #tissueclearing #preprint uses a custom mouse behaviour + deep-learning c-Fos analysis pipeline to compare several different Serotonin receptor agonists / antagonists in mice.
Concerted modulation of spontaneous behavior and time-integrated whole-brain neuronal activity by serotonin receptors
Friedmann et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.08.02.606282#lightsheet #microscopy #serotonin #neuroscience #preprint #brainmapping
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New #tissueclearing paper checks oligodendrocyte distribution throughout the entire mouse brain. Looks pretty neat!
Brain-wide mapping of oligodendrocyte organization and oligodendrogenesis across the murine lifespan
Xu et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.09.06.611254Github: https://github.com/yxu233/Xu_Bergles_brainwide_oligo_map
#neuroscience #lightsheet #microscopy #preprint #oligodendrocyte #myelination
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New #tissueclearing paper checks oligodendrocyte distribution throughout the entire mouse brain. Looks pretty neat!
Brain-wide mapping of oligodendrocyte organization and oligodendrogenesis across the murine lifespan
Xu et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.09.06.611254Github: https://github.com/yxu233/Xu_Bergles_brainwide_oligo_map
#neuroscience #lightsheet #microscopy #preprint #oligodendrocyte #myelination
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This preprint looks like a conceptual advance for deeper staining (also in human tissue) and multi-round multiplexed immunostaining with BABB clearing.
INSIHGT: Accessible multimodal systems biology with quantitative molecular phenotyping in 3D
Yau et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.05.24.595771#tissueclearing #lightsheet #microscopy #neuroscience #FluorescenceFriday
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Landmarking via UV-activatable dye makes mapping between light-sheet and confocal imaging possible
Correlative multiscale 3D imaging of mouse primary and metastatic tumors by sequential light sheet and confocal fluorescence microscopy
Zheng et al., preprint at biorxiv 2024
https://doi.org/10.1101/2024.05.14.594162 -
Interesting new #preprint about #tissueclearing and #lightsheet #microscopy in mouse ovaries. Complete with #napari-based deep-learning pipeline and detailed build instructions for 3D-printed sample chambers for solvent-cleared samples, so they can be viewed under a #confocal!
OoCount: A machine-learning based approach to mouse ovarian follicle counting and classification
Folts et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.05.13.593993v1 -
Interesting new #preprint about #tissueclearing and #lightsheet #microscopy in mouse ovaries. Complete with #napari-based deep-learning pipeline and detailed build instructions for 3D-printed sample chambers for solvent-cleared samples, so they can be viewed under a #confocal!
OoCount: A machine-learning based approach to mouse ovarian follicle counting and classification
Folts et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.05.13.593993v1 -
Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains.
Paper: https://www.nature.com/articles/s41592-024-02245-2
Code: https://github.com/erturklab/delivr_cfos
Docker containers, test dataset, handbook: https://www.discotechnologies.org/DELiVR/ -
Very excited that our whole-mouse-brain analysis pipeline - DELiVR - is published now at Nature Methods. With DELiVR, we built an open-source, easy-to-use pipeline for analyzing image stacks from cleared mouse brains.
Paper: https://www.nature.com/articles/s41592-024-02245-2
Code: https://github.com/erturklab/delivr_cfos
Docker containers, test dataset, handbook: https://www.discotechnologies.org/DELiVR/ -
Check out our simple solution for imaging between the #zebrafish eyes (or other hard-to reach sample regions) during #lightsheet microscopy:
https://www.biorxiv.org/content/10.1101/2024.04.05.588276v2 -
Check out our simple solution for imaging between the #zebrafish eyes (or other hard-to reach sample regions) during #lightsheet microscopy:
https://www.biorxiv.org/content/10.1101/2024.04.05.588276v2 -
Interesting #preprint: New mouse brain atlas links high-resolution MRI and light-sheet imaging, finally placing Allen Brain Atlas coordinates in stereotaxic space.
#tissueclearing was done via LifeCanvas and includes 17 common neuron type markers:
Preprint: https://www.biorxiv.org/content/10.1101/2024.03.28.587246v1.full
Atlas + webviewer here (requires registration): https://civmimagespace.civm.duhs.duke.edu
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Interesting #preprint: New mouse brain atlas links high-resolution MRI and light-sheet imaging, finally placing Allen Brain Atlas coordinates in stereotaxic space.
#tissueclearing was done via LifeCanvas and includes 17 common neuron type markers:
Preprint: https://www.biorxiv.org/content/10.1101/2024.03.28.587246v1.full
Atlas + webviewer here (requires registration): https://civmimagespace.civm.duhs.duke.edu
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Our paper on Oblique #lightsheet #Microscopy with dynamic remote focusing is now online!
Also, all the relevant data is public on Zenodo, because open data is great!
If you are a fellow microscopist and are attending FOM 2024, i will be giving a talk about it at 11, come say hi!Paper doi: https://doi.org/10.1117/1.JBO.29.3.036502
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Very cool new #tissueclearing #preprint - a clearing protocol for marine invertebrates aptly named See-Star.
Works on echinoderms and molluscs (i.e. sea stars, sea urchins, slugs and cuttlefish). I wonder whether it also works on terrestrial snails then?
See-Star: a versatile hydrogel-based protocol for clearing large, opaque and calcified marine invertebrates
Clarke et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.03.16.585344v1 -
Interesting preprint on using a #machinelearning frame interpolation technique originally developed for videos on biomedical image stacks (for spatial interpolation): They claim broad applicability for #MRI, #lightsheet microscopy, #histology and #cryoEM image stacks.
Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping
Joshi et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.03.07.583909v1 -
Interesting preprint on using a #machinelearning frame interpolation technique originally developed for videos on biomedical image stacks (for spatial interpolation): They claim broad applicability for #MRI, #lightsheet microscopy, #histology and #cryoEM image stacks.
Generative interpolation and restoration of images using deep learning for improved 3D tissue mapping
Joshi et al., preprint at biorxiv 2024
https://www.biorxiv.org/content/10.1101/2024.03.07.583909v1 -
Hey, it's #FluorescenceFriday !!! Have a look at the fluorescence from the chlorophyll of these tiny little happy algae. Image courtesy of our oblique #lightsheet microscope! In their DYE-ART project the awesome @alessiacandeo and Barbara Menin are going to make these little guys super efficient at capturing CO2 from the atmosphere.
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Hey, it's #FluorescenceFriday !!! Have a look at the fluorescence from the chlorophyll of these tiny little happy algae. Image courtesy of our oblique #lightsheet microscope! In their DYE-ART project the awesome @alessiacandeo and Barbara Menin are going to make these little guys super efficient at capturing CO2 from the atmosphere.
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Very nice work on #tissueclearing and #lightsheet #microscopy:
This technique (TESOS) brings resin embedding to solvent-cleared samples. The resulting #organogels are stable enough to allow block-face imaging with an oblique LSM. Already pretty big with whole adult mice, but I'd love to see this scaled up to human-organ size.
Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system
Yi et al., Cell Research 2024
https://doi.org/10.1038/s41422-023-00867-3 -
Really cool #lightsheet #microscopy application:
An atlas of the developing mouse brain (DevATLAS from Yongsoo Kim's lab), combined with a new neuronal activity reporter line (Npas4-Cre), shows the order in which brain regions become active in the first postnatal weeks.
(And they have #ephys and #rnaseq too!)
Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation
Xue et al., preprint on biorxiv, 2024
https://doi.org/10.1101/2024.01.03.572456 -
Check out the first #preprint from my research in Politecnico! Trying to make oblique #lightsheet fluorescence #microscopy easier and less expensive using tunable lenses. Now may the peer review be ever in our favor!
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Oh, wow, what a warm reception! the fediverse science community may be small but is definitely welcoming!
As many suggested, here is my #introduction : I am a physicist developing optical microscopy methods for biomedical applications at the Politecnico di Milano University, in Italy. I will try to fill the fediverse with colorful images of squishy biological things. Apparently, I am also the new resident #opendata manager, so expect some posts on that!
#microscopy #lightsheet #optics -
@PhiloNeuroScie Nice find! #Tissueclearing and #lightsheet #microscopy work on human brain (sections) too :)
Human brain samokes are normally quite hard to properly image because they are dense with lipofuscins, super autofluorescent and not very permeable to antibodies. That they managed to pull this off using the more-or-less standard iDISCO protocol (even with "just" a 400 µm thick section and high antibody concentrations) is quite impressive.
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@ottiswimmers I haven't tried this yet, but there is a recent biorxiv paper on a DIY #lightsheet #microscope that uses a FLIR Grasshopper 3. They have controller code on github too, designed to run on an Nvidia Jetson Nano, I assume that would be running Linux.
Paper:
https://www.biorxiv.org/content/10.1101/2023.05.31.543173v2.fullController code on github:
https://github.com/tomerlab/pLSM-Control -
Check out our lab's #newpaper in @cellpress Cell:
We found that the skull is special - its marrow is a special immunologic niche. Skull #Immune #cells can move to the meninges via skull-meninges connections, which we found both in mice and humans with #tissueclearing and #lightsheet #microscopy.
We also bring #proteomics and #PETimaging to the mix!Paper: https://doi.org/10.1016/j.cell.2023.07.009
Explainer thread:
https://bird.makeup/users/erturklab/statuses/1689293936185991169 -
Preprint alert! Our lab developed targetable #DNA origami #nanoparticles, which we then image throughout the entire (transparent) mouse body using #lightsheet #microscopy.
Our DNA origami were able to target immune cells, as well as a subset of cancer metastases in the lung.
Preprint:
https://www.biorxiv.org/content/10.1101/2023.07.24.550304v1.full.pdfExplainer thread:
https://bird.makeup/users/erturklab/statuses/1686331791022448640 -
Happy to introduce our latest gizmo from the lab: pLSM !
https://www.biorxiv.org/content/10.1101/2023.05.31.543173v1A big shoutout to our brilliant grad student, Yannan Chen, who led this work.
In short, pLSM is a plug-and-play, cost-effective and easy-to-scale light sheet microscopy platform. More than 20 times cheaper, with imaging quality comparable to high-end systems.
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We are so excited to have Kevin Dean visit next week as our first in-person Janelia+EMBL Bioimaging Series invited speaker. @markkitti #lightsheet
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I'm excited to announce that our cephalic furrow paper is out! We investigated the function of this enigmatic invagination using live imaging and modeling and found that it plays a mechanical role during fly gastrulation https://www.biorxiv.org/content/10.1101/2023.03.30.534554
#CephalicFurrow #Drosophila #MechanoBiology #TissueMechanics #Flies #PrePrint #DevBio #Lightsheet
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My postdoc work at Isaac Bianco's lab is finally out on @eLife !
https://elifesciences.org/articles/78381Combining #lightsheet volumetric functional imaging and a spiking network simulation, we were able to show that a simple connectivity motif in the #zebrafish #optictectum explains multiple features in ongoing population dynamics, their impact on trial-to-trial variability, and trends in experience dependent behavior.
It is a neat example of how #networkdynamics can explain why neuronal and behavioural responses vary, or how past activity sets the ever-changing background for new input (that, in turn, will make its own long-lasting splash)
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#Zebrahub is not only about #scRNAseq data. We also imaged zebrafish embryonic development using two complementary #lightsheet microscopes (#OpenSiMView & #DaXi) to be able to follow as accurately as possible tens and hundreds of thousands of cells in embryos. 8/n
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We present #Zebrahub: a timecourse atlas of zebrafish embryonic development, combining #scRNAseq time-course data with #lightsheet live imaging. Explore our seq. and imaging datasets interactively at
https://www.biorxiv.org/content/10.1101/2023.03.06.531398v1.article-info
zebrahub.org
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