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Nikita Vladimirov

@nvladimus.bsky.social
433 followers 221 following 95 posts

Imaging scientist, light-sheet aficionado, #mesoSPIM developer, open source contributor. Building cool microscopes for cool people. www.mesospim.org www.github.com/nvladimus

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Reposted by Nikita Vladimirov
James Manton @jamesdmanton.bsky.social · 29/09/2026
I've been working on a fast, high-ratio image compressor to try and alleviate the data storage issues myself and some of my colleagues have recently been facing. Before I 'release' version 1, it'd be great to gain some feedback regarding performance and missing features. github.com/jdmanton/rad...
github.com
GitHub - jdmanton/radelta
Contribute to jdmanton/radelta development by creating an account on GitHub.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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napari @napari.org · 26/09/2026
🚀 napari is hiring Remote Developers-in-Residence! Join us to build the future of interactive n-dimensional data visualization in Python. 💻 60% Dev / 20% Maintenance / 20% Community & Outreach ⏱️ Contract, 14–35 hrs/wk 🌍 Global 100% Remote Learn more and apply today: napari.org/island-dispa...
napari.org
We’re hiring Developers-in-Residence! — napari blog documentation
Organization: napari (a NumFOCUS Sponsored Project) Position Type: Independent contractor agreement. Global, 100% Remote. Duration: One year, possibility to extend. Commitment: 0.4 to 1.0 FTE…
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voigtvision.bsky.social @voigtvision.bsky.social · 03/09/2026
📢 Superhappy to announce that I've been awarded a 2.5M€ @erc.europa.eu Starting Grant for the project "KALEIDOSCOPE - metasurface-based brain observatories" 🥳🔬 🧠 🐟🥳 📢. The grant will support starting my lab ( voigt-lab.org ) at @mpi-scienceoflight.bsky.social. erc.europa.eu/news-events/...
erc.europa.eu
Starting Grants 2026: Examples of projects
The European Research Council (ERC) has announced the awarding of 421 Starting Grants to outstanding early-career researchers across Europe, as part of the Horizon Europe programme. To illustrate the ...
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Laura Baudis @lbaudis.bsky.social · 30/08/2026
Tomorrow, August 31 at 4 pm CEST, the XENON Collaboration will host a live presentation about new findings from the XENONnT experiment. You can learn more at agenda.infn.it/event/53372/. Please note that registration is required for the event!
A picture of the XENONnT experiment underground at LNGS.The announcement for the new results from XENONnT.
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Marco Dalla Vecchia @marcodv.bsky.social · 27/08/2026
Interested in image analysis and a service role in a dynamic and growing facility? Come and joy our image analysis team! Feel free to reach out for any questions or doubts. ista.ac.at/en/job/?titl...
ista.ac.at
Job details
Job details
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voigtvision.bsky.social @voigtvision.bsky.social · 12/08/2026
🚨 Now out in @aaas.org Science Advances 🚨: aDISCO: a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue by Anna Maria Reuss! 🧠🔬#lightsheet #Microscopy @mesospim.bsky.social @ptrrupprecht.bsky.social www.science.org/doi/10.1126/...
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Aafke Gros @aafkegros.bsky.social · 24/07/2026
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell. A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 22/07/2026
New features in the latest #mesoSPIM - control release: - group tiles and channels the way you like. Adjust acquisition parameters for many tiles at once. - record timelapse, eg for light-sheet imaging of live organisms (embryos and plants). Because why not? 1/2
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 15/07/2026
At the next #NGFFCafe, Marvin Albert (ETH Zurich) will present 𝗺𝘂𝗹𝘁𝗶𝘃𝗶𝗲𝘄-𝘀𝘁𝗶𝘁𝗰𝗵𝗲𝗿, a Python package for scalable stitching/alignment/fusion of multi-view, tiled & multimodal image acquisitions. Join us! 🗓️ Thursday, July 30 🕚️ 11 am CEST 📍 Online Register⤵️ us02web.zoom.us/meeting/regi...
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voigtvision.bsky.social @voigtvision.bsky.social · 06/07/2026
🚨 New Preprint! 🚨: A new method for quantifying #tissue #clearing and a next-get #lightsheet #Microscope - the #mesoSPIM ultra by Marko Pende, @jcregg.bsky.social, @murawalalab.bsky.social @mdibl.org & many more! Preprint: www.biorxiv.org/content/10.6... Github: github.com/mesoSPIM/mes...
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Peter Rupprecht @ptrrupprecht.bsky.social · 02/07/2026
Looking forward to #FENS2026 next week in Barcelona! I will present a poster on effects of locus coeruleus and arousal on astrocytes and neurons in hippocampus: PS06-09PM-201 PhD student Shinjini Ghosh will present a poster on a Theremin-based auditory virtual environment for mice: PS04-08PM-568
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Joel Lüthi @joelluethi.bsky.social · 29/06/2026
Want to learn about converting data into OME-Zarr and the design choices behind different tools built for it? Join the Open Bioimaging Practices Meeting tomorrow: Tuesday, June 30th 2026, 4pm CEST. Learn more about the event here: www.biovisioncenter.uzh.ch/en/events/Up... (1/3 🧵)
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup June 30th 2026
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Zimeng Wu @zimengwu33.bsky.social · 08/12/2025
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]
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Reese Richardson @reeserichardson.bsky.social · 05/06/2026
See my original blog post on the situation, featuring @sholtodavid.bsky.social's initial observation of something being afoot: reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 450 instances of apparent data manipulation in Thermo’s catalog
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Reese Richardson @reeserichardson.bsky.social · 05/06/2026
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
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James Manton @jamesdmanton.bsky.social · 02/06/2026
We present: Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution www.biorxiv.org/content/10.6...
Image of first two pages of manuscript.
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Ali Shaib @alishaib.bsky.social · 01/06/2026
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
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voigtvision.bsky.social @voigtvision.bsky.social · 26/03/2026
🚨New Lab Alert!🚨 Superhappy to announce that I will start my lab combining photonics & neuroscience at the Max Planck Center for Physics & Medicine in Erlangen & @mpi-scienceoflight.bsky.social in January 2027! Reach out if you're interested in internships, BSc, MSc & PhD & postdoc projects!
Max Planck Center for Physics and Medicine buildingMax Planck Instittute for the Science of Light building
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MwahahahahahadScientist @mads100tist.bsky.social · 16/03/2026
It's out! Happy to present ITEC, a semi supervised algorithm with an extremely low error rate that can track cells in files of any size (think Terabytes!). We used it in many organisms, including zebrafish, to study how organs form and linked it to gene expression www.biorxiv.org/content/10.6... +🧪
biorxiv.org
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Science Magazine @science.org · 16/03/2026
The 35th Ig Nobel Prize ceremony held in Boston in September 2025 will be the last in the United States—at least for now. This year, the beloved spoof on science Nobel Prizes will take place in Zürich, kicking off a potentially permanent change to European-hosted ceremonies. scim.ag/4siO2lS
scim.ag
After 35 years, Ig Nobel ceremony to leave the U.S.
Finances and Trump policies underlaid the decision to move the satirical science event to Switzerland
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Nature Methods @natmethods.nature.com · 16/03/2026
SeeDB-Live is a tissue-clearing approach for live tissue slices or brains, improving image quality while having minimal effects on electrophysiological properties of neurons. @imailab.bsky.social www.nature.com/articles/s41...
nature.com
Isotonic and minimally invasive optical clearing media for live cell imaging ex vivo and in vivo - Nature Methods
SeeDB-Live is a tissue-clearing approach for live samples such as tissue slices or the in vivo brain. It improves image quality while having minimal effects on electrophysiological properties of neuro...
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Benjamin Judkewitz @benjulab.bsky.social · 16/03/2026
How do fish localize sound without interaural cues? @johve.bsky.social et al. found a behavioral algorithm for directional hearing that predicts behavior from a pressure/motion phase comparison and accounts for how this relationship varies with distance. www.cell.com/current-biol...
cell.com
An algorithm underlying directional hearing in fish
Veith et al. show how a fish—Danionella cerebrum—can reliably startle away from sound. It uses the relative phase between particle motion and pressure to infer the direction of sound. This sensorimoto...
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James Manton @jamesdmanton.bsky.social · 13/03/2026
Myself and @immunoah.bsky.social are looking to hire a postdoctoral scientist to build a next-generation high-throughput high-resolution light sheet microscope for imaging entire cleared organs/tissues and to further develop live & fixed tissue clearing methods. www.nature.com/naturecareer...
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Benjamin Judkewitz @benjulab.bsky.social · 12/03/2026
Tiny, transparent, and now charted! Our brain atlas of adult Danionella cerebrum includes >200 annotated regions, 29 whole-brain in situs, and male/female reference volumes – openly available, versioned and extendable. Work by @nkadobyansky.bsky.social and team. www.biorxiv.org/content/10.6...
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 09/03/2026
Thanks to AI, the comprehensive #mesoSPIM-control documentation is finally here 🎇 mesospim.github.io/mesoSPIM-con...
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Constantin Pape @cppape.bsky.social · 05/03/2026
Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx Part of sfb1690.uni-goettingen.de to study hearing, vision, and more. Plus, you can create pretty pictures as the one below :).
A cochlea imaged in light-sheet microscopy (right) with staining for spiral ganglion neurons (red) and inner hair cells (blue). You will develop AI-based methods to analyze these structures, for example via segmentation of the individual cells (right) that will support gene therapy development for hearing loss and a better overall understanding of the anatomy of hearing.
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Science Magazine @science.org · 05/03/2026
Writers for the Superman, Star Trek, and Mission Impossible franchises all dreamed up the idea of storing libraries of data in glass. Now, Microsoft researchers say they are bringing this vision closer to reality. Learn more: scim.ag/4cZ9aJd
This glass wafer could back up your phone—and last 10,000 years
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Stephan Saalfeld @herrsaalfeld.bsky.social · 20/02/2026
If your imaging system has poorly characterized constant distortions leading to chromatic aberration, shoddy stitching, or false measurements (the answer is likely yes), you may want to give this tool a try. Native installers for Linux, Mac, Win under Releases github.com/saalfeldlab/...
github.com
GitHub - saalfeldlab/lens-correct: Correcting lens-distortion in confocal stacks
Correcting lens-distortion in confocal stacks. Contribute to saalfeldlab/lens-correct development by creating an account on GitHub.
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Kevin Dean @kevin-dean.bsky.social · 05/02/2026
In @elife.bsky.social: A high-resolution, easy-to-build light-sheet microscope for subcellular imaging doi.org/10.7554/eLif...
doi.org
A high-resolution, easy-to-build light-sheet microscope for subcellular imaging
An accessible light-sheet microscope delivers subcellular-resolution, multicolor volumetric, and live-cell imaging, lowering barriers to state-of-the-art performance.
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Reto Fiolka @retof.bsky.social · 27/01/2026
We have two funded postdoctoral positions available. Topics encompass: -Next gen light-sheet fluorescence microscopy instrumentation -Structured illumination microscopy and other approaches to extend the resolution limit. -Nonlinear microscopy combined with adaptive optics / phase conjugation
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napari @napari.org · 24/12/2025
Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 21/11/2025
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2) forum.image.sc/t/bigvolumeb...
forum.image.sc
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 16/10/2025
The 10 Years of #mesoSPIM Symposium was a blast! 🔟🎂The excitement was palpable, and we were all inspired. Three days flew by fast! Thanks to all the attendees, speakers, organizing team, and our sponsors for making it such a memorable event! Let's shape the next 10y of microscopy together! 💪❤️🔬
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🍁 Bryan Heit, PhD 🍁 @bryanheit.bsky.social · 09/10/2025
This is insane. 13 years ago we bought a million dollar #microscope to do this type of super-resolution imaging. Today, all you need is a smartphone and a few hundred bucks of off-the-shelf components 🤯 www.nature.com/articles/s41...
nature.com
Direct single-molecule detection and super-resolution imaging with a low-cost portable smartphone-based microscope - Nature Communications
Loretan and colleagues present a low-cost smartphone-based microscope capable of detecting single-molecule fluorescence. This approach opens doors to personalised and widely distributed applications in diagnostics, biosensing, and science education.
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 10/10/2025
Job opportunity at the University of Zurich! 📢 We are looking for a 𝐋𝐚𝐛𝐨𝐫𝐚𝐭𝐨𝐫𝐲 𝐓𝐞𝐜𝐡𝐧𝐢𝐜𝐢𝐚𝐧 / 𝐑𝐞𝐬𝐞𝐚𝐫𝐜𝐡 𝐀𝐬𝐬𝐢𝐬𝐭𝐚𝐧𝐭 (𝟒𝟎%) to join our Microscopy Innovation Platform (MIP), an open-source initiative focused on advancing and making light-sheet and multiphoton microscopy accessible to researchers. 1/3
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Jean-Yves Tinevez @jytinevez.bsky.social · 07/10/2025
Job alert! We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? See also on the forum: forum.image.sc/t/research-e...
forum.image.sc
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
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Crick BioImage Analysis Symposium @cbias.bsky.social · 23/09/2025
The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there! 🔗⬇️ www.crick.ac.uk/whats-on/cri...
CBIAS2025 flier, showing the conference logo, listing the topics, confirmed speakers and sponsors. On the top right corner, a QR code is available to access the registration page.
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Joel Lüthi @joelluethi.bsky.social · 18/09/2025
Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...
forms.gle
2025 OME-NGFF Workflows Hackathon application
The 2025 OME-NGFF Workflows Hackathon has a limited number of seats. A selected number of applicants will be invited to participate by the organizing committee from their application. The hackathon is...
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Heather Brown-Harding @microscopyed.bsky.social · 15/09/2025
6 of my papers are on the list...
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Crick BioImage Analysis Symposium @cbias.bsky.social · 28/08/2025
Last few days to submit an abstract for #CBIAS2025 (deadline 31/08)! We invite submissions on all topics related to #bioimageanalysis, from new software tools to discoveries made using existing methods. Early career researchers are especially encouraged to submit! www.crick.ac.uk/whats-on/cri...
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 27/08/2025
Is it possible to stain specific proteins and cell types in old formalin-fixed human tissues and make them transparent for light-sheet imaging and clinical 3D diagnostics? 🧵 1/3
Image presenting two of the speakers for the 10 Years of mesoSPIM symposium. Background of the image is a microscopy picture showing blood vessels in magenta and glial cells in cyan on a black field. On the top left, the photo of the first speaker is contained in a white-rimmed circle. On the top right the text reads: "Hei Ming Lai, The Chinese University of Hong Kong, HK" followed by the talk title "Customizing mesoSPIM-based workflows for clinical 3D tissue Diagnostics". On the lower part of the image, the second speaker is presented in a specular manner. On the lower left, text reads “Anna Maria Reuss, University Hospital, Zurich, Switzerland”, followed by the talk title “aDISCO - A Broadly Applicable Method for 3D Microscopy of Archival Paraffin-Embedded Human Tissues”. On the lower left, the photo of the second speaker is contained in a white-rimmed circle. On the bottom right it reads “10 Years of mesoSPIM Symposium”
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Joel Lüthi @joelluethi.bsky.social · 25/08/2025
We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)
Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland
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voigtvision.bsky.social @voigtvision.bsky.social · 22/08/2025
One of the people I'm indebted the most for creating stunningly beautiful #mesoSPIM samples was Martina Schaettin - who tragically passed away in March this year. To honor her memory, Elkhan Yusifov created an award - submit your best #microscopy images & videos! www.linkedin.com/company/mart...
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 22/08/2025
📣We have opened our official User Forum: forum.image.sc/tag/mesospim In this forum you can connect with 🔬developers and the image analysis experts. Ask your burning questions about the #mesoSPIM hardware, software, and image processing, or help the beginners to get started! Tip: use project tags!
forum.image.sc
Topics tagged mesospim
Topics tagged mesospim
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 20/08/2025
How to image across scales from organs to synapses, unravel biological mechanisms and handle massive data? Learn more from @adamkglaser.bsky.social, senior scientist at the Allen Institute and the lead developer of #ExA-SPIM technique, at the #mesoSPIM2025 Symposium, Oct 13-15.
Image presenting one of the speakers for the 10 Years of mesoSPIM symposium. Background of the image is a microscopy picture showing blood vessels in magenta and glial cells in cyan on a black field. On the left, the photo of the speaker is contained in a white-rimmed circle. On the right the text reads: "Adam Glaser, Allen Institute, WA, USA" followed by the talk title "New technologies for mapping centimeter scale tissues with nanoscale resolution". On the bottom right it reads “10 Years of mesoSPIM Symposium”
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 18/08/2025
💥How can light-sheet help reveal dark matter?💥 Join Prof. Laura Baudis @lbaudis.bsky.social at #mesoSPIM Symposium, Oct 13–15 in Zurich or online, to see how light-sheet fluorescence microscopy 🔬 is used to image nuclear ☢️ recoil tracks to detect elusive particles! Register now: t.uzh.ch/1Ss
mage presenting one of the speakers for the 10 Years of mesoSPIM symposium. Background of the image is a microscopy picture showing blood vessels in magenta and glial cells in cyan on a black field. On the left, the photo of the speaker is contained in a white-rimmed circle, on the right text reads: "Laura Baudis, University of Zurich, Switzerland" followed by the talk title "Probing dark matter and neutrinos with light sheet microscopy". On the bottom right reads "10 Years of mesoSPIM Symposium”
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voigtvision.bsky.social @voigtvision.bsky.social · 13/08/2025
#Deeplearning-based #CRISPR DNA integration and editing by Thomas Naert & Sören Lienkamp & Co with lots of @mesospim.bsky.social #lightsheet #Microscopy data of tadpoles (and some taken with the #Schmidt #multiimmersion objective prototype!) 🔬🐸 www.nature.com/articles/s41...
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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 12/08/2025
We’re excited to welcome @kevin-dean.bsky.social to the #mesoSPIM2025 Symposium! Explore his innovations in Multiscale Cleared-Tissue Axially Swept Light-Sheet Microscopy for imaging from organ to subcellular levels. 🗺️Oct 13–15 | Zurich & hybrid Interested? Register now: t.uzh.ch/1Ss
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