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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

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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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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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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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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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...

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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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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

voigtvision.bsky.social @voigtvision.bsky.social · 28/02/2026

🚨Preprint alert🚨 Mapping of 3D collagen architecture with #tissueclearing, @mesospim.bsky.social #lightsheet #Microscopy, the Schmidt #multiimmersion microscope objective & #deeplearning in healthy tissue & wound healing by Wout Houbart & Thomas Naert & Co! www.biorxiv.org/content/10.6...

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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

Doug Shepherd @dpshepherd.bsky.social · 10/12/2025

We're still exploring how to improve LSFM performance with "big" detection air objectives, where field curvature often limits achievable FOV. Here, Steven introduces curvedASLM, a method to dynamically correct field curvature (along one axis) in axially scanned setups www.biorxiv.org/content/10.6...

Schematic on how to correct field curvature along light-sheet propagation axis.

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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

Kevin Dean @kevin-dean.bsky.social · 03/12/2025

Fun to see photos from the @mesospim.bsky.social Symposium this last October.

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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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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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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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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 22/08/2025

Final program of the 10-year #mesoSPIM2025 Anniversary Symposium, October 13-15 in Zurich! Amazing lineup of speakers: biologists, physicists, developers, computer scientists and industry experts! Join us to learn, present, and connect! Registration until Sept. 15. www.adabd.uzh.ch/en/events/me...

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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

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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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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 14/07/2025

Abstract Submission Deadline: TOMORROW, July 15-th 🎇

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 03/07/2025

🎉 Call for Abstracts! 🎉 Abstract deadline approaching! 10 years of #mesoSPIM initiative – join us at the symposium for talks, demos & posters on microscopy, tissue clearing, and data analysis! 📆 October 13-15, 2025 🗺️ Zurich, Switzerland, but also online. www.adabd.uzh.ch/en/events/me...

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 12/06/2025

🎉 Call for Abstracts! 🎉 We’re celebrating 10 years of #mesoSPIM #opensource initiative – join us at the symposium for talks, demos & posters on open-source light-sheet microscopy, tissue clearing, and imaging! Dates: October 13-15, 2025 Location: Zurich, Switzerland Registration: ema.uzh.ch/R7YRN

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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

ierp-inrae.bsky.social @ierp-inrae.bsky.social · 10/06/2025

🔬 On June 6, we inaugurated the first #MesoSPIM in France at INRAE Jouy-en-Josas & ENS Paris-Saclay! A big thanks to @nvladimus.bsky.social , @mgarbelli.bsky.social ,Angeliki Vavladeli & all speakers and sponsors. Exciting step forward for #opensource imaging & interdisciplinary science! #microscopy

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 07/06/2025

Did you know that Universite Paris Saclay has its own Benchtop #mesoSPIM? Interdisciplinary team lead by @christellelangevin.bsky.social has built their own setup, the first in France, and organized an inauguration symposium! Cleared baby sturgeon or trout? They have it! French bioimaging is strong!

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Jason Kirk 🔬📷 @jasonmileskirk.bsky.social · 03/06/2025

New chamber mount design for our @mesospim.bsky.social - magnetic kinematic bases from @thorlabs.bsky.social for the win! 3D printed (for now) bases hold the chamber snugly for precise positioning between experiments. Fill port on the front allows for media addition without disturbing imaging.

Stainless Imaging chamber for mesoSPIM with 3D printed kinematic mounts

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voigtvision.bsky.social @voigtvision.bsky.social · 16/05/2025

Looking forward to the @mesospim.bsky.social #lightsheet #Microscopy anniversary symposium in October with @preibischs.bsky.social @adamkglaser.bsky.social @christellelangevin.bsky.social & many more! And to the next mesoSPIM decade! 🔬 Thanks @nvladimus.bsky.social & Co for organizing it!

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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

Jon Daniels @jsdaniel02.bsky.social · 15/05/2025

I'm excited to be able to be in Zurich for the mesoSPIM symposium. This is a really fantastic project.

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voigtvision.bsky.social @voigtvision.bsky.social · 27/05/2025

The culmination of years of hard work by Anna Maria Reuss & Co: aDISCO - a protocol for clearing & antibody-staining human formalin-fixed paraffin-embedded (FFPE) tissue! With lots of @mesospim.bsky.social #lightsheet #Microscopy @ptrrupprecht.bsky.social & many more! www.biorxiv.org/content/10.1...

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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

christellelangevin.bsky.social @christellelangevin.bsky.social · 29/04/2025

Have you heard about #MesoSPIM microscopy platforms for imaging cleared tissue? Join us to learn more about this #opensource #lightscheet device specific features, applications and discuss current challenges with experts in the field. #3Dimaging #LightSheet #TissueClearing #AI #DataScience #R&D

🕘 6th of June
🗺️ Jouy-en-Josas, France
👉 https://mesospim-upas.sciencesconf.org/?lang=fr

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 29/04/2025

Want to learn about #mesoSPIM imaging initiative and network with microscopy and data analysis experts? Come to Paris-Saclay on June 6-th! Meet our team there! Registration is still open (and free)! mesospim-upas.sciencesconf.org

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Reposted by mesoSPIM: Clear Images. Big samples. Open source.

MDI Biological Laboratory @mdibl.org · 10/03/2025

This is an image of a healthy mouse kidney, imaged on the MesoSPIM 4x objective. #microscopymonday #microscopy #fluorescentproteins #lightsheet 🧪 🤝 🍎 👩‍🔬 #NephSky #RenalSky Image courtesy of @mdibl-lmf.bsky.social

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 10/03/2025

New release of #mesoSPIM control software! Major bug fixes and performance improvement. github.com/mesoSPIM/mes...

### Performance :rocket:
- implementation of time lapse function via script. See example script at `mesoSPIM/scripts/timelapse.py` for details.
- images can now be displayed at full resolution during either live mode or acquisition, with no performance penalty. Deprecated config parameters:
``` python
'camera_display_live_subsampling': 2,
'camera_display_acquisition_subsampling': 2,
```
to enjoy full-resolution image in real time. The corresponding GUI elements for controlling the downsampling were removed.

### Bugfixes :bug:
- duplication of sub-stacks while writing large H5 files (>0.5 TB) and freezing at the end of acquisition. Fixed by replacing signal/slot mechanism for CameraWindow image update to deque mechanism. Boosted performance and stability.
- `MAX` projection is always on by default, if the dataset is asvaed in TIFF or RAW format. No need to check the box in the Image Processing Wizard. This generates maximum intensity projection as TIFF file for each stack in the acquisition list.
- explicit initialization of the first raw in Acquisition Manager, to avoid undefined GUI widget states.

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 14/02/2025

Some good news: 3 new Benchtop #mesoSPIM are being built! Scientists in China, USA, and Czech Republic are building the beautiful open-source beasts for their research. South America, what are you waiting for? Australia? Greenland? mesospim.org/setups/

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 05/02/2025

New experimental feature: timelapse for #mesoSPIM! Because why not? You can now image live specimen, such as developing organisms. Checkout this SW version at: github.com/mesoSPIM/mes... and let us know how it works for you. Be brave!

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MDI Biological Laboratory @mdibl.org · 24/01/2025

"Zebrafish head" In this captivating image, we can see the labeling of blood vessels in the head of a #zebrafish. Taken by Marko Pende on the #mesoSPIM in December 2022. #flourescencefriday 🐟🎸 🧪🤝 #microscopy #fluorescentproteins #lightsheet

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voigtvision.bsky.social @voigtvision.bsky.social · 27/01/2025

In 2019, the #mesoSPIM and #ctASLM #lightsheet #Microscopy papers appeared back-to-back in @naturemethods.bsky.social - now Jinlong Lin, @zacsimile.bsky.social & @kevin-dean.bsky.social & Co introduce the MCT-ASLM - a chimera of both for smart multiscale #imaging! www.biorxiv.org/content/10.1...

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 20/01/2025

Did you know? Our Center for Microscopy and Image aAalysis (ZMB) website has detailed step-by-step instructions how to operate and troubleshoot your #mesoSPIM microscope. Prepared by @mgarbelli.bsky.social and José Maria Mateos Melero for users like you! zmb.dozuki.com/c/Lightsheet...

zmb.dozuki.com

Lightsheet Microscopy

Lightsheet fluorescence microscope enables long term imaging of large biological samples. It delivers optical sections of large samples, with virtually no phototoxicity or bleaching and with high temp...

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mesoSPIM: Clear Images. Big samples. Open source. @mesospim.bsky.social · 20/01/2025

The #mesoSPIM project highlights in 2024, The Year of Benchtop. mailchi.mp/dced0daca419... (image courtesy Tchern Lenn)

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