mesoSPIM: Clear Images. Big samples. Open source.

Abstract Submission Deadline: TOMORROW, July 15-th 🎇

🎉 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...

Speakers include @voigtvision.bsky.social @adamkglaser.bsky.social @christellelangevin.bsky.social @preibischs.bsky.social @jsdaniel02.bsky.social @nvladimus.bsky.social and many others! Poster design by @mgarbelli.bsky.social, cover image by Anna Maria Reuss.

Highlights:
🗣️ Keynotes & lightning talks
👩‍🔬 Maker Day for microscope builders
🤝 Meet devs, users & industry
Join us to shape the future of open-source microscopy!
#mesoSPIM2025 #openscience

Submit your work in any of these areas:
🧠 Bio/Neuro/Phys imaging
🧼 Tissue clearing techniques
🖥️ Image analysis tools (open or commercial)
🔧 Hardware and software (open or commercial)
Talks, posters & demos welcome!
Abstract submission: ema.uzh.ch/R7YRN

🎉 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

Happy imaging!

🔬 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

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!

Stainless Imaging chamber for mesoSPIM with 3D printed kinematic mounts

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.

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!

We are looking forward to your visit! And thanks for being our sponsor!

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

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...

We are thrilled to announce the 10-year #mesoSPIM2025 Anniversary Symposium, October 13-15 in Zurich! Amazing lineup of speakers: biologists, physicists, developers, computer scientists and industry experts! Register now: www.ema.uzh.ch/R7YRN Join us to learn, present, and connect!

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

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

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

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

### 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.

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

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/

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!

"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

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...

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...

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...

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

Benchtop mesoSPIM: a next-generation open-source light-sheet microscope for cleared samples - Nature Communications In 2015, we launched the mesoSPIM initiative, an open-source project for making light-sheet microscopy of large cleared tissues more accessible. Meanwhile, the demand for imaging larger samples at hig...

The next-generation open-source "Benchtop" #mesoSPIM light-sheet microscope, with open access to everyone. Find the detailed blueprints on how to build your own, and examples of applications, from neuroscience to astrophysics!
link.springer.com/article/10.1...