Joel Lüthi
joelluethi.bsky.social
Joel Lüthi
@joelluethi.bsky.social
Head of Research and Development of the BioVisionCenter at the University of Zurich
Pinned
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 🧵)
What an incredible two days!
Reposting this with so much appreciation for everyone who made the 2025 International OME-NGFF workshop such a special event. Thanks everyone for coming & especially everyone of the BVC team to help pull this off!
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
November 13, 2025 at 9:48 PM
Reposted by Joel Lüthi
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
Reposted by Joel Lüthi
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:

jobs.uzh.ch/job-vacancie...

It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
UZH: Head of the Center for Microscopy and Image Analysis (Core Facility)
The Center for Microscopy and Image Analysis (ZMB) is a nationally and internationally recognized Core Facility at the University of Zurich (UZH), providing access to state-of-the-art light and electr...
jobs.uzh.ch
November 12, 2025 at 6:42 PM
Reposted by Joel Lüthi
Very happy to share our latest work extending iterative immunofluorescence to in toto imaging of early zebrafish embryos (3D-4i), integrated with a 3D-dedicated image analysis pipeline! 🐟🔬📊
Huge kudos to Max Hess for this PhD milestone! 💪
@lucaspelkmans.bsky.social shorturl.at/cO0u7
Let's zoom in!
October 29, 2025 at 2:20 PM
Reposted by Joel Lüthi
The #mesoSPIM symposium really opened my eyes to the power of open source hardware. I've highlighted some of the surprising outcomes in a new blog post:

How Open Source Microscopy is Solving the Funding Crisis: Insights from the mesoSPIM 10-Year Symposium

www.syglass.io/blog/how-ope...
October 23, 2025 at 4:17 PM
Reposted by Joel Lüthi
Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!
October 14, 2025 at 9:31 PM
Reposted by Joel Lüthi
We’ve upgraded ShapeEmbed 🎉 ShapeEmbedLite decodes latent codes via an MLP to guarantee valid EDMs, making it lighter and ideal for small microscopy datasets or limited compute. Hear more at my BIC workshop talk or poster at #ICCV2025! Try it out at github.com/uhlmanngroup...
October 17, 2025 at 7:35 AM
Reposted by Joel Lüthi
The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social

www.biorxiv.org/content/10.1...
October 11, 2025 at 1:30 PM
Reposted by Joel Lüthi
🚀Join Helsinki BioImaging as an Image Analysis Specialist🖥️to support cross-disciplinary image analysis projects. If you love coding and are interested in working at the crossroads of computer science and biology, apply by 🗓️ November 15, 2025⤵️
jobs.helsinki.fi/job/Helsinki...
#jobopening
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
Image Analysis Specialist/Engineer/Coordinator, Helsinki Bioimaging
jobs.helsinki.fi
October 10, 2025 at 1:58 PM
Reposted by Joel Lüthi
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
October 10, 2025 at 8:58 AM
Reposted by Joel Lüthi
@nfdi4bioimage.bsky.social Task Area Leaders Josh Moore and Christian Tischer will introduce participants to the history and basics of OME-Zarr at the international 2025 OME-NGFF Symposium from November 10–11 in Zurich, SW.
Register here:
👉 www.ema.uzh.ch/de/register/...
Picture by BioVisionCenter
October 8, 2025 at 12:21 PM
Reposted by Joel Lüthi
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...
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...
forum.image.sc
October 7, 2025 at 12:39 PM
Reposted by Joel Lüthi
We’re looking for an enthusiastic postdoc to join our team. 😊

The project focuses on protein design and cryo-EM applied to cancer research. 🔬🧪

The position is fully funded for 3 years.

Please share 🙏

Job description and application details (deadline: October 11th): www.cnio.es/en/empleo/po...
Postdoctoral Research Assistant for the Biomolecular Design and Structural Nanomedicine Group
DescriptionWe are looking for a Postdoctoral Researcher to join Roger Castells-Graells’ lab at the Spanish National Cancer Research Centre (CNIO). The successful candidate will work on innovative biom...
www.cnio.es
October 5, 2025 at 2:32 PM
Reposted by Joel Lüthi
napari 0.6.5 is out! 🚀

Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: napari.org/dev/release/...
October 2, 2025 at 11:44 AM
Reposted by Joel Lüthi
BioImage analysis friends - King's are recruiting for a full-time, permanent facility position! Come and work with fun microscopes and fun people (and me!) - please share! www.kcl.ac.uk/jobs/126345-...
Bioimage Analysis Specialist | King's College London
www.kcl.ac.uk
September 29, 2025 at 9:48 AM
Reposted by Joel Lüthi
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 8:32 AM
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...
September 18, 2025 at 9:42 AM
Reposted by Joel Lüthi
Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org

@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev
September 18, 2025 at 7:23 AM
Are you working with OME-Zarrs in Switzerland?
We're running a series of community events in the context of the BioFAIR project of the BioVisionCenter: Monthly Open Bioimaging Practices Meetups with presentations by us & community members. Starting off with 3 cool events this fall (see image) (1/6)
September 16, 2025 at 7:46 AM
Reposted by Joel Lüthi
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9)

www.nature.com/articles/s41...
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
www.nature.com
September 10, 2025 at 9:37 AM
Reposted by Joel Lüthi
We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊
📄 joss.theoj.org/papers/10.2110… (1/3)
ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets
Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882
joss.theoj.org
August 15, 2025 at 1:07 PM
Reposted by Joel Lüthi
Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden

Wednesday, 27th of August, 2pm CEST
August 20, 2025 at 3:04 PM
Reposted by Joel Lüthi
Once is an exception, twice is a trend, thrice is a tradition!

Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!

Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!
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 🧵)
August 25, 2025 at 1:50 PM
Reposted by Joel Lüthi
I'll be there! Giving a talk! and hacking on _something_ for a few days!
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 🧵)
August 25, 2025 at 9:32 AM
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 🧵)
August 25, 2025 at 9:07 AM