Joel Lüthi

Toward better 2D - 3D registration in BigWarp BigWarp has so far focused on 2D-2D or 3D-3D registration, and not on 2D-3D registration. After a conversation with @Christian_Tischer , we thought some simple UI changes could make the support for 2...

Do you have 2D-to-3D image registration challenges? Let me know about them here
forum.image.sc/t/toward-bet...

I am still digesting all the info from the OME-NGFF hackathon last week.

So I decided to make a little UI for some of the code created there (just to play around), which one can easily show to interested colleagues 😜.

CZI --> OME-ZARR with some options ...

By far not perfect but still fun!

OME-Zarr is the answer. The question was: How do we enable interactive visualisation, FAIR sharing & image analysis at the TB scale?

Lorenzo Cerrone demoing visualizing HCS plates stored as OME-Zarr

Joel presenting Fractal

CytoData 2025 audience

It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!

GitHub - czimaginginstitute/zarr-particle-tools: Particle extraction and reconstruction from OME-Zarr tilt series. Particle extraction and reconstruction from OME-Zarr tilt series. - czimaginginstitute/zarr-particle-tools

Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?

Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!

📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...

📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee

📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY

Go read Joel's thread on the hackathon last week in Zürich! If you have any level of interest in OME-NGFF, there are so many exciting things happening. I had a great time meeting some of my favorite people in the world - It was equal parts rewarding, fun and exhausting 🙃️

Very happy to share some more pics! What an amazing week! I am still recovering!

Thank you so much to you all❤️‍🩹🥲

Hackathons need power adapters!

Workflow group hacking

Plus more hacking pictures I forgot to attach to the workflows effort 😅

So grateful for this community, and very excited for what’s coming next for OME-Zarr. 🚀

(14/14 🧵)

More amazing organisers & helpers!
@tischi.bsky.social @vladimirulman.bsky.social @normanrz.com @perlman.bsky.social @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social @cfusterbarcelo.bsky.social & Valentina Marcelli

(13/14 🧵)

And none of this would have been possible without all the organizers & helpers, who kept things running smoothly. Huge thanks to everyone who made the hackathon happen — you are the reason this community keeps thriving.
@joshmoore.bsky.social @jo-soltwedel.bsky.social

Continued ...

(12/14 🧵)

This event would not have been possible without the generous support of the University of Zurich and of swissuniversities' Programme Open Science II. Thank you so much for giving us the resources to promote and develop FAIR practices in bioimaging!

(11/14 🧵)

Konrad introducing capability manifests

Jonas discussing OME-Zarr Zip

Johannes discussing NGFF authorship structures

Tons of additional work on ZIP-Zarr, Java libraries, capability manifests, conformance testing, Open Seadragon, bug fixing, prototyping, brainstorming and general OME-Zarr spec discussions

(10/14 🧵)

Dave showing new ViZarr UI

Daniela showing new Vizarr features

Joris showing new Vizarr plate loading

So many fixes and additions to the ViZarr viewer to ensure it's a good basis to rely on as an OME-Zarr web viewer going forward

(9/14 🧵)

Daniel showing new napari Fractal task plugin

A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer

(8/14 🧵)

Vlado showcasing new FIJI drag & drop functionality

Exciting developments to make OME-Zarr even more accessible from FIJI: Keep an eye out for an update site to empower more drag & drop opening of OME-Zarrs in FIJI

(7/14 🧵)

John introducing RFC 5

Norman introducing collections

Transforms group hacking

Collections group hacking / discussing

Big progress on the Transformations and Collections RFCs: Setting the stage for the next developments in the spec and towards OME-Zarr 1.0

(6/14 🧵)

Discussions in the documentation group

Kiya presenting the documentation goals

Kiya presenting the documentation group outcomes

A major refresh of the OME-NGFF website (ngff.openmicroscopy.org), making it clearer, more accessible, and easier to navigate

(5/14 🧵)

The energy, the generosity, and the collaborative spirit were amazing to see.

A few highlight outcomes of the hackathon (longer form to follow later):

(4/14 🧵)

Participants at hackathon Pizza dinner

Selection of Pizzas at the Pizza dinner

Hackathon discussion

Hackathon mood

50 developers, researchers and image analysis experts from across the OME-Zarr ecosystem came together to prototype, break things, fix things, design new ideas, and have the conversations that only happen when everyone is in the same room (or around the same dinner table).
(3/14 🧵)

This followed the great OME-NGFF symposium Monday-Tuesday last week: bsky.app/profile/virg...

(2/14 🧵)

Hackathon participants group picture

We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵

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!

This is what hacking *actually* looks like. #OME_NGFF_Hackathon

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...

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.

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!

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...

A flyer for the Bioimage Analysis Beginnings Bootcamp - blue and white with a picture of cells on the top. It says "Learn core bioimage analysis skills using open-source tools for light microscopy. Open to participants at all skill levels." It also says it will be held a the Broad Institute, 415 Main Street, Cambridge MA USA, on Monday to Friday January 12th-16, 2026, from 9-5pm. Registration is $750 academic, $1250 industry, and applications are open at broad.io/BAB3

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!

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...

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...