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)

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 🧵)

🛠️ Fractal 2.14 brings powerful new features:
• Flexible filters at workflow submission
• Advanced subset processing
• Smarter, scalable run history
• Easier tracking of granular processing steps
Perfect for testing workflows and pinpointing issues fast.

🚀 We just released a major Fractal update!
More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr.
Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...

The hackathon highlighted the power of in-person collaboration - new connections, shared learnings, and a strong community effort to keep developing OME-Zarr!

📸 Group picture

🧵 (10/15)

We also explored:

📊 Benchmarking chunk sizes and sharding configurations
📌 Using Xarray to store transformations

📌 Figure 7

🧵 (9/15)

Meanwhile, in the 🐍 Python space 🐍, we started yet another OME-Zarr library (yes, again 😅):

🔗 ome-zarr-models-py → github.com/ome-zarr-mod...

…but this one will actually reduce fragmentation, we promise!

🧵 (8/15)

In the ☕ Java group ☕, we:

✅ Pushed key libraries for Zarr v3 support
✅ Improved ways to open OME-Zarrs more easily in Fiji

📽️ A demo of our progress!

🧵 (7/15)

In the workflow group, we showed that a single processing task can run in Fractal, Nextflow, Snakemake, and even via two napari plugins - highlighting the power of OME-Zarr for interoperable workflows!

📌 Figures 4 & 5

🧵 (6/15)

We had a great introduction to:

📌 How Zarr isn’t really a file format but more of an API
📌 How the Requests for Comment (RFC) process is used to evolve the OME-Zarr spec

🔗 doi.org/10.5281/ZENO...

📸 RFC screenshot

🧵 (4/15)

At the hackathon, OME-Zarr 0.5 was released, bringing support for Zarr v3 and the long awaited sharding feature to reduce file numbers of OME-Zarr.

🧵 (3/15)

Over five days, we tackled four key topics:

1️⃣ The OME-Zarr specification
2️⃣ Interoperable workflows using OME-Zarr
3️⃣ The OME-Zarr Java ecosystem
4️⃣ The OME-Zarr Python ecosystem

📌 Figure 1 gives an overview!

🧵 (2/15)

We also couldn't do such a hackathon with travel grants & catering without the support from German BioImaging
(through funding from NFDI4BIOIMAGE) and travel grants through CZI Science.
Finally, we'd also like to thank our industry sponsor
Yokogawa. (3/3)

This week, we're hosting the #OME_NGFF_Hackathon 2024 at the BioVisionCenter at the University of Zurich. We're bringing together 40 motivated researchers and specialist for #OMEZarr workflows, #OMEZarr Python tools & #OMEZarr Java tools. (1/3)