Joel Lüthi
@joelluethi.bsky.social
Head of Research and Development of the BioVisionCenter at the University of Zurich
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!
November 20, 2025 at 1:03 PM
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!
Plus more hacking pictures I forgot to attach to the workflows effort 😅
November 17, 2025 at 1:25 PM
Plus more hacking pictures I forgot to attach to the workflows effort 😅
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 🧵)
(10/14 🧵)
November 17, 2025 at 1:24 PM
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 🧵)
(10/14 🧵)
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 🧵)
(9/14 🧵)
November 17, 2025 at 1:24 PM
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 🧵)
(9/14 🧵)
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 🧵)
(8/14 🧵)
November 17, 2025 at 1:24 PM
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer
(8/14 🧵)
(8/14 🧵)
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 🧵)
(7/14 🧵)
November 17, 2025 at 1:24 PM
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 🧵)
(7/14 🧵)
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 🧵)
(6/14 🧵)
November 17, 2025 at 1:24 PM
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 🧵)
(6/14 🧵)
A major refresh of the OME-NGFF website (ngff.openmicroscopy.org), making it clearer, more accessible, and easier to navigate
(5/14 🧵)
(5/14 🧵)
November 17, 2025 at 1:24 PM
A major refresh of the OME-NGFF website (ngff.openmicroscopy.org), making it clearer, more accessible, and easier to navigate
(5/14 🧵)
(5/14 🧵)
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 🧵)
(3/14 🧵)
November 17, 2025 at 1:24 PM
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 🧵)
(3/14 🧵)
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 🧵
1/14 🧵
November 17, 2025 at 1:24 PM
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 🧵
1/14 🧵
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 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
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 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 🧵)
📅 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
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 🧵)
📅 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.
• 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.
April 29, 2025 at 8:23 AM
🛠️ 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.
• 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...
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...
April 29, 2025 at 8:23 AM
🚀 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...
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)
📸 Group picture
🧵 (10/15)
March 11, 2025 at 11:59 AM
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)
📸 Group picture
🧵 (10/15)
We also explored:
📊 Benchmarking chunk sizes and sharding configurations
📌 Using Xarray to store transformations
📌 Figure 7
🧵 (9/15)
📊 Benchmarking chunk sizes and sharding configurations
📌 Using Xarray to store transformations
📌 Figure 7
🧵 (9/15)
March 11, 2025 at 11:59 AM
We also explored:
📊 Benchmarking chunk sizes and sharding configurations
📌 Using Xarray to store transformations
📌 Figure 7
🧵 (9/15)
📊 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)
🔗 ome-zarr-models-py → github.com/ome-zarr-mod...
…but this one will actually reduce fragmentation, we promise!
🧵 (8/15)
March 11, 2025 at 11:59 AM
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)
🔗 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)
✅ Pushed key libraries for Zarr v3 support
✅ Improved ways to open OME-Zarrs more easily in Fiji
📽️ A demo of our progress!
🧵 (7/15)
March 11, 2025 at 11:59 AM
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)
✅ 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)
📌 Figures 4 & 5
🧵 (6/15)
March 11, 2025 at 11:59 AM
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)
📌 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)
📌 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)
March 11, 2025 at 11:59 AM
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)
📌 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)
🧵 (3/15)
March 11, 2025 at 11:59 AM
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)
🧵 (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)
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)
March 11, 2025 at 11:59 AM
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)
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)
(through funding from NFDI4BIOIMAGE) and travel grants through CZI Science.
Finally, we'd also like to thank our industry sponsor
Yokogawa. (3/3)
November 20, 2024 at 10:31 PM
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)
(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)
November 20, 2024 at 10:31 PM
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)