iiinova — where your digital self keeps evolving

Learn more about the event series and register for the events and the event mailing list: www.biovisioncenter.uzh.ch/en/events/Op... (🧵 10/10)

Open Bioimaging Practices Meetups

000

Join our Cloud HD Video Meeting

These meetings are hybrid. Join us in person in Zurich/Basel to get snacks & drinks after the event, or connect via Zoom: uzh.zoom.us/j/6665982770... (🧵 9/10)

uzh.zoom.us

Zoom is the leader in modern enterprise cloud communications.

100

Spatial OMICs in OME-Zarr Date: November 19, 2026 4:00 PM CET Catch up with the latest developments from the Spatial OMICs space. Learn both about the Python and R side of SpatialData and the current developments, then dive into user stories of seeing them in action. (🧵 7/10)

100

Hear from the people building them: @rhornb.bsky.social, @nrepina.bsky.social & Flurin Sturzenegger. Learn more here: www.biovisioncenter.uzh.ch/en/events/Up... (🧵 6/10)

Open Bioimaging Practices Meetup, October 2026

Multiplexed image analysis in OME-Zarr Date: October 27, 2026 4:00 PM CET Discover workflows processing multiplexed imaging data and the open source libraries that enable them. (🧵 5/10)

100

Hear from the people building this: Stefan Hahmann, @bogovicj.bsky.social, @tischi.bsky.social, Eugene Katrukha, Vladimír Ulman & Will Moore. Learn more here: www.biovisioncenter.uzh.ch/en/events/Up... (🧵 4/10)

Open Bioimaging Practices Meetup, September 2026

121

And hear about OME-figure (formerly Omero figure, now working with standalone OME-Zarrs) (🧵 3/10)

100

OME-Zarr viewers, part 2; "The FIJI strikes back" Date: September 30, 2026 4:00 PM CEST Learn about many of the recent developments in the FIJI space (new update site, drag & drop OME-Zarr into FIJI, writing OME-Zarrs from FIJI, MoBIE, BigVolumeViewer & scripting with OME-Zarrs) ... (🧵 2/10)

100

I'm happy to announce the fall 2026 Open Bioimaging Practices Meetup schedule. We'll have 3 exciting meetings about developments in the OME-Zarr space: - OME-Zarr viewers - Multiplexed Image analysis in OME-Zarr - Spatial OMICs in OME-Zarr See www.biovisioncenter.uzh.ch/en/events/Op... (🧵 1/10)

Open Bioimaging Practices Meetups

152

Joel Lüthi @joelluethi.bsky.social · 18/09/2026

It's been great to join #IbSB2026 in Jena this week, to learn about all the great image analysis being done here & share our work on OME-Zarr & Fractal with the community. Thank you Marc Thilo Figge & team for the organisation, this meeting is worth taking the DB adventures to make your way to Jena

020

Reposted by Joel Lüthi

Carl-Magnus Svensson @cmsvensson.bsky.social · 18/09/2026

Second day of #IbSB2026 is about to start. Looking forward to talks from @tingyingpeng.bsky.social, @joelluethi.bsky.social and many others her at @leibniz-hki.de.

011

Reposted by Joel Lüthi

Virginie Uhlmann @virginieuhlmann.bsky.social · 11/09/2026

Research software is costly and time-consuming to produce because it requires focused time from developers who have invested years learning to master their craft, just like art. There is nothing to celebrate about relinquishing intellectual expertise and mastery in favor of fast and cheap.

12711

Reposted by Joel Lüthi

FMI science @fmiscience.bsky.social · 01/09/2026

📣 Applications are now open for the FMI PhD and MD-PhD Programs! Train in a collaborative, international environment with cutting-edge technology, courses, scientific retreats and career-development opportunities — in Basel, a leading European life sciences hub. Apply at www.fmi.ch/education-ca...

063

Reposted by Joel Lüthi

napari @napari.org · 26/08/2026

🚨🚨🚨 napari 0.9.0 is out! 🚨🚨🚨 This is a huge release for us and for our community, with over 30 people contributing new features, improvements, and bug fixes in the 6 weeks since 0.8.0! Release notes here: napari.org/stable/relea... and some highlights in the thread below! 👇

napari.org

napari 0.9.0

Tue, Aug 25, 2026 We’re happy to announce the release of napari 0.9.0! napari is a fast, interactive, multi-dimensional image viewer for Python. It’s designed for browsing, annotating, and analyzing l...

13612

Reposted by Joel Lüthi

Image Cooperative @image.coop · 27/08/2026

The next OME-Zarr Office Hours is coming up in just over 2h! 8am SFO / 11am NYC / 5pm Paris. Come ask any questions about OME-Zarr, and/or watch @kevinyamauchi.bsky.social live-convert an HCS (High Content Screening) dataset to RFC-8 syntax! ngff.openmicroscopy.org/community/#o...

053

Reposted by Joel Lüthi

napari @napari.org · 20/08/2026

Sizzling Summer Series 4 - global 🌍️ napari 0.9.0 is about ready to fly out the door! ✈️ We would be grateful if you tried out the pre-release: Install into an environment with `pip install "napari[all]>=0.9.0rc1"` or try with uv in a temp environment with `uvx "napari[all]>=0.9.0rc1"`.

1199

Joel Lüthi @joelluethi.bsky.social · 19/08/2026

Join the Open Bioimaging Practices Meetup all about OME-Zarr viewers on Monday, August 24th, 4pm CEST. Learn about ViZarr, napari & VolE & hear user stories on how they handle OME-Zarrs. More info here: www.biovisioncenter.uzh.ch/en/events/Up...

0118

biovisioncenter.notion.site

Applications are open until September 15th, and selected participants will be confirmed latest in early October. Learn more about the event and apply here: biovisioncenter.notion.site/2026-ome-zar... (5/6 🧵)

2026 OME-Zarr Hackathon | Notion

Picture: 2025 OME-NGFF workflows hackathon

121

The in-person 2026 OME-Zarr Hackathon has a limited number of seats. A selected number of applicants will be invited to participate by the organizing committee from their application. (4/6 🧵)

Learn more about the kinds of work done at this hackathon in the 2024 OME-NGFF workflows hackathon preprint: osf.io/preprints/bi... (3/6 🧵)

osf.io

OSF

This is the 4th annual OME-Zarr hackathon in Zurich and it's a great place to push the OME-Zarr spec forward. This year, we'll focus on OME-Zarr RFCs, the OME-Zarr V1 effort, OME-Zarr viewers, OME-Zarr in Python, OME-Zarr in Java and workflows with OME-Zarr. (2/6 🧵)

130

Cornelia Schwayer @cschwayer.bsky.social · 03/08/2026

We're excited to announce the 2026 OME-Zarr hackathon 🎉 📅 Date: November 2nd - November 6th 2026 📍 Location: University of Zurich, Zurich, Switzerland 💻 Virtual participation: possible for Monday afternoon, 1:00 PM CET 6:00 PM CET biovisioncenter.notion.site/2026-ome-zar... (1/6 🧵)

11414

Reposted by Joel Lüthi

I will be opening my research group at the Max Delbrück Center later this year to unravel the principles governing the unique context sensing capacity of the liver www.mdc-berlin.de/schwayer and am looking for enthusiastic PhD applicants.

mdc-berlin.de

Schwayer Lab

The mammalian liver possesses a regenerative capacity that is unmatched by any other organ. Following injury, liver epithelial cells can proliferate or even change their identity, enabling the organ t...

55218

Reposted by Joel Lüthi

napari @napari.fosstodon.org.ap.brid.gy · 31/07/2026

RE: fosstodon.org/@napari/1166165047810… And it's a wrap! The hackathon was a fantastic success! 🥳 You can look forward to a longer post about all we did, and one of our biggest releases yet in 0.9.0! Huge thanks to all the participants 🤩, and we hope to see you at the next one!

Hackathon participants discussing a new feature demo.

Jules Vanaret shows off slicing of volumes with non-orthogonal transforms.

The naPLari hackathon crowd: Wouter-Michiel Vierdag, Grzegorz Bokota, Tim Monko, Giannis Liaskas, Draga Doncila Pop, Lorenzo Gaifas, Aroj Hada, Brian Northan, Jules Vanaret, Zuzana Čočková, Curtis Rueden, Juan Nunez-Iglesias, and Margot Chazotte.

Celebratory drink after the last full day of the hackathon. 🍻

0144

The meeting is taking place hybrid: In person at the FMI in Basel Switzerland and virtually via Zoom. For anyone attending in person, there will be drinks & snacks at the end. Learn more about the meeting & sign up here: www.biovisioncenter.uzh.ch/en/events/Up... (5/5 🧵)

Open Bioimaging Practices Meetup August 2026

010

Third, we'll be introduced to the Vol-E viewer (vol-e.allencell.org) by members of the Allen Cell Vol-E team as well as a user story about Vol-E and the Timelapse Feature Explorer (timelapse.allencell.org) by a member of the Allen Cell Vol-E team or Max Hess. (4/5 🧵)

vol-e.allencell.org

Vol-E

GitHub - BioNGFF/vizarr: A minimal Zarr image viewer based on Viv.

First, we will hear about the ViZarr viewer (github.com/BioNGFF/vizarr) from @davehorsfall.bsky.social and Alex Surtees from Newcastle University, as well as a ViZarr user story about the ViZarr ROI annotation plugin by Luca Anceschi from IHB Roche. (2/5 🧵)

github.com

A minimal Zarr image viewer based on Viv. Contribute to BioNGFF/vizarr development by creating an account on GitHub.

Do you want to learn more about OME-Zarr viewers, where they stand today and what's being developed at the moment? On August 24th at 4pm CEST, we will hear about 3 different OME-Zarr viewers and user stories for each. www.biovisioncenter.uzh.ch/en/events/Up... (1/5 🧵)

Open Bioimaging Practices Meetup August 2026

11511

Reposted by Joel Lüthi

Shayan Shamipour @shamipourshayan.bsky.social · 03/07/2026

🚀Excited to share our latest efforts in bringing highly multiplexed whole-mount imaging to intact multicellular systems! Shield-4i: an integrated platform to study multi-scale information flow in 3D embryos and embryo-like systems. Kudos to @rhornb.bsky.social for this major milestone in the lab!🚀

13613

Reposted by Joel Lüthi

Constantin Pape @cppape.bsky.social · 30/06/2026

Want to learn about the latest trends and developments in bioimage analysis? Join us for the GLOBIAS workshop in Dortmund this November! I will be hosting a session on foundation models / AI. www.globias.org/activities/g...

globias.org

GloBIAS2026 Workshop Dortmund

GloBIAS 2026 Bioimage Analysts' Workshop Registration is open! Register with this link! 10-13 November, 2026 - Tuesday to Friday Leibniz-Institut für Analytische Wissenschaften – ISAS – e. V. (https...

01510

fractal-analytics-platform.github.io

Learn more about the plugin and its functionality here: fractal-analytics-platform.github.io/news/2026-06... (5/5 🧵)

napari plugins to handle Fractal-created OME-Zarrs - Fractal Analytics Platform

010

2. A way to interactively draw and save new regions of interest tables. Want to limit labels you load to specific regions? Or prepare an OME-Zarr with small ROIs for further processing? Draw them in napari & save them as ngio ROI tables. (4/5 🧵)

In this newest release, I've polished the existing widgets and added 2 new major widgets: 1. A way to save labels back to OME-Zarrs: Save full labels back to an OME-Zarr. Or just edit a smaller region of interest of a large OME-Zarr, edit it and update the OME-Zarr labels. (3/5 🧵)

100

fractal-analytics-platform.github.io

I've just released a significant update to the napari-ome-zarr-navigator plugin (github.com/fractal-napa...). The navigator plugin loads labels & tables from OME-Zarr and helps you navigate OME-Zarr HCS plates. (2/5 🧵)

napari plugins to handle Fractal-created OME-Zarrs - Fractal Analytics Platform

100

Joel Lüthi @joelluethi.bsky.social · 29/06/2026

Working with OME-Zarrs in @napari.org ? Check out the newest release of napari-ome-zarr-navigator to make your life easier & allow more interactive ways to write back to OME-Zarrs. Follow the thread for more (1/5 🧵)

1178

Have your own data you want to convert? Bring it along (preferably smaller datasets for testing). After the inputs, we'll have time to try live OME-Zarr conversion on your data. If you can attend in-person, support for it will be easier. (3/3 🧵)

010

Joel Lüthi @joelluethi.bsky.social · 29/06/2026

Learn from Bugra Oezdemir about EuBI-Bridge, from @lorenzocerrone.bsky.social about ome-zarr-converters-tools and from Flurin Sturzenegger about the ZMB facility perspective. (2/3 🧵)

Joel Lüthi @joelluethi.bsky.social · 29/06/2026

Want to learn about converting data into OME-Zarr and the design choices behind different tools built for it? Join the Open Bioimaging Practices Meeting tomorrow: Tuesday, June 30th 2026, 4pm CEST. Learn more about the event here: www.biovisioncenter.uzh.ch/en/events/Up... (1/3 🧵)

Open Bioimaging Practices Meetup June 30th 2026

173

Reposted by Joel Lüthi

Helena Klara Jambor @helenajambor.bsky.social · 19/06/2026

What a week! My first Points of View was published @natmethods.nature.com Happy to start the series in 🏳️‍🌈 month with "On Color scales and the birth of Viridis" - looks good, allows naming of regions, AND is perceptually uniform 🎁 rdcu.be/fnPhk www.nature.com/articles/s41... #dataviz

A mountain ridge shown in different color sclales. Picture:
Andres Passwirth - Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=17166331

44616

Reposted by Joel Lüthi

Anna Foix @afoix.bsky.social · 15/06/2026

BIC @eccv.bsky.social 2026 is OPEN! Show us your new CV, AI & Bio work🦠🔬 🚪: openreview.net/group?id=the... Thanks organisers for making it possible @alex-krull.bsky.social Peter Bajcsy @janfunkey.bsky.social @florianjug.bsky.social Qingjie Meng @virginieuhlmann.bsky.social @maweigert.bsky.social ✨

openreview.net

ECCV 2026 Workshop BIC

Welcome to the OpenReview homepage for ECCV 2026 Workshop BIC

0108

Reposted by Joel Lüthi

Image Cooperative @image.coop · 16/06/2026

Keeping track of OME-Zarr support across the ecosystem isn't always easy. Over the past few weeks, we've been speaking with stakeholders about experiences, successes, and remaining gaps. Here is our snapshot of where things stand and where effort may be most valuable next: image.coop/blog/posts/2...

image.coop

OME-Zarr Pulse Check: Spec, Tooling, and Community – Image Cooperative

Feedback and insights from chatting to the community and analysing ecosystem data over the last six weeks.

076

Joel Lüthi @joelluethi.bsky.social · 01/06/2026

Want to work with us at the BioVisionCenter on building new cool OME-Zarr image analysis workflows? Apply to our Bioimage Analyst position!

055

Reposted by Joel Lüthi

Image Cooperative @image.coop · 29/05/2026

Some initial results from the live survey at the recent #OME-Zarr Community Call for you to ponder over the weekend. Thoughts, as always, welcome! 🤔

Slide titled "What keeps you engaged with OME-Zarr?" with colored boxes sized to match the number of responses:

## Community (15)
- Great people!
- Delightful people
- Very knowledgable approachable people in the community
- Job, but also exciting to support the community
- People care
- Friendly community
- open communication with the community
- Awesome community
- The community x7

## Value & Trajectory (13)
- moving towards 1.0
- we're almost there :)
- The momentum
- It is the future
- hope
- Love the vision
- finally having the One True Format
- Format is useful and things are happening!
- very promising to handle large data in the future, nothing else seems to provide this
- Data is too big for anything else
- Better format to handle big data
- Potential to solve difficult/modern data problems.
- Obvious value of ome zarr

## Outreach (4)
- very good outreach!
- I'm new here but I will be back! :)
- Curiosity
- Staying updated

## Open (2)
- Open
- Open source

## Flexible (2)
- Versatile
- Flexible

## Misc. (9)
- Useful
- Fair data
- Right technology
- Making hard problems easier
- Need to be able to support end users
- I want to be able to access the benefits
- Scverse uses OME-Zarr as a backbone for Spatialdata object
- "pressure" from the repos, as the only accepted format
- The fame and money

Slide titled "What keeps you engaged with OME-Zarr?" with colored boxes matching the number of responses.

# Large data / Scalability (13)
- Dealing with large images
- Large data support
- large data handling
- Sharing large datasets
- scalability x4
- Big data x3
- Scalable x2

## Cloud native (9)
- Works in the cloud and locally
- Cloud support
- Cloud data native
- Cloud native brick storage
- cloud native x3
- Native cloud support x2

## Remote access (5)
- Streaming support x2
- streamable
- deposit data once and everything else just uses the S3-URL
- deposit somewhere once, access/index it from everywhere

## Community (5)
- It is represented by an international community
- Large Community support and buy in
- Community support
- good community support
- community driven

## Performance (5)
- Efficient storage, transfer and sharing
- Lazy Loading
- Rapid loading over network
- Parallel IO
- Easy browsing and parallel computing on large datasets

## Standardisation (3)
- Standardisation x2
- Standardization

## Chunking (3)
- Chunking
- Data in chunks
- Multiscale, chunked access

## Flexible (3)
- Flexible x2
- Extensible

## Open (3)
- Openness x2
- Open

## FAIRness (2)
- FAIRness x2

## Misc. (8)
- Multimodal images
- Independence on compute hardware
- Interoperability
- Remote visualization
- Easy visualisation
- Human readable
- vendor agnostic
- growing acceptance

Slide titled "What are the drawbacks of OME-Zarr?" with colored boxes sized to match the number of entries:

## Tooling Support (14)
- Tools have unclear incompatibilities
- Lack of generalised processing tools
- Too many libraries with different features
- lack of a single cannonical library for python
- "unclear tool eco-system / unclear features / important features missing"
- Most easy to use tools focus on visualisation only, not processing
- not yet enough interoperability with different tools, but it gets more
- What tool and version supports what and how to choose reasonable settings
- Easy to Load in FIJI
- Fiji support
- Using traditional Fiji 2D algorithms on OME Zarr is not efficient
- OMERObility
- OMERO support incomplete
- Traditional orthogonal 3D viewer is still lacking

## Evolving spec. (13)
- evolving spec x4
- Not stable enough yet
- Unstable spec
- Not finished
- not stable
- Not meeting all requirements yet
- Changing specification
- Might there be massive (potentially breaking) changes in future?
- Missing metadata
- Missing flexibility

## User accessibility (9)
- Too technical x2
- Complexity x2
- user comfort
- Difficult to access for end users
- Hard to use if not computationally comfortable
- giving access to s3 to biologists
- Not entirely supporting biologists

## File systems (7)
- Too many files
- Many small files
- Many files
- inodes
- Amount of files
- problem on traditional filesystem
- HPC use

## Version confusion (4)
- Fracture between Zarr v2 v3, omezarr v4, v5
- confusion with versions of zarr and versions of ome-ngff
- Hard to know which tool and version supports what
- Is ome NGFF equal to ome.zarr?

## Infrastructure (4)
- Authentication
- lack of good data management tools (auth, groups, etc)
- lack of object storage infrastructure
- Network performance/overhead

## Compression (3)
- No RGB compression
- No lossy compression
- Codec support

## Vendor support (3)
- No vendor support
- Missing features for vendors
- not y…

193

Joel Lüthi @joelluethi.bsky.social · 27/05/2026

Find more about the event series here: www.biovisioncenter.uzh.ch/en/events/Op...

Open Bioimaging Practices Meetups

000

Joel Lüthi @joelluethi.bsky.social · 27/05/2026

On June 30th at 4pm, we will get an overview of different OME-Zarr conversion approaches with Bugra Özdemir and a chance to "bring your data" for live OME-Zarr conversion at the end of the talks. See details here: www.biovisioncenter.uzh.ch/en/events/Up...