iiinova — where your digital self keeps evolving

Reposted by Joel Lüthi

Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026

🚨New release: NGFF specification 0.6 🚨 Last week, we formally released the latest version of the NGFF specification: 0️⃣.6️⃣( ngff.openmicroscopy.org/specificatio...) Let's take a small tour through the things possible with #ome-zarr 0.6 now that this is out! 👇

ngff.openmicroscopy.org

Version 0.6 — NGFF documentation

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Joel Lüthi @joelluethi.bsky.social · 21/09/2026

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)

biovisioncenter.uzh.ch

Open Bioimaging Practices Meetups

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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

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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.

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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.

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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...

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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...

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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...

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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"`.

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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...

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Joel Lüthi @joelluethi.bsky.social · 14/08/2026

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 🧵)

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

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...

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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. 🍻

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Joel Lüthi @joelluethi.bsky.social · 24/07/2026

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 🧵)

biovisioncenter.uzh.ch

Open Bioimaging Practices Meetup August 2026

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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!🚀

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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...

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Joel Lüthi @joelluethi.bsky.social · 30/06/2026

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 🧵)

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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 🧵)

biovisioncenter.uzh.ch

Open Bioimaging Practices Meetup June 30th 2026

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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

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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

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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.

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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!

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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…

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

I'm happy to announce the summer 2026 Open Bioimaging Practices meetings schedule. Before the summer holidays, we have 2 exciting meetings planned to learn about all things OME-Zarr.

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Simon F. Nørrelykke @simonfn.bsky.social · 06/05/2026

The SwissBIAS Annual Meeting is taking place on June 3rd in Bern. Registration deadline: Friday, May 15th, so make sure to secure your spot now! We look forward to seeing you all there for a fantastic day of science, networking, and inspiration. @swissbias.bsky.social tinyurl.com/SwissBIAS2026

eventbrite.com

SwissBIAS annual meeting 2026

It is the time of the year to make veterans meet new members, discuss to foster feedback on existing activities and promote new initiatives.

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Erick Ratamero @erickratamero.com · 30/04/2026

I reposted this but want to add some comments: the OME community is my "scientific home", a place rooted on mutual respect, trust and looking out for each other. #OME2026 was 2/3 first-time attendees and it was amazing to see they immediately "got it". Extremely rewarding as an organizer.

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Virginie Uhlmann @virginieuhlmann.bsky.social · 30/04/2026

Thank you all for the incredible energy and inspiration! The OME community is a real treasure ❤️

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Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 30/04/2026

Back from ICLR 2026 in Rio! 🇧🇷 Highlights: presenting my poster at the LMRL workshop, Copacabana sunsets☀️, and the best coincidence: finding out my best friend got in too without us even planning it! 👯‍♀️ So grateful to @virginieuhlmann.bsky.social for the support. Where to next? 🚀

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 30/04/2026

#OME2026 is coming to an end. It has been a truly welcoming, motivating, and inspiring experience full of intensive exchange and shaped by an exceptionally open and collaborative spirit. Grateful for the many insightful discussions, new connections, and shared ideas. Thank you!

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Joel Lüthi @joelluethi.bsky.social · 29/04/2026

Amazing to be at #OME2026 & talk about the future of OME-Zarr. @virginieuhlmann.bsky.social @lorenzocerrone.bsky.social & I were very happy to present the BioVisionCenter, ngio and Fractal yesterday. If you want to learn more, check out today’s ngio workshop: github.com/BioVisionCen...

Virginie Uhlmann giving a talk titled “Towards interoperable bioimage analysis at scale

Lorenzo Cerrone presenting the ngio poster

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Johannes Soltwedel @jo-soltwedel.bsky.social · 28/04/2026

🚨ngff-spec release candidate out🚨 Just out: ngff specification version 0.6.dev4 (github.com/ome/ngff-spe...), which will be the last dev version (!) and mark the beginning of the 🚧spec-phase🚧 (see also forum.image.sc/t/ngff-weekl...) This means: let's develop some implementations 👷‍♀️👷‍♂️ #OME2026 👋

github.com

Release 0.6.dev4 · ome/ngff-spec

What's Changed fix: avoid non-unicode characters (dev) by @jo-mueller in #121 specification: Tie down possible output for coordinate transformation… by @jo-mueller in #109 Improve readability of m...

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 28/04/2026

Day 1 at #OME2026 is coming to an end with stimulating discussions during the poster session. It's been a wonderful first conference day. Looking forward to tomorrow with highlights including workshops and our keynote speaker Carole Goble. Stay tuned.

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 28/04/2026

Great talks and fruitful discussions on day 1 of the #OME2026 Community Meeting in Düsseldorf with demonstrations of using OMERO, OME-Zarr, and other OME tools in material sciences, palynology, spatial omics and more. Now starting: The Poster session. 📜💬🗨️

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Johannes Soltwedel @jo-soltwedel.bsky.social · 28/04/2026

A painful truth well put by @virginieuhlmann.bsky.social at #OME2026 😬 Striving for software #interoperability will make all our lives easier in the future!

A fictional article title of a new segmentation article, claiming to be the best

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 28/04/2026

A significant moment at #OME2026: Thanking Prof. Jason Swedlow, the founder of OME, who shaped this remarkable community work since the beginning of the millenium. His work & leadership were honored - even with a nod to his famous blue shirts by OME's Interim Board, nominated by Jason in Oct '25.

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Tiago Lubiana @tiagolubiana.bsky.social · 28/04/2026

nice to see fellow Latin American presenting on how the Smithsonian Tropival Research Institute (STRI) is using OMERO to manage data on ancient polen from the Amazon forest (at #OME2026) "the solution I have been waiting my whole life"

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Stefan Terjung @stefanterjung.bsky.social · 14/04/2026

We are looking for an experienced light microscopy specialist, motivated to support our users in the Advanced Light Microscopy Facility at EMBL Heidelberg. embl.wd103.myworkdayjobs.com/en-US/EMBL/j... -closing date 11 May 2026 @eurobioimaging.bsky.social @globalbioimaging.bsky.social

embl.wd103.myworkdayjobs.com

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Crick BioImage Analysis Symposium @cbias.bsky.social · 09/04/2026

🚨🔬🚨🔬🚨 We are pleased to announce that registration for the 7th edition of the Crick BioImage Analysis Symposium #CBIAS 2026 is now open! 🕐November 23rd-24th, 2026📍The Francis Crick Institute, London. We look forward to seeing as many of you as possible there (or online 😀)

crick.ac.uk

Crick BioImage Analysis Symposium 2026

We use cookies to track usage and preferences.

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James Briscoe @jamesbriscoe.bsky.social · 01/04/2026

A question I get asked all the time by @dev-journal.bsky.social authors "Why does it cost so much to publish a paper?" We break down the finances and explain where the money goes Spoiler: quality publishing takes a village (people + infrastructure) journals.biologists.com/dev/article/...

journals.biologists.com

‘Why is publishing so expensive?’

For many of us who work in scientific publishing, the title of this Editorial is a question we hear all the time when we're out talking to academics. And it's a perfectly reasonable one. After all, re...

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Joel Lüthi @joelluethi.bsky.social · 31/03/2026

We have just released the latest Fractal update: Bringing workflow template support to Fractal with Fractal server 2.20 This allows users to create workflow templates & share it with others. Learn more about it here: fractal-analytics-platform.github.io/news/2026-03...

fractal-analytics-platform.github.io

Fractal Workflow Templates - Fractal Analytics Platform

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napari @napari.fosstodon.org.ap.brid.gy · 24/03/2026

napari 0.7.0 is available now! 🚀🎉 It's a BIG release so read the full release notes, with highlights: napari.org/stable/release/release_0… We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant […] [Original post on fosstodon.org]

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Joel Lüthi @joelluethi.bsky.social · 26/03/2026

🔬 Next Open Bioimaging Practices Meetup (OBPM) – Mar 31, 16:00 CET Hybrid: FMI Basel & Zoom Talk by @jo-soltwedel.bsky.social : Transforming OME-Zarr: What’s coming in v0.6 Plus short updates from the BVC & time for discussion www.biovisioncenter.uzh.ch/en/events/Up...

biovisioncenter.uzh.ch

Open Bioimaging Practices Meetup: March 2026

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Image Cooperative @image.coop · 16/03/2026

Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...

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David Stansby @dstansby.bsky.social · 13/03/2026

The paper that sums up what I've been working on and running for the last three years was published this week 🎉 www.science.org/doi/10.1126/...

science.org

The Human Organ Atlas

The Human Organ Atlas provides open access to 3D images of human anatomy spanning whole organs to cellular scale resolution.

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Brandy A Freitas @brandy-syglass.bsky.social · 12/03/2026

Streaming OME-Zarr data directly into syGlass for #3DThursday🌍🔬 With #syGlass v2.6.0, datasets can stream from disk, S3, or HTTPS with no massive downloads required. Huge thanks to the community building open imaging standards: @openmicroscopy.org #OMEZarr #Microscopy #OpenScience #Bioimaging

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Virginie Uhlmann @virginieuhlmann.bsky.social · 10/03/2026

If you've been wondering what our current obsession with OME-Zarr and lego blocks is about, I have good news for you: the Fractal preprint is out! Thanks to @joelluethi.bsky.social , all co-authors, and the Fractal developers and users community for making this beautiful project a reality ❤️

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Josh Moore @joshmoore.bsky.social · 11/03/2026

Help shape the future of @openmicroscopy.org! 🔮 The OME 2026 community survey is open—tell us what’s working, what isn’t, and what you'd like to see next. Takes just a few minutes 👇 forum.image.sc/t/ome-2026-c...

forum.image.sc

OME 2026 Community Survey

Calling all OME Community members, contributors, and lurkers! This year in April, the 19th OME Community Meeting will be gathering to determine the "Future and Governance of OME" during the final mee...

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Erick Ratamero @erickratamero.com · 10/03/2026

Calling all OME Community members, contributors, and lurkers! Please take a minute to answer the OME 2026 Community Survey (docs.google.com/forms/d/e/1F...) to help us prepare for discussing the future of OME governance during the OME 2026 Community Meeting at the end of April.

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