iiinova — where your digital self keeps evolving

Reposted by Josh Moore

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 06/10/2026

Curious to see what a malaria parasite looks like during different stages of cytokinesis? 🫣 In this month’s @nfdi4bioimage.bsky.social calendar, we present a dataset of Plasmodium falciparum in EMPIAR and available as OME-Zarr via the @bioimagearchive.bsky.social, both hosted by @ebi.embl.org.

This composite from EMPIAR-10392 features FIB-SEM images of the malaria parasite Plasmodium falciparum 3D ultrastructure during different cytokinesis stages: (i) mid-segmentation, (iii) Parasitophorous Vacuole Membrane rupture, (ii+iv) post-PVM rupture.

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Reposted by Josh Moore

Image Cooperative @image.coop · 02/10/2026

Last call for abstracts (deadline Tue Oct 6) for the 29th Australian Conference on Microscopy & Microanalysis! www.acmm29.org Feb 1-4, 2027 in Sydney, Australia! 🐨 #ACMM29

The ACMM29 banner image: a composite of the Sydney Opera House at night time, with glowing microscopy images overlaid on each sail.

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Reposted by Josh Moore

Sebi @sebi06.bsky.social · 02/08/2026

czitools 0.20.1 is out! 🎉 Improved CZI/HCS → OME-Zarr export, lazy Dask reading, lighter imports, better napari notebook support, and NDV visualization. Github: github.com/sebi06/czito... PyPi: pypi.org/project/czit...

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 11/09/2026

I'm always very happy to see the #Fiji gang & co, this time during the OME-Zarr Java hackathon in Dresden (imglib2/BDV motherland?). My personal progress: increasing max # of volumes in #BigVolumeViewer from 15 to ~200. Still not high enough, but there was not enough time.

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Reposted by Josh Moore

John Bogovic @bogovicj.bsky.social · 24/09/2026

Here's a whimsical example of what you can achieve with #bigwarp and the brand new #ome-zarr 0.6!

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Reposted by Josh Moore

Martin Panknin @mpanknin.bsky.social · 24/09/2026

Multichannel rendering in Kiln v0.4.1 beta. This is a fruit fly brain. Unlike the ones currently all over your feed, it doesn't play Beat Saber. It just sits there, streamed from OME-Zarr in native WebGPU and rendered at full 16-bit precision across four fluorescence channels. #OME-Zarr #WebGPU

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Reposted by Josh Moore

Sebi @sebi06.bsky.social · 30/09/2026

Hi all, prototype of a napari-zenapi-streaming plugin is working using @zeiss-microscopy.bsky.social and @napari.org. - stream pixels from ZEN into multi-dim array and display live - stream pixels from ZEN directly into OME-ZARR (see video) For viewing I used: find-nuclei.github.io

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Josh Moore @joshmoore.bsky.social · 25/09/2026

ICYMI: OME-Zarr 0.6 is out! 🎉 This is big, years in the making. @bogovicj.bsky.social & @jo-soltwedel.bsky.social perseverance brought transformations into this next major step on the road to OME-Zarr 1.0. 👏👏👏 Huge congratulations to the Johns — and to everyone who helped get us here! 🥳🙌

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Reposted by Josh Moore

Merlin Lange @merlinlange.bsky.social · 15/09/2026

🔬🧪 We're hiring postdocs&engineers at Institut de la Vision in AMAZING Paris 🇫🇷!! Join a dynamic team working at the nexus of retina developmental biology, spatial omics & advanced imaging Ambitious science in a supportive & young inclusive team 🚀 DM me for more info & please share 🙏 #academicsky

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Reposted by Josh Moore

German BioImaging @gerbi-gmb.de · 28/08/2026

"What the heck is…OME-zarr/NGFF" Demystifying bioimaging tech: no jargon, no judgment, just real conversation with @jo-soltwedel.bsky.social on the latest tools & trends. 📅 Sept 3, 1–2:30 PM (Zoom) Register: t1p.de/0byxl | Infos: t1p.de/zkcnd #opensource #ngff #ome #bioimaging

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Reposted by Josh Moore

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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Reposted by Josh Moore

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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Reposted by Josh Moore

Image Cooperative @image.coop · 19/08/2026

Our next office hours session is coming up in just under 22h! 2026-08-20 at 9am Paris/12:30pm Delhi/5pm Melbourne. Ask us anything about OME-Zarr and/or watch @jni.codes attempt to live-release the experimental 0.9dev1 version (including RFCs 3 & 4) with @joshmoore.bsky.social's help!

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Reposted by Josh Moore

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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Reposted by Josh Moore

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 07/07/2026

📆 New month – new data publication featured in the @nfdi4bioimage.bsky.social wall calendar! The calendar image for July, taken by Pauline Wanjiku Kibui, shows testicular tissue, with the seminiferous tubules depicted in red, the cell nuclei in green, and the actin in the smooth muscle in blue.

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Josh Moore @joshmoore.bsky.social · 03/07/2026

I very much hope we can get T.H. to play @bogovicj.bsky.social when the time comes to make NGFF: The Movie 🎥 ❤️

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Josh Moore @joshmoore.bsky.social · 03/07/2026

Johannes joined @gerbi-gmb.de with a clear first major task: help lead the completion of #NGFF RFC-5. Today, just before heading off on a well-earned holiday and just shy of his one-year anniversary, 0.6 has a release candidate. Kudos, @jo-soltwedel.bsky.social! 🍻🏝️🚀

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Johannes Soltwedel @jo-soltwedel.bsky.social · 02/07/2026

That's one satisfying github notification list to end the day with 🏝️ Now just one more thing to do...

A github notification list with many fixed issues and merged pull requests.

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Reposted by Josh Moore

Image Cooperative @image.coop · 01/07/2026

Earlier in June, we had our first in-person meeting at @embl.org (thank you for hosting us!), joined by representatives from Glencoe, Fideus Labs, @gerbi-gmb.de, and @scalableminds.com (+Dundee & Janelia on zoom) to start our OME-Zarr 1.0 project. More details to come, but it was fun and productive!

OME-Zarr collaborators having lunch together at the EMBL cafeteria

OME-Zarr working group discussing in a meeting room

Juan talking about Image Cooperative at an EMBL seminar room

hackathon participants having dinner in Heidelberg

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Reposted by Josh Moore

German BioImaging @gerbi-gmb.de · 29/06/2026

🚨 TiM2027 Deadline Extended! More time to submit your workshop! New deadline: July 14, 2026 Don’t miss your chance. 🔗 Apply now #TiM2027 #DeadlineExtended #Microscopy

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Reposted by Josh Moore

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 19/06/2026

You can't spell AI without FAIR❗ Here are the presentation slides from @jo-soltwedel.bsky.social talk, "You Can't Spell AI Without FAIR: How Data Management Leaves Footprints in Image Analysis," presented at the #ELMI2026 conference. 👉 Find the presentation on Zenodo: doi.org/10.5281/zeno...

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Reposted by Josh Moore

Johannes Soltwedel @jo-soltwedel.bsky.social · 17/06/2026

🚨New release 🚨 We just released ome-zarr-py 0.18 (pypi.org/project/ome-...), which brings an all new, shiny API for reading and writing #OME-ZARR data. Check out the documentation 📚 for more hints: ome-zarr.readthedocs.io/en/stable/ @openmicroscopy.org @will-j-moore.bsky.social

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Reposted by Josh Moore

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 16/06/2026

At the #ELMI2026 Core Facility Day, @schmchris.bsky.social presented the BAND (BioImage Analysis Desktop) service by @nfdi4bioimage.bsky.social on behalf of its core developer Yi Sun from EMBL Heidelberg: low-barrier access to powerful compute resources for bioimage analysis available in the cloud.

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Reposted by Josh Moore

Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Great interactive talk about surveys/interactive survey about talks and cognitive biases from my colleague @lisa-schaefer.bsky.social from @gerbi-gmb.de at #ELMI2026

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Reposted by Josh Moore

Chris Schmidt @handle.invalid · 16/06/2026

@jo-soltwedel.bsky.social presenting about how important FAIR data management is for efficiently leveraging AI in a trustworthy manner. Small differences in underlying data annotation and metadata can effect AI-based analysis output a lot. #ELMI2026 @gerbi-gmb.de #OME-Zarr

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Reposted by Josh Moore

Johannes Soltwedel @jo-soltwedel.bsky.social · 16/06/2026

Just gave a talk at #ELMI2026 and a panel discussion about how #FAIR data impacts #AI and its use in #bio-image-analysis 🔬🧪- and what we at @gerbi-gmb.de do about it 👷👷‍♀️ Slides available here: zenodo.org/records/2070...

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Reposted by Josh Moore

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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Reposted by Josh Moore

German BioImaging @gerbi-gmb.de · 16/06/2026

So excited for #ELMI2026 getting started! First act: The core facility day full of enlightening talks tailored around the world of Core Facilities. We’re happy to having contributed to make this day happen!

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Tiago Lubiana @tiagolubiana.bsky.social · 26/05/2026

this is a map of the OME-Zarr contributors so far! nice to see different regions — and the opportunities for the community growth are you in one of the gray countries and interested in advanced microscopy data projects? talk to me :) +

map of the world in equal earth projection showin the contributors to OME-Zarr

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Reposted by Josh Moore

Virginie Uhlmann @virginieuhlmann.bsky.social · 01/06/2026

📢📢 We are hiring a Bioimage Analyst at the BioVisionCenter! 📢📢 Join our collaboration with the Flow Cytometry Facility and contribute back to the international efforts on open standards for bioimaging data! More information here, reach out if you have any question: jobs.uzh.ch/job-vacancie...

jobs.uzh.ch

UZH: Bioimage Analyst

The University of Zurich is the largest university in Switzerland and one of the most prominent in Europe. For research purposes the Biovision Center and Flow Cytometry Facility offer services to supp...

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Reposted by Josh Moore

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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Reposted by Josh Moore

Image Cooperative @image.coop · 26/05/2026

Getting to know who's in the room at the first session of the #OME-Zarr Community Call. If you missed it, join for the second session to share your thoughts. Let's grow that 'curious' bubble! 🫧 forum.image.sc/t/join-us-fo...

Screenshot of a mentimeter poll titled, "How are you involved with OME-Zarr? Select all that apply". The results are:

3 - Curious/not actively using OME-Zarr. 12 - Tool developer. 11 - Spec contributor. 12 - OME-Zarr data user/Analyst. 6 - Other

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Reposted by Josh Moore

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 22/05/2026

📅 Find the story behind the May image in the @nfdi4bioimage.bsky.social wall calendar and read more about what it takes to make bioimaging data truly reusable here: 👉 nfdi4bioimage.de/en/community... To the corresponding dataset on @bioimagearchive.bsky.social: 👉 www.ebi.ac.uk/biostudies/b...

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Reposted by Josh Moore

Image Cooperative @image.coop · 22/05/2026

We want to hear from you about your experience using the OME-Zarr ecosystem and how we can improve it! We are joining the upcoming OME-NGFF community call to introduce ourselves to the community and to collect your feedback (May 26, 9AM and 5PM CET). See you there! forum.image.sc/t/join-us-fo...

forum.image.sc

Join us for the next OME-NGFF Community Call on Tuesday May 26, 2026 9:00 CET and 17:00 CET!

Dear all, We are delighted to announce our Q2 OME-NGFF Community Call to be held on Tuesday May 26! As usual, we will repeat the agenda over two time slots to welcome participants from everywhere aro...

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Reposted by Josh Moore

Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 21/05/2026

New release of #BigVolumeBrowser (0.1.1) adds support for (multiscale) OME-Zarr (thanks to libraries from @bogovicj.bsky.social, Stefan Hahmann, Vladimir Ulman). And midi gizmo navigation (from @herrsaalfeld.bsky.social ), shown below.

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 20/05/2026

You can now register for the Boosting Biodata Bootcamp 2026! Gain insights into research data management and data analysis, and learn how to advance your research and make your data and tools #FAIR. To the registration: 👉 events.hifis.net/event/3702/r...

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Reposted by Josh Moore

Global BioImaging @globalbioimaging.bsky.social · 11/05/2026

Global BioImaging & German BioImaging launch Spotlight on DATA: 💡 Built by the Image Data Management WG 📊 Featuring a practical “10 Steps” framework 🌍 Community-driven, real-world focus 📅 Live: 28 May | 17:00 CEST 🔁 Replay:29 May | 08:00 CEST 👉 Register/contribute: docs.google.com/forms/d/e/1F...

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Reposted by Josh Moore

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 07/05/2026

The Cimini lab is hiring for both postdocs and interns! The postdoc role will cover bioimage analysis projects and educational material creation; the intern will be working on our Bilayers project for helping distribute and access deep learning tools for bioimage analysis. Click below to learn more!

forum.image.sc

Postdoctoral Associate and Data Science Intern roles - Broad Institute, Cambridge MA USA

The Broad Institute Imaging Platform (the team behind CellProfiler, Piximi, and Bilayers) is currently hiring for postdoctoral and intern roles! Postdoc role: we are looking for 1-2 candidates who ha...

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Tiago Lubiana @tiagolubiana.bsky.social · 06/05/2026

Erin Diel now presenting on the mutualistic relation of Glencoe Software and the Open Microscopy Environment and the contributions of Glencoe towards OME-Zarr 1.0 #GIDE2026

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Tiago Lubiana @tiagolubiana.bsky.social · 06/05/2026

Tim Olsen from XNAT showing the 27 years of progress of a platform used all over the world for clinical and pre-clinical imaging (a "DICOM repository" and much more) #GIDE2026

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 06/05/2026

What's new in Ome-Zarr 0.6? Ome-Zarr is a cloud-optimised next-generation file format #NGFF for bioimaging, aiming to increase #FAIR access and remove barriers in the scientific process. The latest version offers numerous improvements and features. 👉 Find out more on Zenodo: doi.org/10.5281/zeno...

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Image Cooperative @image.coop · 06/05/2026

Member Eric Perlman takes the stage at @embl.org to announce our launch as an international worker co-op for #OSS scientific imaging software. First task supported by @biohub.org is accelerating #OMEZarr towards a 1.0 alpha early 2027. Stay tuned! image.coop #GIDE2026 @gideproject.bsky.social

A screenshot of Eric's title slide, saying "The role of COOPeration in global imaging. Eric Perlman. Member, Image Cooperative" in Atkinson Hyperlegible font in black on white. The footer is a subtle pink-to-green bar with the hexagonal ball as a separator. The text in the footer says "Image Cooperative Ltd."

A photo of Eric behind the mic at EMBL with the first slide as described in the other image being shown by the projector.

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Josh Moore @joshmoore.bsky.social · 05/05/2026

„Writing good data is like writing a good book. Someone will read it.„ -Dongmin Kang, S. Korea 🙇‍♂️📖🎉

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Tiago Lubiana @tiagolubiana.bsky.social · 05/05/2026

today we also saw the vision of a bioimage index project with AI-readiness at the raw data level a nice presentation by Chi-Li Chiu (@biohub.org), and right in time to share the hot news on the @os4science.org fund

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Josh Moore @joshmoore.bsky.social · 05/05/2026

„RDM … is becoming the scientific process itself.„ - Chris Wood, Mexico ❤️

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Josh Moore @joshmoore.bsky.social · 05/05/2026

„A data ecosystem is not only about sharing data, but about creating trust, capacity, and value in the communities where data originates.“ -Andrea Lara, Guatemala 🤩👏🏼

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