iiinova — where your digital self keeps evolving

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

OME-Zarr 0.6 allows to compose multi-modal image data across dimensionalities into a joint dataset and ingest it into a supporting viewer of your choice. Combining image data across scales from µm 🧫 to cm 🧠 and beyond will be much easier now! Dataset source: rodare.hzdr.de/record/3131

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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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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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Johannes Soltwedel @jo-soltwedel.bsky.social · 17/08/2026

One cool feature in the latest #ome-zarr spec are "projectAxis" transforms 📽️: Projecting images into higher dims (i.e. 2D->3D) is absolutely transformative for some use cases! Now to do this with maaaany more slides 🔬 Dataset from rodare.hzdr.de/record/3131 cc @napari.org

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Johannes Soltwedel @jo-soltwedel.bsky.social · 25/06/2026

Just the occasional this-thing-is-really-easy-in-ome-zarr-0.6 kind of post: Stitching in napari @napari.org with napari-stitcher (@m-albert.bsky.social) and napari-ome-zarr (@will-j-moore.bsky.social) (WIP) : (Sample data from the awesome big-stitcher tool github.com/JaneliaSciCo...)

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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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CCP-volumeEM @ccp-volumeem.bsky.social · 17/06/2026

In March, CCP-volumeEM hosted an OME-NGFF hackathon, bringing the community together to collaborate, share ideas and advance tools for volume electron microscopy. 🔬💻 Read about what we worked on and hear directly from two attendees about their experiences: www.ccp-volumeem.ac.uk/hackathons/h...

ccp-volumeem.ac.uk

OME-NGFF Hackathon March 2026 — CCP in vEM

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

ICYMI (I did 🫣) 💚

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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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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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OME @openmicroscopy.org · 03/05/2026

#OME2026 has come to an end—what an inspiring and collaborative few days. Huge thanks to @nfdi4bioimage.bsky.social for documenting the meeting so thoroughly—definitely worth a look back through their posts! But first, enjoy the wrap-up video presented already during the closing session! 🤩

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

now @will-j-moore.bsky.social and the new developments in ome-zarr.js github.com/BioNGFF/ome-... #OME2026

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

Finally turning a lot of Github handles into real-world acquaintances and meeting many friends from the field 😀 Looking forward to three days of @openmicroscopy.org #OME2026

A title slide for the OME 2026 meeting in Düsseldorf

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Josh Moore @joshmoore.bsky.social · 22/04/2026

Really excited to finally share this more widely. This is exactly the kind of work we hoped the cooperative could support—helping turn strong community momentum around #OMEZarr into something more coordinated and sustained. Very curious to hear what people think.

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Utz Ermel @uermel.bsky.social · 20/04/2026

Excited to share our paper about copick, a dataset API and toolkit for collaborative annotation and analysis of #cryoET data! Whether you're picking particles or curating segmentations, copick reduces friction and brings #OME-Zarr to cryoET without breaking pipelines. 🧵👇 doi.org/10.1002/pro.70578

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will-j-moore.bsky.social @will-j-moore.bsky.social · 17/04/2026

Looking forward to our workshop "OMERO.figure embraces OME-Zarr" at #OME2026 in just over a week. You can just have a go with the app at ome.github.io/omero-figure/

ome.github.io

OMERO.figure

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Martin Panknin @mpanknin.bsky.social · 27/03/2026

Kiln also has experimental OME-Zarr support. This is the Beechnut — a 3 GB micro-CT scan streamed directly from a public OME-Zarr store into the browser. No preprocessing, no conversion. github.com/MPanknin/kil... #WebGPU #OMEZarr #VolumeRendering

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Juan Nunez-Iglesias @jni.codes · 16/03/2026

So… um… I (and Draga Doncila Pop and Eric Perlman and @joshmoore.bsky.social and @kevinyamauchi.bsky.social) started a thing! We are excited and terrified in equal measures, and look forward to working with you all in our amazing scientific imaging community! ❤️‍🔥 Read the linked post for the lowdown.

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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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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/03/2026

I'm a simple man. I see lazy streaming of chunked bio-image data from a remote @openmicroscopy.org #ome-zarr image to a virtual reality #VR framework, I repost. Seriously, this is *so* cool! 🤯

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Joel Lüthi @joelluethi.bsky.social · 10/03/2026

We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows. Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis. (1 / 10🧵) www.biorxiv.org/content/10.6...

biorxiv.org

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Robert Haase @haesleinhuepf.bsky.social · 07/03/2026

I had a great time at Uni Copenhagen giving a talk about How Generative AI impacts Bio-Image Data Science this week. You find my slides online and a recording will be shared soon! doi.org/10.5281/zeno... Big thanks to @danishbioimaging.bsky.social, @claraprats.bsky.social and team for hosting me!

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Ulrike Boehm @ulrikeboehm.bsky.social · 02/03/2026

𝗘𝘅𝗰𝗶𝘁𝗶𝗻𝗴 𝗗𝗲𝘃𝗲𝗹𝗼𝗽𝗺𝗲𝗻𝘁𝘀 𝗶𝗻 𝗠𝗶𝗰𝗿𝗼𝘀𝗰𝗼𝗽𝘆 𝗥𝗲𝗽𝗼𝗿𝘁𝗶𝗻𝗴! If you're involved in creating, processing, or publishing microscopy data, take a look at the new checklist for reporting requirements provided by @quarep-limi.bsky.social in @jcb.org 🔗 rupress.org/jcb/article/...

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OME @openmicroscopy.org · 26/02/2026

We have integrated the Allen Institute's BioFile Finder app with IDR. You can quickly Group and Filter all images in a study. Data is served by the IDR search engine and supports up to a million images at a time. BioFile Finder links are on each study page e.g. idr.openmicroscopy.org/study/idr0056/

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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 24/02/2026

Mohsen Ahmadi presents his poster, "FAIR bioimaging data management workflow for plasma medicine by integrating #OMERO, eLabFTW, and Adamant via #Jupyter notebook," at the annual meeting of the @researchdataall.bsky.social (#rdade2026). 👉 Find out more about the workflow: zenodo.org/records/1845...

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Talley Lambert @talley.codes · 06/02/2026

One of the funniest conversations I've ever had with Claude... stick with it through the third image to watch it slowly realize it's broken, try to "play it cool", fail spectacularly, then attempt self-aware commentary and immediately faceplant again. it's worth it, I promise.

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Philippe Bastin's Lab @bastinlab.bsky.social · 29/01/2026

Very emotional symposium in memory of our dear Spencer Shorte @pasteur.fr His legacy will be with us for ever, many thanks to Nathalie Aulner and all speakers @krogersiooi.bsky.social @freddyfrischknecht.bsky.social @jytinevez.bsky.social @yarareis-gbi.bsky.social @stratocore.bsky.social

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German BioImaging @gerbi-gmb.de · 22/01/2026

Great news for German #BioImaging! 🤝 #GerBI & #de.NBI just signed an MoU to launch a GerBI #OMERO platform. de.NBI brings the cloud, GerBI handles ops, support & community. 🧩 A testbed + training hub for everyone. Stronger data, stronger science. More soon!

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German BioImaging @gerbi-gmb.de · 22/01/2026

19th #OME Community Meeting, Düsseldorf · 28–30 April 2026 Registration is now open! Join researchers, developers, and imaging facility staff to connect, share experiences, and discuss the future of OME tools. Details & registration (deadline: 31 March 2026): gerbi-gmb.de/event/ome-20...

gerbi-gmb.de

19th OME Community Meeting - German BioImaging

Join us for the 19th Open Microscopy Environment (OME) Community Meeting from 28.-30.4.2026, in the Haus der Universität Düsseldorf. Invited Speakers Carole Goble – Keynote – Jean-Marie Burel Josh Moo...

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Lucien Hinderling @lhinderling.bsky.social · 07/01/2026

Won best thesis award with this video! 4 years of research and play in 3 minutes :') youtu.be/so0fPlK1-LM

youtu.be

Smart microscopy, computer vision, and controlling cells with light -- my PhD thesis in 3 minutes

YouTube video by Pertz Lab

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Johannes Soltwedel @jo-soltwedel.bsky.social · 07/01/2026

Kind of flew under the radar, BUT we released napari-omero 0.6 recently 🥳 @openmicroscopy.org You can now down-/upload ROIs from and to OMERO inside @napari.org 🤩Bringing the power of napari for annotation to the management of OMERO :) Thanks @psobolewskiphd.bsky.social and other maintainers!

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will-j-moore.bsky.social @will-j-moore.bsky.social · 05/01/2026

Very pleased to announce the release of #OMERO.figure 7.3.0 including ROI Labels, Colorbars and lots of bug fixes. Thanks to contributors: Rémy Dornier, @tom-bssnnt.bsky.social, Jens Wendt, Niraj Kandpal. www.youtube.com/watch?v=cUy5...

youtube.com

OMERO.figure: ROI Labels and Colorbars: New in 7.3.0

YouTube video by Open Microscopy Environment

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will-j-moore.bsky.social @will-j-moore.bsky.social · 16/12/2025

As I prepare the next #OMERO.figure release (apologies, it's been a while) I found a video for the last release that I never published! youtu.be/Jj-XjIhaQF4 shows Interactive Inset panels, borders, Hilo LUTs, label re-ordering etc.

youtu.be

OMERO.figure new features in 2024

YouTube video by Open Microscopy Environment

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paveltomancak.bsky.social @paveltomancak.bsky.social · 13/12/2025

#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question 🙃, because the #preprint. Software is available in every #Fiji near you. www.biorxiv.org/content/10.6...

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Zimeng Wu @zimengwu33.bsky.social · 08/12/2025

Pleased to say that Jonas Hartmann (bs-less) and I have finally released DySTrack (“diss track”) - Dynamic Sample Tracking. It’s a Python-based, modular tool that brings smart microscopy to everyday imaging on commercial systems. Preprint: www.biorxiv.org/content/10.6... [1/6]

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OME @openmicroscopy.org · 21/11/2025

Idr0168: Prediction of protein subcellular localization in single cells from www.nature.com/articles/s41... by Zhang et al. Images in idr0168 are OME-Zarrs converted by the submitter. idr.openmicroscopy.org/search/?quer...

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Virginie Uhlmann @virginieuhlmann.bsky.social · 19/11/2025

So nice to see this!!!

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Jacob Tomlinson @jacobtomlinson.dev · 18/11/2025

For Python package management I use a mixture of pixi, uv and conda depending on the task I'm doing. I wrote up a long form post about the history of these tools, why each one exists, and why I settled on these choices in my workflow. jacobtomlinson.dev/posts/2025/p...

jacobtomlinson.dev

Python package managers: uv vs pixi?

When I talk to people about Python package management in 2025 I see the following tools in active use; uv, pixi, pip, conda, mamba, micromamba and poetry. There may be others, but I don’t hear much ab...

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Johannes Soltwedel @jo-soltwedel.bsky.social · 12/11/2025

This is what hacking *actually* looks like. #OME_NGFF_Hackathon

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Joel Lüthi @joelluethi.bsky.social · 20/11/2024

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)

Hackathon group picture in the lecture room

Hackathon group picture in the restaurant (where not everyone fit on the picture unfortunately)

Josh Moore giving a talk at the hackathon

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Erick Ratamero @erickratamero.com · 11/11/2025

Been busy in Zürich für the last 24h or so. Talks have been great so far, and I have a talk too. Still find it weird to see my name on a poster.

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will-j-moore.bsky.social @will-j-moore.bsky.social · 11/11/2025

Morning run to explore Zurich and grab breakfast

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will-j-moore.bsky.social @will-j-moore.bsky.social · 11/11/2025

Some great talks on the first day of the #NGFF symposium in Zurich yesterday, including this lovely slide from Matthew Hartley, #ome-zarr

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David Stansby @dstansby.bsky.social · 04/11/2025

Today I'm announcing a new digital textbook 📖🖥️, "An Introduction to OME-Zarr for Big Bioimaging Data". ome-zarr-book.readthedocs.io

ome-zarr-book.readthedocs.io

An Introduction to OME-Zarr for Big Bioimaging Data

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Stephen Royle @steveroyle.bsky.social · 04/11/2025

I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way. quantixed.org/2025/11/04/a...

quantixed.org

Adventures in Code VII: getting started with napari – quantixed

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will-j-moore.bsky.social @will-j-moore.bsky.social · 31/10/2025

Another #OME-Zarr RFC, another implementation! Started a basic display of OME-Zarr Collections (RFC-8) in ome-ngff-validator at github.com/ome/ome-ngff...

Screenshot of ome-ngff-validator showing a hierarchy of OME-Zarr thumbnails in a Collection

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