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.

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

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! 🤯

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...

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!

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/...

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/

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...

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.

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

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!

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...

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

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!

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...

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.

#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...

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]

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...

Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2) forum.image.sc/t/bigvolumeb...

So nice to see this!!!

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...

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

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)

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.

Morning run to explore Zurich and grab breakfast

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

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

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...

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...

Today, napari users can’t fully leverage Xarray’s labeled metadata, as slider names, units & dimensions often get out of sync. That’s changing. At SciPy 2025, napari, Xarray & CellProfiler devs began a collab to build true metadata-aware visualization across sciences. earthmover.io/blog/scienti...

The comedy Wildlife photography competition come at the perfect time each year www.comedywildlifephoto.com/gallery/fina...

If you've ever worked with OME things, it is worth reading this update from Jason Swedlow on image.sc about the evolving OME governance. The TL;DR is that an interim leadership team has been assembled and new governance structures are coming sooner rather than later. forum.image.sc/t/ome-transi...

Over at `ome-zarr-models` we're working on implementing support for the new coordinate systems too - here's an example of a transformation graph from multiple tiled images that can be transformed into a common "world" coordinate system. 🟥 ➡️ 🌎

Those sample datasets are public, so you can try them yourselfs. Links can also be found at github.com/ome/ome-ngff...

The #OME-Zarr RFC-5 proposal allows you to transform multiple images into the same coordinateSystem. Trying this out with napari at github.com/will-moore/n.... Cool that you can offset T-dimension as well as XYZ!

The connectome of the entire male Drosophila central nervous system is out!! Acquired using FIB-SEM @ 8x8x8nm, we aligned 7.5 mio 2D images aligned into one seamless 3D volume, which was used to segment & proofread neurons and synapses. @hhmijanelia.bsky.social www.biorxiv.org/content/10.1...

Very nice! Your Affine Transform blog post is really neat and just what I needed right now 👍 for #OME-Zarr RFC-5. I also want to try out marimo and Web Assembly 😍

Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org @tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev

Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...

hey bluesky 👋 visa hurdles mean I’m looking for opportunities outside the US. I’m a computational biologist (bacterial + phage genomics, postdoc in Koonin’s group @ NIH). I am interested in teaming up on funding apps. reach out if this resonates!

What to do if you have extraordinary size data but no extraordinary local memory? 😱 At the @grcib2025.bsky.social, @joshmoore.bsky.social addressed this issue in the talk “When Data Doesn’t Fit – A Bioimaging Story from Files to FAIR”. 👉 Interested? zenodo.org/records/1708...

Honoured to be featured - and even prouder of what the @bioimagearchive.bsky.social team is building together for the life sciences community.

From #ome-ngff-validator you can open open #OME-Zarr images in a bunch of viewers, and neuroglancer's rendering of multi-channel images just got a lot nicer: ome.github.io/ome-ngff-val... - See github.com/google/neuro...

new blog post: in which I talk (briefly) about getting a new job and moving back to Europe, getting a VPS, and self-hosting my code and my personal website. pages.erickratamero.com/personal-web...

You are an OME-Zarr developer yourself? Join us at the hackathon! Help push OME-Zarr towards 1.0, work on RFCs to the spec, contribute to tooling in Java or Python or build workflows using OME-Zarrs. Find out more & apply to the hackathon here: biovisioncenter.notion.site/2025-OME-NGF...

We’re excited to share that ez_zarr now supports Zarr v3! 🚀 Huge thanks to @mbstadler.bsky.social & @csoneson.bsky.social who took on the challenge of creating this open-source tool for fast, programmatic access to OME-Zarr file sets + easy plotting 📊 📄 joss.theoj.org/papers/10.2110… (1/3)

Currently working on #OMERO web-based import of public #OME-Zarr images github.com/ome/omero-we...

Poster Session at #CoRDI2025. Here is @joshmoore.bsky.social presenting how cloud-ready next-generation file formats like #OME-Zarr enable federated repositories with large N-dimensional arrays at peta-scale. #OME-NGFF @nfdi4bioimage.bsky.social Find the poster on C.A.R.L level 2 @rwth.bsky.social

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...