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...

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

#microscopycommunity- do you use BioFormats, OMERO, OME-TIFF, OME-Zarr or are you interested in open source and microscopy? Then you should check out the recordings from OME2025! buff.ly/fgUxoQf @openmicroscopy.org @gerbi-gmb.de‬. @jacksonlab.bsky.social‬ @mblscience.bsky.social

🌟 #MeetOurDataSteward: #3: Riccardo Massei #DataSteward at NFDI4Bioimage and researcher @ufz.de. He makes high-content screening data FAIR and cloud-ready using #OMERO, #Python, #Galaxy, and #Jupyter. Questions? Get in touch! 👉https://nfdi4bioimage.de/about-us/data-stewardship-team/massei/

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube: www.youtube.com/watch?v=frEo...

For a list of the OME-Zarr images in idr0170, see github.com/IDR/idr0170-... where the metadata can be viewed in BioFile Finder (bff.allencell.org) - use Chrome!

It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇

New landing pages have landed for every study in the Image Data Resource (IDR)! Now, you can easily see clear details of the study - including how to download the data! To access the landing page for a study, just click on its thumbnail from the homepage (idr.openmicroscopy.org).

As good as a time as any to announce: After a great time at @poldresden.bsky.social I'm looking forward to starting my new position at @gerbi-gmb.de as a software developer for @openmicroscopy.org 🔬😀! Scalable #RDM solutions in the ome-zarr-verse, here we come!

#TiM2023 and #TiM2025 data is now publicly available! Find the data collected and annotated at the Trends in Microscopy conference in an OMERO-based framework introduced by I3D:bio '23 and extended in '25, supported by the @nfdi4bioimage.bsky.social data stewards. 👉 nfdi4bioimage.de/news/news-de...

FINALLY just released the @napari.org clusters-plotter 0.9.0 🤗 pypi.org/project/napa... The latest version comes with a complete overhaul of the entire codebase to make #microscopy data introspection and browsing even more accessible, intuitive and versatile! #bioimaging Let's have a look 👇🧪💻🔬

Michele Bortolomeazzi, Christian Schmidt and Jan-Philipp Mallm at @nfdi4bioimage.bsky.social have developed a new OMERO-web plugin: OMERO-vitessce. It enables the visualization of datasets hosted in #OMERO with the #Vitessce multimodal data viewer. Find the poster here: 👉 zenodo.org/records/1483...

"What #FAIR #RDM tools are available to you in your laboratory or facility?" State of the #bioimaging #community captured during #ELMI2025 Core Facility Day

@joshmoore.bsky.social presenting at #ELMI2025 about the #Bioimaging community's immense efforts to pave the way to OME-Zarr 1.0 - Stable cloud-readiness for bioimage data is getting real. Slides available in Zenodo: doi.org/10.5281/zeno... @gerbi-gmb.de @nfdi4bioimage.bsky.social

What a special atmosphere! #ELMI2025 Poster Session 1 on Helix A last night. The perfect environment to exchange with friends & colleagues about #bioimaging #RDM: - OMERO-vitessce - IO-FAST initiative - @nfdi4bioimage.bsky.social Data Stewardship Talks, Workshops & Poster Session 2 up ahead today!🔬

Great stimulating discussions about #bioimage data organization in #OMERO led by @tom-bssnnt.bsky.social from #i3dbio at #ELMI2025

Metadata & Standards Developer – FAIR Bioimaging We seek a developer to advance metadata standards for imaging data (e.g. OME-Zarr, NGFF) 📌 Schema design (JSON-LD, RDF, SHACL), FAIR principles, open dev 🤝 Work with RO-Crate, ELIXIR, RDA & global partners 🌍 Remote | TVöD 13–14 | Deadline: 30.06

🛠️ Job Alert: Project Coordinator (50-100%, fully remote) We're seeking a dynamic and proactive professional who's passionate about science, communication and community building to join and strengthen our management office team. Apply by 30 June 2025! Full posting: gerbi-gmb.de/resources/ca...

Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST! Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...

E11 Bio is launching Volara: an open-source Python library for block-wise processing of large volumetric microscopy datasets! 🧪🔬 Volara features block-wise task abstractions, making scalable image processing more accessible, robust, and repeatable. Read more: e11.bio/blog/volara

We invite you to our next #NFDITalk about "Cloud based image data science". 🗓️ 2 June, 4 PM – Online 🎤 Speakers: Josh Moore and Yi Sun #NFDI4BIOIMAGE ➡ Join the Zoom Meeting: www.nfdi.de/talks ➡ YouTube stream: www.youtube.com/live/bzfmE29... #NFDI #fdm #rdm #datascience #forschungsdaten

Secondly, which I think is very cool: You can now draw annotations in napari and upload them to OMERO. Hopefully this makes annotating large datasets a lot less painful! 💥 (Nevermind my shonky drawing - don't annotate like me 😄) Looking forward to feedback/bug reports: github.com/tlambert03/n...

New release: napari-omero 0.5.0 😀@openmicroscopy.org @napari.org thanks to some big contributions from @psobolewskiphd.bsky.social , @will-j-moore.bsky.social and of course @talley.codes. Some features in spotlight 👇 First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:

@nfdi4bioimage.bsky.social Data Steward Riccardo Massei presented an #OMERO framework for the management of image flow cytometry data at the @helmholtzhmc.bsky.social Conference to enable pollen classification. 🌿 More about Riccardo's research: www.researchgate.net/profile/Ricc...

More examples of @zarr.dev OME-Zarr data being used for cool stuff!

at pycon! wrote a bit about exceptions and borrowing good ideas from python for typescript on the plane today... trevorma.nz/blog/catch-e...

(almost) every talk from OME 2025 is now on YouTube! If you care about microscopy data and about open-source, you should definitely check them out. www.youtube.com/playlist?lis...