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

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...

Scientific Data Visualization with Xarray and Napari - Earthmover Ian Hunt-Isaak Xarray Community Developer Tim Monko Neuroscience PhD & napari community manager This blog was also published on the xarray blog and the napari blog. TL;DR Making Napari and Xarray work...

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...

OME Transition-- Update Dear All- Over the past two decades, OME has grown into a vibrant and global community dedicated to developing open standards, tools, and resources for the management, sharing, and analysis of micros...

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 😍

Christian Tischer addresses the online participants of the EMBO Advanced methods in biomage analysis course before starting his tutorial on OME-Zarr.

Christian Tischer gets prepared to start his tutorial on OME-Zarr in front a full classroom.

Christian Tischer gives the first intructions to the onsite and the online participants of the EMBO Advanced methods in biomage analysis course for his tutorial on OME-Zarr.

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...

2025 OME-NGFF Workflows Hackathon | Notion Date: November 12th - 14th, 2025

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...

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets Barbiero et al., (2025). ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. Journal of Open Source Software, 10(109), 7882, https://doi.org/10.21105/joss.07882

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)

Screenshot of OMERO.web showing OME-Zarr import page

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...

Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland

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 🧵)

OME logo in Red Green and Blue, followed by At sign and letters MBL

#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/

YouTube video by SciPy Abdennur, Lekschas, & Manz - Bring your __repr__’s to life with anywidget | SciPy 2024

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube:

www.youtube.com/watch?v=frEo...

GitHub - IDR/idr0170-rose-mibitof Contribute to IDR/idr0170-rose-mibitof development by creating an account on GitHub.

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!

Interview: How a Hearing-Loss Grant Got Cut in the Fight Over DEI “It felt like the floor dropped out,” researcher Uri Manor said after the sudden suspension of his lab’s award.

undark.org/2025/07/11/i...