@will-j-moore.bsky.social
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...)
🚨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
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...
OME-NGFF Hackathon March 2026 — CCP in vEM
ccp-volumeem.ac.uk
Our omero-biofilefinder app is now available at github.com/ome/omero-bi..., so you can open your OMERO data in BioFile Finder
GitHub - ome/omero-biofilefinder: OMERO.web plugin for opening data in BioFile Finder
OMERO.web plugin for opening data in BioFile Finder - ome/omero-biofilefinder
github.com
Rita Strack@ritastrack.bsky.social · 2mo agoIf you love imaging metadata, do I have something for you -- Search, organize, aggregate and share image data with BioFile Finder (BFF) | Nature Methods share.google/9UxsAcpaWhbu...
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
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...
#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! 🤩
NFDI4BIOIMAGE@nfdi4bioimage.bsky.social · 3mo ago#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!
#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!
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. 📜💬🗨️
now @will-j-moore.bsky.social and the new developments in ome-zarr.js github.com/BioNGFF/ome-... #OME2026
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
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.
Image Cooperative@image.coop · 4mo agoOur first project is live. ✨ With support from @biohub.org, @image.coop is coordinating work across the #OMEZarr community to help move the standard toward 1.0—supporting both implementation and the coordination needed to get there. More details in our latest post: image.coop/blog/posts/2...
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
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/
OMERO.figure
ome.github.io
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
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.
Image Cooperative@image.coop · 5mo agoHello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
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! 🤯
Brandy A Freitas@brandy-syglass.bsky.social · 5mo agoStreaming OME-Zarr data directly into syGlass for #3DThursday🌍🔬 With #syGlass v2.6.0, datasets can stream from disk, S3, or HTTPS with no massive downloads required. Huge thanks to the community building open imaging standards: @openmicroscopy.org #OMEZarr #Microscopy #OpenScience #Bioimaging
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
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...
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...
gerbi-gmb.de
Won best thesis award with this video! 4 years of research and play in 3 minutes :') youtu.be/so0fPlK1-LM
Smart microscopy, computer vision, and controlling cells with light -- my PhD thesis in 3 minutes
YouTube video by Pertz Lab
youtu.be
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!
