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/
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.
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! 🤯
Fantastic work @joelluethi.bsky.social and the Fractal team! Q: I couldn't see the Supplementary Videos in the pre-print?
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!
Admins can now upload and update the OMERO.script (used for figure export) directly from the OMERO.figure app. github.com/ome/omero-fi...
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
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
Matt McCormick asking a question
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.
