Sign in

OME

@openmicroscopy.org
293 followers 4 following 38 posts

OME is a consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data. www.openmicroscopy.org

PostsRepliesMedia
Reposted by OME
Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026
🚨New release: NGFF specification 0.6 🚨 Last week, we formally released the latest version of the NGFF specification: 0️⃣.6️⃣( ngff.openmicroscopy.org/specificatio...) Let's take a small tour through the things possible with #ome-zarr 0.6 now that this is out! 👇
ngff.openmicroscopy.org
Version 0.6 — NGFF documentation
12310
Reposted by OME
Johannes Soltwedel @jo-soltwedel.bsky.social · 03/07/2026
There are bound to be more 🤯-kind of use cases waiting to be implemented and published. Follow us on the image.sc dev thread forum.image.sc/t/ngff-weekl... for information about cool datasets, upcoming implementations across the @openmicroscopy.org OME-verse and get in touch 👉
forum.image.sc
NGFF weekly dev update thread
Done and dusted: 🎁 ngff specification 0.6 🥳 (rc0) Alright, everyone here it is: I just released the ngff specification 0.6(rc0) 🤔 ...Why rc0? Ultimately, we need to abide by the results and constrai...
041
OME @openmicroscopy.org · 03/05/2026
#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! 🤩
094
OME @openmicroscopy.org · 31/03/2026
Two new studies available in the Image Data Resource (IDR, idr.openmicroscopy.org). Plus, IDR welcomes a new organism - the African green monkey!
idr.openmicroscopy.org
IDR: Image Data Resource
100
OME @openmicroscopy.org · 20/03/2026
One week left for the OME2026 Community Survey! 📣 If you haven't filled it out, please do so. We'll be discussing it live at the #OME2026 meeting in April. bit.ly/ome2026-comm...
bit.ly
OME 2026 Community Survey
This year in April, the 19th OME Community Meeting will be gathering to determine the "Future and Governance of OME" during the final meeting day's guided Discussion Forum / "Unmeeting". This survey...
023
Reposted by OME
Josh Moore @joshmoore.bsky.social · 11/03/2026
Help shape the future of @openmicroscopy.org! 🔮 The OME 2026 community survey is open—tell us what’s working, what isn’t, and what you'd like to see next. Takes just a few minutes 👇 forum.image.sc/t/ome-2026-c...
forum.image.sc
OME 2026 Community Survey
Calling all OME Community members, contributors, and lurkers! This year in April, the 19th OME Community Meeting will be gathering to determine the "Future and Governance of OME" during the final mee...
01311
Reposted by OME
Josh Moore @joshmoore.bsky.social · 12/03/2026
Excited to see direct streaming of @openmicroscopy.org @zarr.dev datasets in #syGlass! Exploring huge images without upfront download is just what we’ve been working toward with cloud-optimized formats. Great to have tools connecting the ecosystem of imaging repositories, now including VR 🙌
0133
OME @openmicroscopy.org · 26/02/2026
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/
1166
OME @openmicroscopy.org · 15/01/2026
Dear all Today we are releasing Bio-Formats 8.4.0 which includes a new file format as well as several fixes and improvements. The full list of changes included in this release is on www.openmicroscopy.org/2026/01/15/b... Please use image.sc in case of questions or problems.
openmicroscopy.org
010
OME @openmicroscopy.org · 21/11/2025
Two new protein localization studies available in the Image Data Resource (IDR, idr.openmicroscopy.org).
100
OME @openmicroscopy.org · 06/08/2025
New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).
idr.openmicroscopy.org
IDR: Image Data Resource
163
OME @openmicroscopy.org · 05/08/2025
Dear all Today we are releasing Bio-Formats 8.3.0 which includes several fixes and improvements. The full list of changes included in this release are on www.openmicroscopy.org/2025/08/05/b.... Please use image.sc in case of questions or problems.
openmicroscopy.org
The Open Microscopy Environment
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
020
OME @openmicroscopy.org · 25/07/2025
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).
151
OME @openmicroscopy.org · 10/07/2025
New study released in the Image Data Resource (IDR, idr.openmicroscopy.org) today! An embryonic patterning study from elifesciences.org/articles/78902 by Clark et al. idr.openmicroscopy.org/search/?quer...
010
OME @openmicroscopy.org · 19/06/2025
The #globalbioimaging couse at IISER Pune continued with an intense and well-received OMERO workshop part 1. The parts 2 and 3 of the OMERO workshoop to come tomorrow.
141
OME @openmicroscopy.org · 18/06/2025
On the #globalbioimaging course globalbioimaging.org/internationa... at IISER Pune, India, the discussions go on after the talk about Microscopy Facility Data Management strategies.
010
Reposted by OME
Josh Moore @joshmoore.bsky.social · 11/06/2025
🚀 We’re hiring again! Join @gerbi-gmb.de as a Software Developer! 💻 Build scalable #bioimaging solutions 🌍 Collaborate globally 🎯 Contribute to open science through #OME #Zarr 📣 Tell your #NGFF friends. Remote, full-time. Apply by 30 June 2025: All submissions via bit.ly/gerbi-jobs-2...
Screenshot of the PDF available at https://cloud.gerbi-gmb.de/s/6LrYfMByymPnHP5/download/2025_OME-Zarr_sw_developer.pdfScreenshot of the PDF available at https://cloud.gerbi-gmb.de/s/y4rBGFM6dXn8Jkr/download/2025_OME-Zarr_web_developer.pdf
01710
OME @openmicroscopy.org · 10/06/2025
🤩
000
OME @openmicroscopy.org · 04/06/2025
On #ELMI2025 an ad-hoc Question&Answer session on OMERO went very well, lively discussion with lot of tips on finding the optimal path to successful OMERO adoption in an Institution.
051
OME @openmicroscopy.org · 28/05/2025
Dear all Today we are releasing Bio-Formats 8.2.0 which includes several fixes and improvements. The full list of changes included in this release are on www.openmicroscopy.org/2025/05/28/b.... Please use image.sc in case of questions or problems.
image.sc
Image.sc Forum
Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).
030
Reposted by OME
Johannes Soltwedel @jo-soltwedel.bsky.social · 12/05/2025
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🔺:
13210
OME @openmicroscopy.org · 09/05/2025
Take a look at the three new studies released in the Image Data Resource (IDR, idr.openmicroscopy.org). 1. 3D-SIM data from www.nature.com/articles/s41... by Szabo et al. idr.openmicroscopy.org/search/?quer...
120
Reposted by OME
Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/04/2025
If you train people in ImageJ, Fiji, whatever, even if it isn't your day job, please let us know, and please share this post! Thanks a ton, we really appreciate it. (2/2) forms.gle/C8dUpg8qZkbD... #bioimaging #microscopy #bioimageanalysis
forms.gle
Open Source Bioimage Analysis Training Survey
We are attempting for a publication to estimate the number of biologists who have attended a tutorial or training course in open source bioimage analysis (especially user friendly tools, but anything ...
13242
Reposted by OME
allen institute @alleninstitute.org · 03/03/2025
🚗🧪 We're coming to the East Coast! We're proud to be a part of the @openmicroscopy.org Environment Community Meeting at @mblscience.bsky.social on Apr. 28 to May 1. 🎟️ Register by Mar. 17 to join us in person: www.bioimagingnorthamerica.org/events/ome-2... @bioimagingna.bsky.social
bioimagingnorthamerica.org
OME2025
Details for OME2025
1133
OME @openmicroscopy.org · 05/03/2025
Dear all Today we are releasing Bio-Formats 8.1.1 which includes several fixes and improvements. The full list of changes included in this release are on [the openmicroscopy website](www.openmicroscopy.org/2025/03/05/b...). Please use image.sc in case of questions or problems.
openmicroscopy.org
The Open Microscopy Environment
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
020
OME @openmicroscopy.org · 21/02/2025
2. Large-scale hyperspectral #electronmicroscopy data from www.nature.com/articles/s44... by Duinkerken et al. idr.openmicroscopy.org/search/?quer...
000
OME @openmicroscopy.org · 21/02/2025
Take a look at the two new studies released in the Image Data Resource (IDR, idr.openmicroscopy.org). 1. Light sheet fluorescence microscopy of Tribolium castaneum embryos from journals.biologists.com/dev/article/... by Strobl et al. idr.openmicroscopy.org/search/?quer...
011
Reposted by OME
Josh Moore @joshmoore.bsky.social · 28/01/2025
And now, support for Zarr v3 & sharding is released as an OME-Zarr specification! 🎉 forum.image.sc/t/ngff-0-5-r... #NGFF #BioImaging #Formats @openmicroscopy.org @zarr.dev
forum.image.sc
NGFF 0.5 Release with support for Zarr v3 & shards! 🎉
Dear @ngff community– After a significant hiatus in NGFF releases, I’m pleased to announce the NGFF 0.5 specification with support for Zarr v3! 🎉 https://ngff.openmicroscopy.org/0.5/ After an inten...
0218
Reposted by OME
DANDI Archive @dandiarchive.org · 09/01/2025
DANDI now supports embargoing Zarr-based data! Zarrs (@zarr.dev) are cloud-optimized for N-dimensional arrays. Zarr v3 adds sharding to reduce file counts. Check out @openmicroscopy.org's OME-Zarr challenge to generate 1 PB of v3 data: github.com/ome/ome2024-ngff-challenge
github.com
GitHub - ome/ome2024-ngff-challenge: Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data - ome/ome2024-ngff-challenge
062
Reposted by OME
Zarr @zarr.dev · 09/01/2025
🎉 Zarr-Python 3 is here! 🎉 - Full support for Zarr v3 spec - Chunk-sharding for more efficient data storage - Major performance boosts with async I/O & parallel compression 💻 pip install --upgrade zarr 💻 conda install --channel conda-forge zarr Blog post: buff.ly/3C3OwYw
25520
OME @openmicroscopy.org · 18/12/2024
Want to help build the future of #bioimaging software?
050
Reposted by OME
Tom Boissonnet @tom-bssnnt.bsky.social · 17/12/2024
🚀My rework of the annotation scripts is now officially part of OMERO.scripts 🚀 github.com/ome/omero-sc... Follow the guide to get started with them: omero-guides.readthedocs.io/en/latest/sc... Many thanks to @will-j-moore.bsky.social @openmicroscopy.org and all the Beta Testers.
omero-guides.readthedocs.io
Walkthrough — OMERO guide latest documentation
084
Reposted by OME
will-j-moore.bsky.social @will-j-moore.bsky.social · 13/12/2024
OMERO.figure 7.2.0 just released with lots of new features, including "live" interactive inset panels, panel borders, HiLo checkbox, panel flipping, ROI Fill-Colour, ROI Points... Full list at github.com/ome/omero-fi... Thanks to @tom-bssnnt.bsky.social, Rémy Dornier, Tehmina Enayat & Jens Wendt!
32310
Reposted by OME
Galaxy Project @galaxyproject.bsky.social · 13/11/2024
At HMC 2024, Galaxy showcased how its platform advances FAIR bioimaging workflows: 🔬Building FAIR pipelines for metadata annotation 💡Integrating OMERO for seamless image analysis & metadata enrichment 🔧Combining image processing & data management in one workflow galaxyproject.org/news/2024-11...
galaxyproject.org
Report from the Helmholtz Metadata Collaboration Conference (HMC) 2024
Galaxy imaging and RDM workflows were presented at the HMC 2024
031
Reposted by OME
NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 10/12/2024
Increasing interoperability of bioimage dataset resources is the main goal of @nfdi4bioimage.bsky.social's project at the 3rd #de.NBI #BioHackathon in Kassel - already in full swing. A great opportunity to develop ideas and solutions #RDF #IDR #OMERO #RO-crate and lots of fun hacking for FAIR data.
092
Reposted by OME
Josh Moore @joshmoore.bsky.social · 06/12/2024
See the things you miss if you’re not on #BlueSci… #Galaxy 🤝 #OMERO
011
OME @openmicroscopy.org · 06/12/2024
The one-day OMERO workshop given as a part of the Imaging course organized by CEITEC - Central European Institute of Technology, Brno, just ended. Very intesive workshop with lively discussions about IDR metadata and OMERO.figure.
131
Reposted by OME
Aafke Gros @aafkegros.bsky.social · 20/11/2024
Messing around with the new #Blender 4.3 volume scatter modes with #microscopynodes, while at the #OME #Zarr hackathon! 😁🤩 Great info and work on the upcoming features of Zarr here :D Transforms, collections, and more! 🙏
0287
OME @openmicroscopy.org · 03/12/2024
#OME is now verified on @bsky.app! Follow to find out more about #Bio-Formats, #OMERO, #OME-TIFF, #OME-Zarr, #IDR, and much, much more. openmicroscopy.org
openmicroscopy.org
The Open Microscopy Environment
A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.
0227
Reposted by OME
will-j-moore.bsky.social @will-j-moore.bsky.social · 28/11/2024
Beautiful image of chick embryo from idr0066 in @zarr.dev v3 format (OME-Zarr 0.5) viewed in vizarr hms-dbmi.github.io/vizarr/?sour.... One of a bunch we just added to idr.github.io/ome-ngff-sam...
151
OME @openmicroscopy.org · 27/11/2024
The recent OMERO.server 5.6.14 release included a bunch of new Look-up tables listed at github.com/ome/openmicr... to add to a growling list! Thanks to Tom Boissonnet and @gerbi.bsky.social
163
Reposted by OME
will-j-moore.bsky.social @will-j-moore.bsky.social · 26/11/2024
The OME team just released OMERO.iviewer 0.15.0 which includes mobile-friendly layout on small screens github.com/ome/omero-iv...
Screenshot of OMERO.iviewer with column layout on mobile device
072