OME

BioFile Finder allows the browsing of image thumbnails which enables launching of images in full view via a range of image viewers. We hope this is useful!

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!

Example idr0170 image shown in OME-NGFF-Validator: ome.github.io/ome-ngff-val...

This public object storage access without a server is highly scalable, allowing IDR to support more users while continuing to make the data searchable and browsable through the IDR server. IDR is now increasingly requesting that all new submissions to IDR convert their data into OME-Zarr format.

This is the first study in IDR where the OME-Zarr images are loaded in OMERO using the omero-zarr-pixel-buffer extension. The data is hosted on public object storage and can be accessed directly by the many tools and viewers that support the cloud-optimised OME-Zarr format.

Idr0170: Released ahead of its publication - Imaging Mass Cytometry Dataset of Small-Cell Lung Cancer tumors and tumor microenvironments by Rose et al. Images in idr0170 are OME-Zarrs converted by the submitter.
idr.openmicroscopy.org/search/?quer...

New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.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.

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.

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).

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...

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.

On the #globalbioimaging course globalbioimaging.org/internationa... at IISER Pune, India, the discussions go on after the talk about Microscopy Facility Data Management strategies.

Screenshot of the PDF available at https://cloud.gerbi-gmb.de/s/6LrYfMByymPnHP5/download/2025_OME-Zarr_sw_developer.pdf

Screenshot of the PDF available at https://cloud.gerbi-gmb.de/s/y4rBGFM6dXn8Jkr/download/2025_OME-Zarr_web_developer.pdf

🚀 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...

🤩

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.

Image.sc Forum Scientific Community Image Forum is a discussion forum for scientific image software sponsored by the Center for Open Bioimage Analysis (COBA).

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.

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🔺:

3. Gene expression data from onlinelibrary.wiley.com/doi/10.1111/... by Alzu'bi et al.
idr.openmicroscopy.org/search/?quer...

2. A morphology and secretome map of pyroptosis from the recently published www.molbiolcell.org/doi/10.1091/... by Lippincott et al.
idr.openmicroscopy.org/search/?quer...

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...

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 ...

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

OME2025 Details for OME2025

🚗🧪 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

The Open Microscopy Environment A consortium of universities, research labs, industry and developers producing open-source software and format standards for microscopy data.

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.

2. Large-scale hyperspectral #electronmicroscopy data from www.nature.com/articles/s44... by Duinkerken et al.
idr.openmicroscopy.org/search/?quer...

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...

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

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

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

🎉 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: https://buff.ly/3C3OwYw

Want to help build the future of #bioimaging software?