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OME

@openmicroscopy.org

230 followers 3 following 28 posts

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

www.openmicroscopy.org

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OME @openmicroscopy.org · Dec 3

#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

The Open Microscopy Environment

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

openmicroscopy.org

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OME @openmicroscopy.org · Aug 6

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!

OME @openmicroscopy.org · Aug 6

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!

GitHub - IDR/idr0170-rose-mibitof

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

github.com

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OME @openmicroscopy.org · Aug 6

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

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OME @openmicroscopy.org · Aug 6

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.

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OME @openmicroscopy.org · Aug 6

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.

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OME @openmicroscopy.org · Aug 6

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...

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OME @openmicroscopy.org · Aug 6

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

IDR: Image Data Resource

idr.openmicroscopy.org

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OME @openmicroscopy.org · Aug 5

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.

The Open Microscopy Environment

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

www.openmicroscopy.org

OME @openmicroscopy.org · Jul 25

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).

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OME @openmicroscopy.org · Jul 10

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...

OME @openmicroscopy.org · Jun 19

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.

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OME @openmicroscopy.org · Jun 18

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

Reposted by OME

Josh Moore @joshmoore.bsky.social · Jun 11

🚀 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.pdf

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

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OME @openmicroscopy.org · Jun 10

🤩

German BioImaging @gerbi-gmb.de · Jun 10

"What #FAIR #RDM tools are available to you in your laboratory or facility?"

State of the #bioimaging #community captured during #ELMI2025 Core Facility Day

Photo of Stefanie Weidtkamp-Peters standing in front of a Slido presentation. There are many smaller answers to the question including "idk", "🤷", "USB stick", and similar but one large green word: "OMERO"

OME @openmicroscopy.org · Jun 4

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.

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OME @openmicroscopy.org · May 28

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 Forum

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

image.sc

Reposted by OME

Johannes Soltwedel @jo-soltwedel.bsky.social · May 12

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🔺:

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OME @openmicroscopy.org · May 9

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

OME @openmicroscopy.org · May 9

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...

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OME @openmicroscopy.org · May 9

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...

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Reposted by OME

Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Apr 8

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

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 ...

forms.gle

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Reposted by OME

Allen Institute @alleninstitute.org · Mar 3

🚗🧪 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

OME2025

Details for OME2025

www.bioimagingnorthamerica.org

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OME @openmicroscopy.org · Mar 5

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.

The Open Microscopy Environment

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

www.openmicroscopy.org

OME @openmicroscopy.org · Feb 21

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