OME
@openmicroscopy.org
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/
https://www.openmicroscopy.org/
Pinned
OME
@openmicroscopy.org
· Dec 3
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
#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
Two new protein localization studies available in the Image Data Resource (IDR, idr.openmicroscopy.org).
November 21, 2025 at 10:18 AM
Two new protein localization studies available in the Image Data Resource (IDR, idr.openmicroscopy.org).
New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).
IDR: Image Data Resource
idr.openmicroscopy.org
August 6, 2025 at 4:28 PM
New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).
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.
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
August 5, 2025 at 3:37 PM
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.
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).
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).
July 25, 2025 at 9:03 AM
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).
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...
An embryonic patterning study from elifesciences.org/articles/78902 by Clark et al.
idr.openmicroscopy.org/search/?quer...
July 10, 2025 at 3:23 PM
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...
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.
June 19, 2025 at 12:48 PM
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.
June 18, 2025 at 1:12 PM
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
🚀 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...
💻 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...
June 11, 2025 at 8:26 AM
🚀 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...
💻 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...
🤩
"What #FAIR #RDM tools are available to you in your laboratory or facility?"
State of the #bioimaging #community captured during #ELMI2025 Core Facility Day
State of the #bioimaging #community captured during #ELMI2025 Core Facility Day
June 10, 2025 at 1:43 PM
🤩
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.
June 4, 2025 at 10:15 AM
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.
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.
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
May 28, 2025 at 3:11 PM
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.
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.
Reposted by OME
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🔺:
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
May 12, 2025 at 11:16 AM
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🔺:
First: napari-omero now supports lazy loading of image pyramids from OMERO🔺:
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...
1. 3D-SIM data from www.nature.com/articles/s41... by Szabo et al.
idr.openmicroscopy.org/search/?quer...
May 9, 2025 at 3:30 PM
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...
1. 3D-SIM data from www.nature.com/articles/s41... by Szabo et al.
idr.openmicroscopy.org/search/?quer...
Reposted by OME
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
April 8, 2025 at 2:32 PM
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
Reposted by OME
🚗🧪 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
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
March 3, 2025 at 6:07 PM
🚗🧪 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
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
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.
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
March 5, 2025 at 4:18 PM
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.
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...
idr.openmicroscopy.org/search/?quer...
February 21, 2025 at 3:37 PM
2. Large-scale hyperspectral #electronmicroscopy data from www.nature.com/articles/s44... by Duinkerken et al.
idr.openmicroscopy.org/search/?quer...
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...
1. Light sheet fluorescence microscopy of Tribolium castaneum embryos from journals.biologists.com/dev/article/... by Strobl et al.
idr.openmicroscopy.org/search/?quer...
February 21, 2025 at 3:36 PM
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...
1. Light sheet fluorescence microscopy of Tribolium castaneum embryos from journals.biologists.com/dev/article/... by Strobl et al.
idr.openmicroscopy.org/search/?quer...
Reposted by OME
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/t/ngff-0-5-r...
#NGFF #BioImaging #Formats
@openmicroscopy.org @zarr.dev
January 28, 2025 at 3:42 PM
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/t/ngff-0-5-r...
#NGFF #BioImaging #Formats
@openmicroscopy.org @zarr.dev
Reposted by OME
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
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 - 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
github.com
January 9, 2025 at 8:53 PM
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
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
Reposted by OME
🎉 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
- 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
January 9, 2025 at 4:28 PM
🎉 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
- 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?
🚀 We're hiring! Join the German BioImaging Team as a Software Developer!
💻 Build scalable #bioimaging solutions
🌍 Collaborate globally
🎯 Contribute to open science through #OMEZarr @openmicroscopy.org
Remote, full-time. Apply by 31 Jan 2025: bit.ly/3Zrd4SR
💻 Build scalable #bioimaging solutions
🌍 Collaborate globally
🎯 Contribute to open science through #OMEZarr @openmicroscopy.org
Remote, full-time. Apply by 31 Jan 2025: bit.ly/3Zrd4SR
Software Developer Wanted – Join the German BioImaging Team!
German BioImaging e.V. invites applications by 31. January for a remote position as
Software Developer (m/f/d)
(100 %, pay grade 13-14 TVöD depending on experience)
Are you an enthusiastic open-...
bit.ly
December 18, 2024 at 7:25 PM
Want to help build the future of #bioimaging software?
Reposted by OME
🚀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.
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.
Walkthrough — OMERO guide latest documentation
omero-guides.readthedocs.io
December 17, 2024 at 4:44 PM
🚀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.
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.
Reposted by OME
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!
December 13, 2024 at 2:09 PM
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!
Reposted by OME
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...
🔬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...
Report from the Helmholtz Metadata Collaboration Conference (HMC) 2024
Galaxy imaging and RDM workflows were presented at the HMC 2024
galaxyproject.org
November 13, 2024 at 3:31 PM
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...
🔬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...