#omero

2025-05-22

Highlights from the Helmholtz Metadata Collaboration (HMC) Conference 🔬

@nfdi4bioimage Data Steward Riccardo Massei from @ufz presented a data management framework using #OMERO for handling image flow cytometry data. Using key-value metadata pairs and integrating #Jupyter with #Galaxy workflows enables pollen classification and demonstrates a powerful experimental pipeline for better understanding pollen ecology.🌿

Read more about Riccardo's research: researchgate.net/profile/Ricca

2025-05-20

Efficient, standards-based #bioimaging data management is essential for research and data reuse. Join @nfdi4bioimage's presentation about “A Journey to #FAIR Bioimage Data,” a contribution to @ells_heidelberg's STANDFLOW project webinar series:

🗓️July 2, 2025 | 02:30–03:30 pm | Online & Free

✅ Local data management: #OMERO & beyond
✅ Annotation: metadata, ontologies, REMBI
✅ Linking images with protocols & results
✅ Cloud storage: ome.zarr
✅ Data publication

👉 Register: ebi.ac.uk/training/events/jour

2025-05-14

#FAIR workflows for image data management! 🧬

As part of @nfdi4bioimage, Riccardo Massei and colleagues showcases how to build workflows with different Workflow Management Systems (WMS) to upload and annotate #HCS image data into #OMERO.

Their goal: to make large scientific imaging datasets FAIR and machine-readable with minimal effort-enabling greater reproducibility and research quality.

👉 Curious how it works? Check out the publication: nature.com/articles/s41598-025

2025-03-13

‪Trends in Microscopy #TiM2025 is starting soon!

If you were lucky to secure a ticket, you'll love the talks & workshops. Great opportunity to learn more about bioimaging #RDM from
@nfdi4bioimage , @i3dbio &
@EuroBioImaging.

There is even an #OMERO server on site! Excited? So are we! 😍

Picture by @GerBI

2025-02-21

My #SPARQL query of the day: List all known organisms in the #uniprot taxonomy database for which the donor of a sample depicted in #OMERO
is a host. Promptly answered
by federating local #OMERO Virtual Knowledge Graph and sparql.uniprot.org/sparql. I love it. CC: @nfdi4bioimage @joshmoore #NFDIrocks.

Screenshot showing the QLever SPARQL query editor, a federated query against the OMERO Knowledge Graph and the Uniprot SPARQL endpoint. Results show the OMERO well number, the taxon annotation, the corresponding scientific name and scientific names of hosted organisms.
2025-01-17

@c4r510

This is so exciting, C! Looking forward to querying #OMERO more.

cc: @Andrawaag

2025-01-17

Linking metadata in electronic lab notebook #OpenBIS with metadata in the
#bioimage resource #Omero: How many images are present in omero for a given sample in OpenBIS?
At #mpievolbio, to answer this and similar questions,
we map both resources to #RDF #KnowledgeGraphs using the #ontop framework,
serve the materialized #KGs via #qLever (qlever.cs.uni-freiburg.de) and run a #SPARQL query. Answered in no time! @nfdi4bioimage #LinkedOpenData #FAIR #MicrobialPopulationBiology @ontop

sparql query and response against a knowledge graph for microbial population biology
2025-01-03

I'm bamboozled by OMERO's APIs.

There seems to be an XML model, a Java (slice? blitz?) API that wraps the XML, a Python wrapper for that Java model (omero.model), an official high-level wrapper for that Python wrapper (omero.gateway), and a third party wrapper for that wrapper (ezomero). Then there's also a JSON API.

#ome #bioimage #omero

2024-12-10

Increasing interoperability of bioimage dataset resources is the main goal of @nfdi4bioimage'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.

2024-12-10

Collaborative Research Centers (SFBs) rely on INF projects for harmonized #RDM. At the recent DINI workshop, K. Krooß shared insights from @nfdi4bioimage.bsky.social. On top, S.Kunis showcased I3D:bio's work highlighting #OMERO’s role in SFB 1557. A great platform for exchanging RDM best practices!

2024-08-16

#Achille e #Patroclo da #Omero alla #Miller

Achille e Patroclo. Insieme per sempre di Andrea #Baserga è un bel saggio nel quale si ricostruisce la relazione tra i due mitici eroi greci.

➡️ paroleglbt.info/2024/08/achill

#️⃣ #Letteratura #Grecia #Mitologia #LGBT

2024-04-30

A 2-day intensive workshop on #FAIR data with structured annotations in #OMERO comes to an end. We enjoyed very much the lively & inspiring discussions from & with the participants who created a lovely atmosphere in this online workshop. 🙏 @nfdi4bioimage.bsky.social @i3dbio #OER material to follow.

2024-04-26

OME's next Annual Community Meeting is May 29-31, 2024 in sunny Dundee!!! Spend 2 days with the community talking all things #OMERO, #OMEZarr, and public bioimage #FAIRdata resources. More info and registration:

openmicroscopy.org/events/ome-

2024-04-22

Today I shut down my #OMERO server.

I have been using it since ~2009 to store and manage all my #microscopy data from my PhD, my first postdoc, and my second postdoc. It holds ~115 GB of images, mostly of cultured human cells in mitosis and larval fly brains.

But it didn’t get any new data since March 2021, when upon finishing my second postdoc I left the bench behind to become a #biocurator. For the past three years, I kept maintaining it, upgrading the server to stay up-to-date with the latest versions.

But as it now quite clear to me that I will most likely not go back to being a wet lab scientist in the near or even not-so-near future (I love my #biocuration job too much), I couldn’t justify to myself the time spent in maintaining a server that I would most likely never use again.

So, I took a final dump of the database, a snapshot of the directory containing the raw images (all 115 GB of them), stored that away, and then shut down the server and removed any trace of it from my machine.

After three years, the last page of my former life as a wet lab scientist is finally turned.

2024-03-18

Are you using #OMERO for bioimage data management and want to get more out of your annotations?
Join our workshop about how to leverage structured metadata in OMERO to benefit image analysis and data publication.

Two-day online workshop on April 29th & 30th
Jointly organized by @i3dbio & @nfdi4bioimage
⬇️
gerbi-gmb.de/i3dbio/i3dbio-tea

2024-03-11

You missed us at #GerBI-GMB Community Meeting in Fulda?
Find here our poster with useful links on microscopy image data management and training material for #OMERO and #metadata. #openaccess #OER #FAIR
zenodo.org/doi/10.5281/zenodo.

2024-03-07

This week, we were at #GerBI-GMB Community Meeting in Fulda discussing bioimage #RDM with the German community of microscopy experts. Thank you for the interest, the exciting exchange about I3D:bio's and our partner project's activities, and the stimulating discussions and ideas from the community.
@nfdi4bioimage #OMERO

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