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#BioImage

1 post1 participant0 posts today

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

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.

Some time ago, we published our #biopixR package in #JOSS

social.anoxinon.de/@RoedigerRG

Now Tim @devTLB and I are working on our review as promised here.

social.anoxinon.de/@RoedigerRG

The good news is, we have done most of the work on it. Now we are just polishing the paper.

We will likely share a link to a preprint server. Let's see how things evolve.

Still amazed to have won this award! 🙌

All winners are devoted to #bioimage data, where spotting manipulation & teaching solutions is possible.

More tricky for numerical data: diverse types, summaries, complexity -> challenging to find errors/define trustworthy visuals. Lot's to do!

TOMORROW, NOV21
🏆 Meet&Greet with the winners of the #EinsteinFoundationAward
Elisabeth Bik
PubPeer's Brandon Stell,
Helena Jambor & Christopher Schmied (PixelQuality)

Register: einsteinfoundation.de/en/insig

Einstein-Stiftung BerlinMeet the winners – Einstein Foundation Berlin

> shadow.org.apache.tools.zip.Zip64RequiredException: archive contains more than 65535 entries.

It's ShadowJar time 😎

(cramming a Java codebase, all its Java dependencies, their transitive Java dependencies, their C++ dependencies, compiled C++ libraries and machine learning models into one Jar archive for some reason that remains unknown to me)

Course on "Quantitative Imaging: From Acquisition to Analysis"

Application deadline: January 31st

Course dates: April 1-16

Location: Cold Spring Harbor

Instructors: Jennifer Waters, @bethcimini @florianjug Hunter Elliott, Talley Lambert, Suliana Manley.

Financial aid is available to help offset tuition costs.

meetings.cshl.edu/courses.aspx

meetings.cshl.edu Quantitative Imaging: From Acquisition to Analysis 2024 | CSHL Cold Spring Harbor Meetings and Courses - Long Island, New York. Scientific Conferences and Courses For Research and Education