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#BioImage

1 post1 participant0 posts today
Public
c4r510

In this blog post at s.gwdg.de/m5Bu3L I showcase the #NFDI4BIOIMAGE (@nfdi4bioimage@nfdi.social, @nfdi4bioimage@bird.makeup) #knowledgegraph and its function as a registry for public #OMERO image data repositories and their respective #SPARQL endpoints. Annotated #bioimage data has become part of the #semanticweb. @joshmoore @Andrawaag #nfdi #metadata #KnowledgeGraphs #ontop #r2rml #rdf

SciComp BlogLinked Open Data for BioimagingThis post demonstrates the NFDI4BIOIMAGE Knowledge Graph (N4BIKG). Many aspects of this project are still very much in the flow including a consensus on which ontologies and terms to employ, how to define various namespaces and much more. These issues left aside, I focus on two components: First, the "core" KG contains information about the NFDI4BIOIMAGE consortium, it's participating institutions and people working in or for NFDI4BIOIMAGE, publications (via zenodo records submitted to the NFDI4BIOIMAGE community) and some more.
Public
c4r510

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
Public
multimeric

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
Public
RoedigerRG

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.

#rstats#bioinformatics#BioImage
Public
Helena Klara Jambor

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
Public
Guillaume Gay

Excellent resource to choose the correct repository to publish your #BioImage #data
in #EOSC and elsewhere:

zenodo-rdm.web.cern.ch/records

Thanks @EuroBioImaging !

ZenodoImage Repository Decision Tree - Where do I deposit my imaging dataDepositing data in quality data repositories is one crucial step towards FAIR (Findable, Accessible, Interoperable, and Reusable) data. Accordingly, Euro-BioImaging strongly encourages sharing scientific imaging data in established, thematic repositories.  To guide you in the selection of appropriate repositories, we have created an overview of available repositories for different types of image data, including their scope and requirements. This decision tree guides you through questions about your data and directs you to the correct repository, and/or provides instructions for further processing to meet the critera of the repositories.  Three seperate trees are provided for different classes of imaging data: open bioimage data, preclinical data, and human imaging data. 
Public
multimeric

> 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)

#java#bioinformatics#bioimage
Public
Albert Cardona

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
#microscopy#imaging#biology
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