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#BioImage

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Fabrizio Musacchio

To wrap this up: Both tools are easy to test. I highly recommend trying them on your own data to see what works best for your use case.

I’ll include #CellSeg3D in our next #Napari #bioimage analysis course (fabriziomusacchio.com/teaching). Curious what impressions and feedback the students will share. 🧪🔍

What I really like about @napari is how well it integrates modern #Python tools. Great to have such a flexible, evolving #opensource platform for (bio) #imageanalysis! 👌

c4r510

In this blog post at s.gwdg.de/m5Bu3L I showcase the (@nfdi4bioimage@nfdi.social, @nfdi4bioimage@bird.makeup) and its function as a registry for public image data repositories and their respective endpoints. Annotated data has become part of the . @joshmoore @Andrawaag

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.
NFDI4BIOIMAGE

Exiting news! 💥

We'll be attending the Helmholtz Imaging Conference in Potsdam, June 25-27.

Our @nfdi4bioimage Task Area Leader @haesleinhuepf from @unileipzig will present a keynote on "Large Language Models for #BioImage Data Science". In addition, Riccardo Massei from @ufz will offer a workshop on "Advances and challenges in zebrafish image and video analysis".

We are looking forward to meeting you there and to the exciting program!

👉 Registration: events.hifis.net/event/2061/ov

c4r510

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

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
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
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. 
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