If you would like to attend a microscopy or bioimage analysis training course in the next 6 months but don’t have funding, check out our Microscopy Training Grant from @J_Cell_Sci and @focalplane_jcs.

Next deadline: 6 June 2025

https://www.biologists.com/grants/jcs-focalplane-training-grants/

#Microscopy #BioimageAnalysis #Bioimage #Biology #Training #Grants

Some time ago @devTLB and I announced that we work on a review about #rstats packages for #bioimage informatics. We think it is fairly complete now.

We would be happy to get some feedback before we submit it.

Here is the link to the draft:

[Update: Copy on Codeberg]
https://codeberg.org/devSJR/Bioimage/src/branch/main/RImageReview.pdf

#Bioinformatics

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: https://events.hifis.net/event/2061/overview

A gentle reminder that the deadline for registration to the True Image Deconvolution, Restoration, and Analysis Workshop is today. The workshop is virtual and free of charge.

#Bioimage #Analysis #Microscopy #Euro-Bioimaging #PSF

We're once again hiring a summer (+?) #bioimage #bioimageanalysis #software intern! Due to requirements of the funding program, you must be a current student, as well as work onsite in MA (+ have US work permission). Details at the link below. Spend your summer making great tools with fun people!

Software engineering intern - ...

Want to make your training materials #FAIR & impactful?🤔

Join the @skills4eosc & @atrium_eu webinar "Making Training Materials Matter: Introducing the FAIR-by-Design Methodology" on March, 14 and then contribute to the development of new #FAIR #bioimage #RDM training resources!

Already community-driven and #FAIR training materials from @nfdi4bioimage can be found here: https://nfdi4bioimage.github.io/training/readme.html

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 (https://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.

#ome #bioimage #omero

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

https://social.anoxinon.de/@RoedigerRG/113340746869808933

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

https://social.anoxinon.de/@RoedigerRG/112773962698337008

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

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: https://www.einsteinfoundation.de/en/insights/events/award/meet-the-winners

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

https://zenodo-rdm.web.cern.ch/records/13945179

Thanks @EuroBioImaging !

New from a huge cast of amazing #bioimage analysts in the Journal of Cell Science - "The crucial role of bioimage analysts in scientific research and publication" journals.biologists.com/jcs/article/... . Hop into 🧵to learn more! (1/x) #bioimaging #microscopy #bioimageanalyst

The crucial role of bioimage a...

Winners of the 2024 WEHI Art of Science Exhibition were announced! You can see the whole gallery here: https://www.wehi.edu.au/art-of-science/2024/

I love this exhibition every year, and it's interesting that this year, the Still Image winner (pictured) was of the Cryo EM mist generator and not biological tissue.

#biology #bioimage #cryoem

Want to use #Python for #imageanalysis? Join the eRImote training course: "Intro to #BioImage Analysis for Life Scientists" organised by #EuroBioImaging Nodes.

🗓️Oct. 7-9

📍Sweden, France, Portugal

Innovative format w/common lectures & on-site experts.

Register⤵️

https://eurobioimaging.eu/events/intro-to-bioimage-analysis-with-python-for-life-scientists-a-distributed-in-person-training-course/

What role does NFDI play for different disciplines? Our series continues with Stefanie Weidtkamp-Peters of @nfdi4bioimage

ℹ NFDI4Bioimage works on building an infrastructure of bioimaging data and supporting researchers in handling, storing, reusing and sharing data.

💡 More about NFDI4Bioimage: https://lnkd.in/eB3VFQrv

ℹ Learn more about the NFDI consortia https://lnkd.in/ejvBb7mu

#fdm #rdm #nfdi #bioimage #researchdata

Hey! We are organizingg a #bioimage analysis #challenge!

Try your skills!!

https://focalplane.biologists.com/2024/02/26/will-your-algorithm-be-the-best-for-this-new-image-data-challenge/

> 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

#FijiSc being prepped to run on #Java 21: give it a try and please report any issues. See the post by Curtis Rueden at the image forum:
https://forum.image.sc/t/jaunch-a-new-java-launcher-test-fiji-with-java-21/92058/1

#java21 #ImageProcessing #Bioimage

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.

https://meetings.cshl.edu/courses.aspx?course=C-QICM&year=24

#microscopy #imaging #biology #bioimage

Do you have a #bioimage #analysis question?

Then bring it to the "Image.sc LIVE! around the world" event and a panel of image analysts will be available, live, to answer your questions and provide #ImageAnalysis support and suggestions.

January 18th (Europe, Africa, Americas)-19th (Asia, Aus, NZ) via GatherTown. Exact timetable TBA.

For more information, visit:
https://forum.image.sc/t/image-sc-live-around-the-world/89596