#Bioimage

2025-06-17

Looking forward to the Helmholtz Imaging Conference in Potsdam, June 25โ€“27!

@haesleinhuepf (ScaDS.AI/NFDI4BIOIMAGE) will give a keynote on #LLMs for #bioimage #data science, and Riccardo Massei (#UFZ) will contribute to the pre-conference workshop on #zebrafish image and video analysis on June 25. Don't miss it.

๐Ÿ‘‰ Register here: events.hifis.net/event/2061/ov

2025-05-13

If you would like to attend a microscopy or bioimage analysis training course in the next 6 months but donโ€™t have funding, check out our Microscopy Training Grant from @J_Cell_Sci and @focalplane_jcs.

Next deadline: 6 June 2025

biologists.com/grants/jcs-foca

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

Microscopy Training Grants

Supporting microscopy training for early-career researchers in cell biology

Apply for a grant of up to ยฃ1,000

Application dates:
6 June 2025
5 September 2025
7 November 2025
devSJR :python: :rstats:devSJR@fosstodon.org
2025-04-16

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]
codeberg.org/devSJR/Bioimage/s

#Bioinformatics

Shows sample page from our review (draft) Exploring Image Analysis in R: Applications and AdvancementsShows sample page from our review (draft) Exploring Image Analysis in R: Applications and AdvancementsShows sample page from our review (draft) Exploring Image Analysis in R: Applications and AdvancementsShows sample page from our review (draft) Exploring Image Analysis in R: Applications and Advancements
2025-04-07

Exiting news! ๐Ÿ’ฅ

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!

๐Ÿ‘‰ Registration: events.hifis.net/event/2061/ov

2025-03-10

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

Beth Cimini ๐Ÿ”ฌ๐Ÿ’ป๐Ÿ“Šbethcimini.bsky.social@bsky.brid.gy
2025-03-07

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 - ...

2025-03-04

Want to make your training materials #FAIR & impactful?๐Ÿค”

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: nfdi4bioimage.github.io/traini

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

2024-11-23

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

Helena Klara Jamborhelenajambor
2024-11-20

Still amazed to have won this award! ๐Ÿ™Œ

All winners are devoted to 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
๐Ÿ† Meet&Greet with the winners of the
Elisabeth Bik
PubPeer's Brandon Stell,
Helena Jambor & Christopher Schmied (PixelQuality)

Register: einsteinfoundation.de/en/insig

2024-11-07

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

zenodo-rdm.web.cern.ch/records

Thanks @EuroBioImaging !

Beth Cimini ๐Ÿ”ฌ๐Ÿ’ป๐Ÿ“Šbethcimini.bsky.social@bsky.brid.gy
2024-10-30

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 ๐Ÿงตto learn more! (1/x) #bioimaging #microscopy #bioimageanalyst

The crucial role of bioimage a...

2024-10-15

Winners of the 2024 WEHI Art of Science Exhibition were announced! You can see the whole gallery here: wehi.edu.au/art-of-science/202

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

EuroBioImagingEuroBioImaging
2024-09-02

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

๐Ÿ—“๏ธOct. 7-9

๐Ÿ“Sweden, France, Portugal

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

Registerโคต๏ธ

eurobioimaging.eu/events/intro

2024-03-26

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

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

๐Ÿ’ก More about NFDI4Bioimage: lnkd.in/eB3VFQrv

โ„น Learn more about the NFDI consortia lnkd.in/ejvBb7mu

#fdm #rdm #nfdi #bioimage #researchdata

2024-02-19

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

It's ShadowJar time ๐Ÿ˜Ž

(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

2024-02-10

#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:
forum.image.sc/t/jaunch-a-new-

#java21 #ImageProcessing #Bioimage

2024-01-09

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

#microscopy #imaging #biology #bioimage

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