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Reposted by Anna Klemm

Jean-Yves Tinevez @jytinevez.bsky.social · 1d

Job alert!

We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks?

See also on the forum:
forum.image.sc/t/research-e...

Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA

Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...

forum.image.sc

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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 6d

Great to see Node staff, #i4A training grantee hernanmn.bsky.social & others at the EMBO "Advanced Methods in BioImage Analysis" course! @ahklemm.bsky.social @perrinegil.bsky.social @jytinevez.bsky.social @france-bioimaging.bsky.social @iemcas.bsky.social
More🔽
www.eurobioimaging.eu/news/success...

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 15d

Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.

If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.

BioImaging North America @bioimagingna.bsky.social · 19d

#HappyFluorescenceFriday!

#microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications!

Learn more & sign up: buff.ly/esGIotD

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Anna Klemm @ahklemm.bsky.social · 19d

@iarganda.bsky.social also on the stage by himself, giving an introduction to BiaPy @biapyx.bsky.social for streamlining deep-learning workflows. A tool tailored to be convenient to use by the full range of bioimage analysis experts.

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Jean-Yves Tinevez @jytinevez.bsky.social · 20d

Do you want to listen to me ramble about Pasteur's Image Analysis Hub (research.pasteur.fr/en/team/imag...)?
Let's meet online next Monday. I will present how we work, and what we have learned in delivering bioimage analysis support in the past 7 years.

GloBIAS @globias.bsky.social · 23d

Next #GloBIAS seminar is coming up: join us on 22nd of September, 4 pm CEST to hear from Jean-Yves Tinevez about: The scientific added value of a core-facility dedicated to Bioimage Analysis services. Want to register? -> www.globias.org/activities/b...

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Ignacio Arganda-Carreras @iarganda.bsky.social · 20d

Day 5️⃣ of our @embo.org course on "Advanced methods in bioimage analysis"! 🔬🖥️📊 @embl.org

@tischi.bsky.social is already launching 🚀 Lecture 4: Introduction to working with OME-Zarr (Tutorial) @openmicroscopy.org @zarr.dev

Christian Tischer addresses the online participants of the EMBO Advanced methods in biomage analysis course before starting his tutorial on OME-Zarr.

Christian Tischer gets prepared to start his tutorial on OME-Zarr in front a full classroom.

Christian Tischer gives the first intructions to the onsite and the online participants of the EMBO Advanced methods in biomage analysis course for his tutorial on OME-Zarr.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 21d

Let's finish the day with the round table discussion 🗣️💬 fantastically led by @ahklemm.bsky.social and Suganya Sivagurunathan from @scilifelab.se & Uppsala University!

So many interesting comments about reproducible science 🧪 and commercial vs open-source software 👩‍💻 in image facility projects 🔬

Panoramic view of the classroom during the round table discussion
led by Anna Klemm and Suganya Sivagurunathan from Scilifelab & Uppsala University, Sweden.

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Ignacio Arganda-Carreras @iarganda.bsky.social · 22d

What better way of celebrating the end of our 2nd day of training classes than with pizza 🍕, refreshements 🍻 and selfies 🤳! 😜

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Florian Jug @florianjug.bsky.social · 26d

🚨 Wow, that really sounds like an amazing opportunity… If I were a bit younger, I would start preparing my application already… 😮

www.scilifelab.se/news/ready-t...

Ready to shape the future of AI in life science?

The next call for DDLS Fellows is opening soon, offering an outstanding opportunity for ambitious young researchers to establish their own internationally competitive research groups. This round has a...

www.scilifelab.se

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Kyle Harrington @kyleharrington.com · Aug 26

Better ML for cryo-ET starts with better benchmarks.

We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.

The result: community models beat expert tools.

Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...

A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods

A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...

doi.org

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Agustin Corbat @acorbat.bsky.social · Aug 26

Thrilled to announce that I'm back in Buenos Aires and open for image & data analysis projects!

My focus is turning images from bioscience, ecology, & more into actionable data. I'm available for collaborations in Argentina and internationally.

Check out my portfolio and contact:
acorbat.github.io

iPortfolio Bootstrap Template - Index

acorbat.github.io

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Anna Klemm @ahklemm.bsky.social · Aug 26

Thank you, Agus! We were learning a lot as well, and we still miss you!

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Virginie Uhlmann @virginieuhlmann.bsky.social · Aug 25

Once is an exception, twice is a trend, thrice is a tradition!

Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich!

Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

Joel Lüthi @joelluethi.bsky.social · Aug 25

We're happy to announce the 2025 International OME-NGFF workshop 🎉

📅 Dates:
- Symposium: Nov 10–11, 2025
- Hackathon: Nov 12–14, 2025

📍 Location: Zurich, Switzerland

Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...

#bioimaging #openscience #OMENGFF #OMEZarr

(1/x 🧵)

Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland

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GloBIAS @globias.bsky.social · Aug 20

Next one in the #GloBIAS seminar series: Behind the Scenes at SciLifeLab BIIF: Lessons from Managing a National Bioimage Analysis Support Unit. Presented by Anna Klemm, head of BioImage Informatics Infrastructure Unit, Uppsala University, Sweden

Wednesday, 27th of August, 2pm CEST

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Dave Barry @david-j-barry.bsky.social · Aug 26

The #CBIAS2025 abstract deadline is this Sunday, August 31st. Submit your #BioImageAnalysis work, whether it’s a new tool or a biological discovery. #EarlyCareerResearchers, this is for you! Short and flash talk slots are up for grabs.

www.crick.ac.uk/whats-on/cri...

Crick BioImage Analysis Symposium 2025 Poster

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BioVoxxel (Jan Brocher) @biovoxxel.de · Aug 13

I am stunned!
First edition of the "Bio-Imaging with Shakespeare" LinkedIn Newsletter (buff.ly/8x7Shiq) is out for 15h and already 130 subscribers.

If you are interested in the topic FOLLOW ME on LinkedIn and Bsky and SUBSCRIBE
on LinkedIn buff.ly/cLPh8eZ

#bioimageanalysis #biovoxxel #fiji

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Nicolas Chiaruttini @nkiaru.bsky.social · Aug 12

A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3)

forum.image.sc/t/qupath-ext...

QuPath extension Spotiflow is now available

Hello @qupath team & users, We are pleased to announce a new qupath-spotiflow-extension to handle spotiflow in QuPath 🎉 ! This extension reproduces the logic behind the qupath-extension-cellpose to ...

forum.image.sc

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Robert Haase @haesleinhuepf.bsky.social · Aug 12

My tutorial materials & slides about #Reproducible #BioImageAnalysis using Python, Napari, Jupyter and #AI are available #openaccess.
Thanks to #EMBOlsm25 for having me! It so great to visit friends at my former academic home campus for a couple of days 🤩
scads.github.io/embo-lsm-bia...

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OME @openmicroscopy.org · Aug 6

New Imaging Mass Cytometry data in the Image Data Resource (IDR, idr.openmicroscopy.org).

IDR: Image Data Resource

idr.openmicroscopy.org

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Virginie Uhlmann @virginieuhlmann.bsky.social · Jul 21

Our project BioFAIR: Towards FAIR Practices in Bioimaging has been selected for funding through the swissuniversities Open Science II Programme (www.swissuniversities.ch/en/topics/op...)!

More OME-Zarr and open microscopy community events on the horizon yay!!! 🔥🔥🔥

Funded Projects - swissuniversities

www.swissuniversities.ch

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · Jul 10

Preprint alert! Want to hear more about the coolest new society on the block? You should check out our new preprint discussing @globias.bsky.social ! Hop into 🧵 for a couple quick highlights (1/x):

GloBIAS: strengthening the foundations of BioImage Analysis

There is a global need for BioImage Analysis (BIA) as advances in life sciences increasingly rely on cutting-edge imaging systems that have dramatically expanded the complexity and dimensionality of b...

arxiv.org

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Laurent Guerard @lguerard.bsky.social · Jul 8

Day 2 of #Zidas2025 is happening!

After a lecture from @ahklemm.bsky.social, it's now time for hands on with @ilastik-team.bsky.social by @benediktbest.bsky.social from Anna Kreshuk's lab and some tracking in the afternoon with #Trackmate from @jytinevez.bsky.social !

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Nav @naveed-ishaque.bsky.social · Jul 2

Did you ever notice discrepancies in benchmarking of bioinformatics tools? We did too! Setting out to benchmark spatial clustering methods, we encountered major reproducibility issues in previous benchmarks and questionable "ground truths".
More in our preprint: www.biorxiv.org/content/10.1...

Beyond benchmarking: an expert-guided consensus approach to spatially aware clustering

Spatial omics technologies have revolutionized the study of tissue architecture and cellular heterogeneity by integrating molecular profiles with spatial localization. In spatially resolved transcript...

www.biorxiv.org

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EPFL Brain Mind Institute @epfl-brainmind.bsky.social · Jun 30

New tool CellSeg3D, from the group of blu.ski/@epfl-brainmind professor Mackenzie Mathis @trackingactions.bsky.social enables self-supervised 3D cell segmentation in fluorescent microscopy,👇 labeling time & 👆quantitative analysis -
paper: elifesciences.org/articles/99848
news: tinyurl.com/y2hpmbb9

Self-supervised, label-free 3D cell imaging is here

EPFL researchers introduce CellSeg3D, a self-supervised tool for 3D cell segmentation in fluorescence microscopy, eliminating the need for manual labeling and enhancing accessibility for various biolo...

actu.epfl.ch

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Jean-Yves Tinevez @jytinevez.bsky.social · Jun 11

Our paper describing the creation of a nationwide core facility for bioimage analysis if out in @plos Computational Biology!
🎉✌️

journals.plos.org/ploscompbiol...

So happy about this paper and how the work turned out.
A small thread 👇

#bioimageanalysis #corefacility

F-BIAS: Towards a distributed national core facility for bioimage analysis †

Author summary We describe our experience in creating a nationwide core facility offering services in bioimage analysis. This virtual facility federates existing resources scattered across the territo...

journals.plos.org

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