Lightnews — Scholar-powered news

Virginie Uhlmann @virginieuhlmann.bsky.social · 7d

I sense a modern Rorschach test candidate right here

Reposted by Virginie Uhlmann

Anna Foix @afoix.bsky.social · 15d

Thrilled to be speaking at #CBIAS2025! 🥳
CBIAS has been my scientific home since the beginning of my PhD, providing a welcoming space for early-career researchers. This year feels extra special, as I’ll be presenting my work in the final year of my PhD.
Join us if you get the chance! 😃

Dave Barry @david-j-barry.bsky.social · 15d

The provisional program for The 6th Crick Bioimage Analysis Symposium (#CBIAS2025) is live!

Join us at the @wellcomecollection.bsky.social in London in November for incredible talks, posters and insightful discussions.

Space is limited - register now!
www.crick.ac.uk/whats-on/cri...

Provisional Program for day 1 of the Crick BioImage Analysis Symposium 2025

Provisional Program for day 2 of the Crick BioImage Analysis Symposium 2025

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Reposted by Virginie Uhlmann

Crick BioImage Analysis Symposium @cbias.bsky.social · 15d

The program for the #CBIAS2025 is now live – space is limited, so register now to secure your spot! 24th-25th Nov, Wellcome Trust, London (UK) - see you there!

🔗⬇️
www.crick.ac.uk/whats-on/cri...

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Virginie Uhlmann @virginieuhlmann.bsky.social · 15d

You may have heard me talk about learned shape representations for a long time, but it took @afoix.bsky.social's hard work to bring it to life 🍾 Catch her at @neuripsconf.bsky.social to find out more!!

Anna Foix @afoix.bsky.social · 15d

Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)

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Reposted by Virginie Uhlmann

Joel Lüthi @joelluethi.bsky.social · 20d

Want to hack with ~40 motivated developers in the OME-Zarr space this fall in Zurich, November 12 - 14th? The application window for the 2025 OME-NGFF workflows hackathon is closing on September 30th! Apply here to be part of this exciting week about OME-Zarr: forms.gle/849cf2fBk1pJ...

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Virginie Uhlmann @virginieuhlmann.bsky.social · 22d

I am in this picture and I don't like it

Wolfgang Huber @wkhuber.bsky.social · 22d

Science: only when you write up the manuscript, you realize what you should have done.

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Reposted by Virginie Uhlmann

The BioImage Archive @bioimagearchive.bsky.social · 23d

🎉 Our paper “MIFA: Metadata, Incentives, Formats and Accessibility guidelines to improve the reuse of AI datasets for bioimage analysis” is out in @natmethods.nature.com!
Community-driven standards to make bioimage data AI-ready & reusable.
👉 www.nature.com/articles/s41... #AI #Bioimaging #FAIRdata

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Virginie Uhlmann @virginieuhlmann.bsky.social · Sep 1

Never in history did a game live up to the hype to that extent.

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Reposted by Virginie Uhlmann

Dave Barry @david-j-barry.bsky.social · Sep 1

The abstract submission deadline for #CBIAS2025 has just closed and, for the first time, we have a near perfect gender-balance in our abstract submissions.

In fact, we have slightly more submissions from women than men.

a man with his arms crossed is smiling and saying noice !

ALT: a man with his arms crossed is smiling and saying noice !

media.tenor.com

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Reposted by Virginie Uhlmann

Erick Ratamero @erickratamero.com · Aug 25

I'll be there! Giving a talk! and hacking on _something_ for a few days!

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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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 🧵)

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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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Virginie Uhlmann @virginieuhlmann.bsky.social · Jul 2

Yes please.

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Virginie Uhlmann @virginieuhlmann.bsky.social · Jun 24

And just like that @katharinaweins.bsky.social and Elvira Isenring managed to make us look cooler than we'll ever be:
www.youtube.com/watch?v=8t8R...

Bioimaging | UZH Research Spotlight

YouTube video by Universität Zürich

www.youtube.com

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Virginie Uhlmann @virginieuhlmann.bsky.social · Jun 3

Hey bioimaging folks, join us for the next OME-NGFF Community Call on June 24 at 9:00 CEST and 17:00 CEST!

Details and agenda on the one and only image.sc here: forum.image.sc/t/join-us-fo...

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Reposted by Virginie Uhlmann

BioImaging North America @bioimagingna.bsky.social · May 2

#HappyFluorescenceFriday

#microscopycommunity. @bioimagingna.bsky.social was at OME205 with @openmicroscopy.org this past week with the makers of BioFormats. OME-TIFF, OME-Zarr and OMERO sharing their work and listening to your challenges.

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Reposted by Virginie Uhlmann

Joel Lüthi @joelluethi.bsky.social · Apr 29

🚀 We just released a major Fractal update!
More flexible workflows, dynamic monitoring, and a new history system for better traceability – built to handle Terabytes of high-dimensional microscopy data in #OME-Zarr.
Full announcement post here: fractal-analytics-platform.github.io/news/2025-04...

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Reposted by Virginie Uhlmann

Jan Funke @janfunkey.bsky.social · Apr 18

How can AI help you to analyze your microscopy images?

Find out at the "Machine Learning for Microscopy Image Analysis" course at the @mblscience.bsky.social in Woods Hole from Aug 22-Sep 6!

Applications are due 🚨 April 30 🚨

Read on for more! 👇

www.mbl.edu/education/ad...

AI@MBL: Machine Learning for Microscopy Image Analysis | Marine Biological Laboratory

The goal of this course is to familiarize researchers in the life sciences with state-of-the-art deep learning techniques for microscopy image analysis and to introduce them to tools and frameworks th...

www.mbl.edu

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Reposted by Virginie Uhlmann

Etch a Cell @etchacell.bsky.social · Mar 27

What an incredible first week for Etch A Cell - ImmunoExplorers! 🚀

✨ 688 volunteers have together contributed 23,474 classifications (and counting!), helping us reach 72% completion of our first dataset.

Join the effort here: 🔗 www.zooniverse.org/projects/h-s...

Thank you 🙌 #CitizenScience

This is a screenshot of the project's landing page, showing the statistics quoted in the tweet - 688 volunteers have made 23,474 classifications

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Reposted by Virginie Uhlmann

Etch a Cell @etchacell.bsky.social · Mar 19

Be a part of groundbreaking research!

🔬 Help us study immune cells & fight transplant rejection:

www.zooniverse.org/projects/h-s...

Together, we can make a difference! 💪 #CitizenScience #KidneyHealth #Zooniverse

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This image shows most of the Etch A Cell - ImmunoExplorers project team at a Christmas Market

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Virginie Uhlmann @virginieuhlmann.bsky.social · Mar 19

Share this with everyone you know and help us hunt the immune cells!!!

Etch a Cell @etchacell.bsky.social · Mar 19

There's a lot we still don’t know about immune cells in rejection:

❓ Which immune cells are there?
❓ Are they activated?
❓ What are they doing?

🧵 (3/6)

This image shows two immune cells in a kidney capillary. The immune cells each have a green box around them

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Reposted by Virginie Uhlmann

Dave Barry @david-j-barry.bsky.social · Mar 17

Calling all...
🔬 Microscopists
💻 BioImage Analysts
👩‍🔬 Life Scientists

📅 Save the Date

The 5th edition of the Crick BioImage Analysis Symposium will take place on November 24/25th 2025.

More details to follow...

#CBIAS2025

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Reposted by Virginie Uhlmann

NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · Mar 11

Building a truly interdisciplinary bioimaging culture! 👯
Our latest article explores how #opendata sharing can create interdisciplinary collaboration and scientific discovery: doi.org/10.1242/jcs....

Find out, how NFDI4Bioimage contributes to this vision: nfdi4bioimage.de/about-us/goa...

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Reposted by Virginie Uhlmann

Joel Lüthi @joelluethi.bsky.social · Mar 11

🌍 Who joined us?

👩‍🔬 43 participants from academia & industry
🏢 40 affiliations
📍 11 countries across Europe & the US

OME-Zarr is a global effort!

🧵 (11/15)

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Virginie Uhlmann @virginieuhlmann.bsky.social · Mar 11

Turns out that when a group of interesting and enthusiastic scientists who care about open standards sit together for a couple of days, they do great things 🔥🔥🔥

Joel Lüthi @joelluethi.bsky.social · Mar 11

🚀 We’re very excited to share our latest preprint on OME-Zarr! 🚀

Our report on the 2024 OME-NGFF Workflows Hackathon is a deep dive into the status of OME-Zarr and the great work that happened last November at the BioVisionCenter in Zurich.

🔗 Read the preprint: osf.io/preprints/bi...

🧵 (1/15)

OSF

osf.io

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