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Reposted by Anna Foix

Benjamin Maier @bdmaier.bsky.social · 3d

Also don’t miss:
🧬👯 @epetsalaki.bsky.social’s talk “From Data to Digital Twins” (Wed, Digital Twin Models)

📊🧬 My poster P03.14 – Towards Data-Driven Executable Models (Wed)

🧩🤖 @alussana.bsky.social’s poster P18.13 – Data-Driven Inference of Functionally Coherent Gene Modules (Mon)

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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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Anna Foix @afoix.bsky.social · 13d

Thank you @zaminiqbal.bsky.social and for all your orevious encouraging! I am sure is going amazing in Bath!

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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Anna Foix @afoix.bsky.social · 15d

@alex-krull.bsky.social thanks for be such an inspiration and huge support during our journey, more to come together 😄!

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Anna Foix @afoix.bsky.social · 15d

I couldn't have asked for a better supervisor, inspiration and support. ShapeEmbed is the proof that science is better when you have team work 👩‍💻👩‍💻 thanks @virginieuhlmann.bsky.social

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Anna Foix @afoix.bsky.social · 15d

A huge thank you 💙 to my supervisor @virginieuhlmann.bsky.social, my co-advisor @alex-krull.bsky.social and my colleague Craig Russell who shared feedback and ideas. And to the community already using ShapeEmbed — it’s inspiring to see it applied in different biological contexts! (N/N)

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Anna Foix @afoix.bsky.social · 15d

Why is ShapeEmbed useful in your research? It can extract shape descriptors to distinguish cell phenotypes and reveal drug-condition induced changes through clustering and latent-space exploration, offering a powerful tool for biological shape analysis. (5/N)

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Anna Foix @afoix.bsky.social · 15d

On top of all of this, the latent space learned by ShapeEmbed is generative: it can be used to generate shapes and compute meaningful shape averages and trajectories, enabling data exploration & visualization—which are useful for both discovery and hypothesis testing. (4/N)

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Anna Foix @afoix.bsky.social · 15d

ShapeEmbed is performant even with very limited data — a huge advantage in biological context where images are scarce and may be costly to acquire. Small microscopy sets are enough to learn useful shape descriptors. (3/N)

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Anna Foix @afoix.bsky.social · 15d

ShapeEmbed encodes Euclidean distance matrices relying on a novel encoder design and a new indexation-invariant loss. Through this, it learns highly-informative shape features that surpass classical approaches and current SotA learning methods. (2/N)

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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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Anna Foix @afoix.bsky.social · 15d

ShapeEmbed encodes Euclidean distance matrices relying on a novel encoder design and a new indexation-invariant loss. Through this, it learns highly-informative shape features that surpass classical approaches and current SotA learning methods.

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John Lees @bacpop.org · 16d

Thanks for all the trainers and attendees on this course, which was a lot of fun to run, and hopefully filled a gap in genomics/modelling training

And especially co-organisers @leonielorenz.bsky.social @sonjalehtinen.bsky.social Joel Hellewell

EMBL-EBI Training @training.ebi.embl.org · 19d

Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.

Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
🧬🧫

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Anna Foix @afoix.bsky.social · 19d

It’s crucial that the bioimage community joins spaces long dominated by computer vision/CS to highlight challenges in microscopy data and how we tackle them. Brilliant talk from @aafkegros.bsky.social showing how biology is both exciting and challenging👩🏻‍💻🔬🧬🦠 #bioimage #microscopy #interdisciplinary

Aafke Gros @aafkegros.bsky.social · 19d

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

Microscopy Nodes: handling large biological volumes — Blender Conference 2025

YouTube video by Blender

youtu.be

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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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Randall Munroe @xkcd.com · Aug 8

Snake-in-the-Box Problem

xkcd.com/3125/

Comic. A snake slithers around a hypercube. No two non-consecutive parts of its coils can be on adjacent corners. [Three small 4-dimensional hypercubes showing disallowed options with one large cube with snake wrapped around it. Dimensions = 4. Max Length - 7.] Snake(N) = Longest snake that can fit in an n-dimensional hypercube. Snake(N=1, 2, 3…8) = 1, 2, 4, 7, 13, 26, 50, 98. Snake(N>8) = UNSOLVED. [caption] It turns out every scientific field has a key thought experiment that involves putting a cute animal in a weird box for no reason. So far, quantum mechanics and graph theory have found theirs, but most other fields are still working on it.

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Dr. Davey F. Wright ⛏️🦕🧬 @daveyfwright.bsky.social · Jul 18

"i asked grok" "i asked chatgpt" yeah well i asked carl sagan and he said the greatest enemy of knowledge is not ignorance but the illusion of knowledge 🧪

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James Sharpe @jamesasharpe.bsky.social · Jul 21

Can robots in a swarm act like the cells of an organism? Thanks to Sedeer El-Showk for the new article in @nature.com, which highlights the work of a number of research groups, including our own, on how “Robots demonstrate principles of collective intelligence”. www.nature.com/articles/d41...

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Alex Kalinin @alxndrkalinin.bsky.social · Jul 8

🔬API-first feature extraction for image-based profiling workflows

If you need to obtain interpretable features from your segmented microscopy images, but want to do it in a fully automated way, we know the struggle.

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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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Albert Dominguez Mantes @albertdm.bsky.social · Jun 6

Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression

Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...

rdcu.be

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Martin Weigert @maweigert.bsky.social · Jun 6

Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7

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Florian Jug @florianjug.bsky.social · Jun 4

Another year, another #BIC Workshop!
This year at #ICCV 2025 in Honolulu, 🌺 🏄‍♀️ 🍹 🌼

Check it here: www.bioimagecomputing.com

Submission deadline: July 4th
Hey, you have a month left to submit your work!!! 👍

Florian Jug @florianjug.bsky.social · Jun 6

Another year, another #BIC Workshop!
This year at #ECCV 2024 in Milan, 🇮🇹.

Check it out here: bioimagecomputing.com
Submission Deadline: July 19th

Get your computational work out, we are looking forward to meet you in October!
🍕 🍷 👩‍🎓 👨‍🎓 ☀️

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Leonie Lorenz @leonielorenz.bsky.social · May 7

Very happy and proud to announce that the first preprint of my PhD is out: arxiv.org/abs/2504.20710

We developed an R package to translate mathematical models in SBML format into executable odin models and visualise models from @biomodels.bsky.social on our website Menelmacar biomodels.bacpop.org

SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences

Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computati...

arxiv.org

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