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Inês Cunha @inesmcunha.bsky.social · 3d

Congratulations!! 🥳🥳🥳

Reposted by Inês Cunha

Christophe 🔬 L @christlet.bsky.social · 21d

Our new preprint is up! This is the main postdoc work of @wiesner-t.bsky.social focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold: www.biorxiv.org/content/10.1...
Read the thread below for a summary of our findings 🧵1/11

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Reposted by Inês Cunha

Sebastian Bauer @sebjbauer.bsky.social · Aug 29

Thank you @smlm-symposium.bsky.social for the opportunity to present at #SMLMS2025! 🎉 Stay tuned for the upcoming preprint! 📄

Heilemann Lab @heilemannlab.bsky.social · Aug 29

Sebastian Bauer @sebjbauer.bsky.social from SciLifeLab Stockholm @juliettegriffie.bsky.social reporting #SMLMS2025

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Reposted by Inês Cunha

Ricardo Henriques @henriqueslab.bsky.social · Jun 27

🧑‍🔬📰🚀 #RxivMaker is here! A framework automating the creation of publication-ready scientific #preprints from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with @guijacquemet.bsky.social's lab

📜: zenodo.org/records/1575...
👨‍💻: github.com/HenriquesLab...

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Reposted by Inês Cunha

Guillaume Jacquemet @guijacquemet.bsky.social · Jun 23

Are you looking for a postdoc?
I will be looking for 2-4 people after the summer to join the lab !!
Do not hesitate to reach out and disseminate !!

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Reposted by Inês Cunha

bioRxivpreprint @biorxivpreprint.bsky.social · May 14

AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI https://www.biorxiv.org/content/10.1101/2025.05.12.653464v1

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Inês Cunha @inesmcunha.bsky.social · May 14

And a big thank you to Dr. Alix Le Marois and Dr. Erik Sahai for providing this amazing dataset❤️(see "Imaging of MAP kinase dynamics reveals endocytic regulation of pulsatile signalling and network re-wiring in response to targeted therapy in EGFR-mutant non-small cell lung cancer")

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Inês Cunha @inesmcunha.bsky.social · May 14

A huge thank you ❤️ to @lucapanconi.bsky.social , @sebjbauer.bsky.social , Emma Latron, Maxime Gestin, Erik Sahai, Alix Le Marois, @juliettegriffie.bsky.social and our funders @cancerresearchuk.org , @kawresearch.bsky.social , @erc.europa.eu
biorxiv.org/content/10.1... (5/5)

AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI

Live-cell imaging provides a unique insight into complex cellular processes including single cell fate, but remains limited by both low-throughput and the lack of generalisable analytics for the multi...

biorxiv.org

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Inês Cunha @inesmcunha.bsky.social · May 14

Our model is small and versatile – this allows us to train it on a common laptop on the whole dataset in under 20 minutes ⚡️😌and use limited manual data annotations✍️ for accurate predictions (4/n)

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Inês Cunha @inesmcunha.bsky.social · May 14

We were able to reliably predict cell fate from the very first frame ⚡️of 3 days long acquisition, and identify relevant biological processes🧬 involved in cancer persister cells, despite their known biological variability (3/n)

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Inês Cunha @inesmcunha.bsky.social · May 14

We propose a fully data-driven approach to early cell fate prediction from a microscopy time-lapse. We combine an adversarial autoencoder architecture with a multi-objective loss function, including contrastive learning, to optimise both cell fate prediction and interpretability (2/n)

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Inês Cunha @inesmcunha.bsky.social · May 14

Our work “AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI” is finally out in
@biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️

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Inês Cunha @inesmcunha.bsky.social · May 12

First research manuscript of my PhD finally submitted!! 🥳❤️ Preprint coming soon... 👀 @juliettegriffie.bsky.social

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Inês Cunha @inesmcunha.bsky.social · Feb 6

Come work with us! 😜 💻🔬

Juliette Griffié @juliettegriffie.bsky.social · Feb 3

📣We are recruiting! If you are interested in developing ML tools (with a focus on interpretable ML & generative AI) for bioinformatics applications @scilifelab.se, look no more😋 1 PhD position su.varbi.com/en/what:job/... & 2 post doc positions (online soon, PM me in the meantime).

PhD student in Bioinformatics

The Department of Biochemistry and Biophysics is mainly located with the other Departments of Chemistry and Life Sciences in the Arrhenius Laboratories for Natural Sciences, which are situated in th

su.varbi.com

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Reposted by Inês Cunha

Ricardo Henriques @henriqueslab.bsky.social · Jan 6

#NanoPyx and #LiquidEngine hitting the national news, highlighting our research @itqbnova.bsky.social

www.rtp.pt/noticias/pai...

📰: www.nature.com/articles/s41...

Investigadores da ITQB NOVA usam IA para analisar imagens biomédicas 100 vezes mais depressa

A inteligência artificial (IA) está a transformar a nossa vida diária desde as áreas mais complexas até às mais rotineiras. E uma das áreas que tem aproveitado esta tecnologia é a investigação médica,...

www.rtp.pt

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Inês Cunha @inesmcunha.bsky.social · Jan 2

What an incredible journey with Bruno and António (not on bsky yet) ❤️ I learned so much with these guys and had a blast working with them. This was truly the dream team ❤️ #NanoPyx

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Inês Cunha @inesmcunha.bsky.social · Jan 2

Video 4: "How to Implement your Liquid Engine Method" youtu.be/gRGEjdT8opY (8/8)

youtu.be

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Inês Cunha @inesmcunha.bsky.social · Jan 2

Video 3: "How to Benchmark your Implementations with the Liquid Engine in 1 minute" (7/n) youtu.be/9hF7nLtFzoo

How to Benchmark your Implementations with the Liquid Engine in 1 minute

YouTube video by Henriques Lab

youtu.be

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Inês Cunha @inesmcunha.bsky.social · Jan 2

Video 2: "How to Build your Liquid Engine Class in 1 minute" youtu.be/QQsXrZ_jFa8 (6/n)

How to Build your Liquid Engine Class in 1 minute

YouTube video by Henriques Lab

youtu.be

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Inês Cunha @inesmcunha.bsky.social · Jan 2

HOW CAN YOU USE #NanoPyx ? We recorded a series of 1-minute video tutorials that showcase how you can use #NanoPyx, and the capabilities of the #LiquidEngine on your own image analysis workflows! Video 1: youtu.be/Dx2lHoRB044 (5/n)

How to Install NanoPyx and Run Jupyter Notebooks Locally

YouTube video by Henriques Lab

youtu.be

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Inês Cunha @inesmcunha.bsky.social · Jan 2

What methods does #NanoPyx offer? We have Image Registration, Denoising, Super-Resolution Image Reconstruction🔬 and Quality Control metrics! (4/n)

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Inês Cunha @inesmcunha.bsky.social · Jan 2

The #LiquidEngine has an AI-powered agent 🤖 that predicts the fastest way of running a specific analysis task, given the input data, the user hardware and task parameters. Incorporating the #LiquidEngine significantly improves the performance of bioimage analysis workflows!(3/n)

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Inês Cunha @inesmcunha.bsky.social · Jan 2

The fastest way of performing any analysis task depends on the user device 💻, the input data 🦠 and the specific task we’re trying to run (2/n).

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Inês Cunha @inesmcunha.bsky.social · Jan 2

And to start 2025 strong… Our work #NanoPyx is out in Nature Methods 😍❤️ DOI: doi.org/10.1038/s415...
#NanoPyx is a Python framework that uses the #LiquidEngine to efficiently accelerate bioimage analysis for any user! (1/n) ⬇️

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