Arrate Munoz-Barrutia
- Reposted by Arrate Munoz-BarrutiaMastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets biorxiv.org/content/10.64898/20…
- Reposted by Arrate Munoz-Barrutia#EPFL has an open faculty position - tenure track or tenured!! - in AI driven biophysics. Deadline is Nov 15th. Please spread the word! www.epfl.ch/about/workin...
- Reposted by Arrate Munoz-BarrutiaI just made an account and voted for this biology laboratory made of LEGO to "promote biological research and inspire more people into the world of biology". They need 10K votes. Reposting and/or voting below would be helpful. 🤗 beta.ideas.lego.com/product-idea...
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- Reposted by Arrate Munoz-Barrutia📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social! Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬 📅 Applications open Oct 6 (deadline: ~Oct 27) 📍 San Sebastian, Spain. 👉 cvpd.github.io/post/2025-09...
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- Reposted by Arrate Munoz-Barrutia⛴️ BiaPy just reached version 3.6.1 💫 (latest release)! github.com/BiaPyX/BiaPy... ➡️ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs 🐞 Let me tell you a bit about what's new 👇
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View full threadReposted by Arrate Munoz-BarrutiaIn the meantime, we have more than 46 pretrained models from ⛴️ BiaPy available now in the 🦒 Bioimage Model Zoo 🫶 @ai4life.bsky.social 🔗 Have a look at: bioimage.io#/models As usual, they are accesible from BiaPy's GUI 🖥️, Colab notebooks 📔 and our API 🤓
- Reposted by Arrate Munoz-Barrutia🚀 Manual mask annotation slowing you down? 💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results. 🔬 Perfect for large biomedical images. arxiv.org/abs/2506.02783 #AI #Bioimaging #ImageJ #OpenSource
- @ai4life.bsky.social & @eu-openscreen.bsky.social link highlighted in the isciii eu infrastructures for health event
- Reposted by Arrate Munoz-BarrutiaWe released version 1.6 of micro_sam: - Improvements for automatic tracking. - A new experimental mode for object classification. - **New versions of the LM and EM models** The models fix artifacts in automatic segmentation, see old vs. new prediction and better 3D segmentation results due to it.
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- Reposted by Arrate Munoz-BarrutiaA nice advance for imaging-based spatially resolved transcriptomics from the Weigert and La Manno labs. Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. www.nature.com/articles/s41...
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- Reposted by Arrate Munoz-BarrutiaInterpolaAI, based on deep learning-based optical flow, restores and interpolates sparse image stacks. This first example is a stack of histological images of a human pancreatic duct. 6 out of 7 images were missing or defective, all now generated. Download here: www.nature.com/articles/s41...
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- My office for the day… Quite an honor I must say…
- This work is part of the results from my sabbatical stay at Prof. Denis Wirtz’s lab at Johns Hopkins during the 2022–2023 academic year. Very grateful to have been part of this exciting collaboration—congrats to the team on the Nature Methods publication!
- Prou (ex-)supervisor & (always) mentor of @ai4life.bsky.social @egomezm.bsky.social Teresa Zulueta Coarasa; @danifranco93.bsky.social @cfusterbarcelo.bsky.social Carlos Garcia Lopez de Haro @uc3m @cienciauc3m
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- Reposted by Arrate Munoz-BarrutiaVery excited about this paper that came online today! InterpolAI can predict missing image data from light microscopy to H&E to MRI for improved volumetric imaging and image analysis.
- Reposted by Arrate Munoz-Barrutia🧠 AI4Life wouldn’t be the same without the amazing BioImage.IO community partners! Now showcasing real-world tools from our partners: DeepIcy, @biapyx.bsky.social, SpotMAX and QuPath. Huge thanks to our collaborators!
- Reposted by Arrate Munoz-Barrutia🔧 Time for our tech-savvy crowd! The afternoon kicks off with a workshop for developers and image analysts: creating, uploading, containerising, and deploying models like a pro.
- Reposted by Arrate Munoz-Barrutia🧩 The dream: FAIR models and data. Only standards can solve the MxN problem, and this session is exactly about that. And we wrap up today’s workshops with a group reflection: Why are FAIR resources essential for scientific progress?
- Reposted by Arrate Munoz-Barrutia📸 Good morning from Helsinki! 🇫🇮 We're back for Day 2 of the AI4Life Community Event and we’re kicking things off with a warm welcome from John Eriksson and @antjekeppler.bsky.social @eurobioimaging.bsky.social
- Reposted by Arrate Munoz-BarrutiaIrina Belaia from the Finnish Advanced Microscopy @eurobioimaging.bsky.social Node shares their experience using AI for user projects. Did you know that they offer open access to image analysis services through @eurobioimaging.bsky.social? @turkubioimaging.bsky.social
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- Reposted by Arrate Munoz-Barrutia💡Success stories from AI4Life: From the BioImage.IO models to @bioimagearchive.bsky.social’s AI-ready datasets, and community resources like the Helpdesk, Open Calls, and Challenges — see how it all connects in one ecosystem!
- Reposted by Arrate Munoz-BarrutiaYay! Well done @danifranco93.bsky.social 🤗 and long life to @ai4life.bsky.social 🤩
- 🧠 AI4Life wouldn’t be the same without the amazing BioImage.IO community partners! Now showcasing real-world tools from our partners: DeepIcy, @biapyx.bsky.social, SpotMAX and QuPath. Huge thanks to our collaborators!
- Reposted by Arrate Munoz-Barrutia💬 After lunch, we’re back with the AI4Life Community: tool builders, research infrastructures, and industry voices. Community tools like @biapyx.bsky.social and SpotMAX show how AI4Life partners are building bridges between developers and end users.
- Reposted by Arrate Munoz-BarrutiaPartner Research infrastructures in AI4Life have been instrumental in the reach of use cases gathered at the open calls. We heard today about some successful projects! @embrc-eu.bsky.social, EU-OPENSCREEN, EMPHASIS and @instruct-eric.bsky.social
- Reposted by Arrate Munoz-Barrutia☁️ Interoperability in action: @ai4eosc.eu’s AI4Life cloud marketplace lets researchers run Bioimage.IO models. A true success story of aligning European infrastructure for science. Thanks to our friends at @ai4eosc.eu for making this possible!
- Reposted by Arrate Munoz-Barrutia📘 Where science meets policy: Stefan Liebler (European Commission 🇪🇺) shares insights on Open Science, AI, EOSC, and how projects like AI4Life support the European research strategy. But also, he showcased notebooks running on the EOSC EU node! 🤖
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- Reposted by Arrate Munoz-Barrutia4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel
- Finally, this is getting serious! #neubiaspasteur2025 @jwpylvanainen.bsky.social @biapyx.bsky.social
- @biapyx.bsky.social & Bioimage Model Zoo making people Happy! 😅 at #neubiaspasteur2025 @jwpylvanainen.bsky.social @ai4life.bsky.social
- No words needed! #neubiaspasteur2025 @iarganda.bsky.social @danifranco93.bsky.social @biapyx.bsky.social Thank you @jwpylvanainen.bsky.social
- Reposted by Arrate Munoz-BarrutiaGreat recipe from @cfusterbarcelo.bsky.social on how to train a DL model
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- Reposted by Arrate Munoz-BarrutiaBIG NEWS - for the first time ever, we're running a Bioimage Analysis Beginnings Bootcamp. Learn #bioimageanalysis from awesome folks, and gain familiarity with some new tools as well as how to pick the right tool in the first place. Aug 4th-8th - apply here (soon!) forms.gle/d2fCXsrWHVP8...
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- Reposted by Arrate Munoz-BarrutiaSo happy to see this finally out! 🤗 Amazing job from an awesome team: @ivanhcenalmor.bsky.social, @aaitorg.bsky.social, @caporalclement.bsky.social, @lmescu.bsky.social, @arratemunoz.bsky.social munoz.bsky.social, & more! Specially proud of @danifranco93.bsky.social that dedicated his PhD to this 🥰
- 🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy
- Reposted by Arrate Munoz-BarrutiaFinally BiaPy is out in Nature Methods! 🥳🥳🥳 A major milestone in my research! I'm incredibly proud of the progress made. Huge thanks to my PhD supervisors, @iarganda.bsky.social and @arratemunoz.bsky.social , for their invaluable guidance and support throughout this journey. Check out the thread🧵👇
- 🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy
- After tons of fun and work! BiaPy is out!
- 🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy
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- Reposted by Arrate Munoz-BarrutiaRegister now: #CytoData2025 🔬 This fall, EU-OPENSCREEN is co-hosting the CytoData Hackathon and Symposium, which will explore the power of #microscopy imaging as a data-rich resource for quantifying cellular phenotypes – with a strong focus on high-content imaging techniques such as #CellPainting.
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