29 May 2025
It was nice to be part of this and have the opportunity of present BiaPy!! 🥳🥳
@BiaPyX
28 May 2025
The AI4Life Community Event comes to a close. We wrapped up with a big-picture discussion around the sustainability of services and the role that AI4Life plays in the EOSC.
Thank you to everyone who joined us in Helsinki and online! 🦒
Stay connected 💚
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15 May 2025
Wow, BiaPy is glowing with the magic touch of
@JwPylvanainen ! 😍
15 May 2025
No words needed! #neubiaspasteur2025 @IgnacioArganda @danifranco93 @BiaPyX Thank you @JwPylvanainen !
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29 Apr 2025
Please check out BiaPy from Muñoz-Barrutia, Arganda-Carreras, and colleagues for user-friendly deployment of deep learning tools for bioimage analysis. nature.com/articles/s41592-0…
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29 Apr 2025
Finally BiaPy is out in Nature Methods! 🥳🥳🥳
A major milestone in my research! Incredibly proud of the progress made. Huge thanks to my PhD supervisors @IgnacioArganda and @ArrateMunoz 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)
🔗 nature.com/articles/s41592-0…
#DeepLearning #BioimageAnalysis #BiaPy
ALT BiaPy logo, showing a depiction of a boat transporting a microscope.
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29 Apr 2025
🌟After tons of fun and work BiaPy is finally out!
🔗nature.com/articles/s41592-0…
Big thanks to all the collaborators, especially to Daniel Franco-Barranco (his brain and heart) and Ignacio Arganda-Carreras (brave co-supervisora).
🚀 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)
🔗 nature.com/articles/s41592-0…
#DeepLearning #BioimageAnalysis #BiaPy
ALT BiaPy logo, showing a depiction of a boat transporting a microscope.
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🙏 Thanks to @naturemethods, @rita_strack , the reviewers, and the awesome bioimage analysis community.
We can't wait to see what you build with BiaPy! 🚀🧠
🔗 nature.com/articles/s41592-0…
#BiaPy #BioimageAnalysis #DeepLearning (7/7)
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🔗 Want to try BiaPy?
Check out the full documentation and tutorials here:
👉 biapy.readthedocs.io/
👉 youtube.com/@BiaPyX
Contribute, test, and join the community — BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
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🧬 BiaPy was built by an international collaboration between researchers from @upvehu, @DIPCehu, @BiofisikaScienc, @UC3M, @scu_lab, @LabOptBio and others — led by @IgnacioArganda and @ArrateMunoz.
A huge thanks to everyone who contributed! 🌟 (5/7)
ALT Screenshot of the BiaPy site showing the pictures of the team: Daniel Franco-Barranco Jesús A Andrés-San Román Ivan Hidalgo-Cenalmor Lenka Backová Aitor González-Marfil Clément Caporal Anatole Chessel Pedro Gómez-Gálvez Luis M Escudero Donglai Wei Arrate Muñoz-Barrutia Ignacio Arganda-Carreras
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💡How is BiaPy different?
• Full multi-GPU support for training and inference
• Efficient memory management for very large datasets (MBs → TBs)
• Single-container installation via Docker
• Integration with @bioimageio for easy model sharing and reuse!
#DeepLearning (4/7)
ALT Visual description of the multiple options available to interact with BiaPy: GUI (with friendly wizard), Google Colab and Jupyter notebooks, Docker container and terminal (library use).
ALT Screenshot of the new BioImage.IO site, showing BiaPy as one of the available tools and community partners.
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⚙️ What can you do with BiaPy?
✅ Instance and semantic segmentation
✅ Object detection
✅ Image classification
✅ Image denoising & super-resolution
✅ Self-supervised learning
✅ Image-to-image translation
From 2D images to full 3D brain scans! 🧠 (3/7)
ALT Overview of BiaPy's available workflows: semantic segmentation, single-image super-resolution, image denoising, self-supervised learning, instance segmentation, object detection, image classification and image-to-image translation.
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🔍 What is BiaPy? 🚢
BiaPy is an open-source framework that simplifies the use of deep learning for microscopy and biomedical images, offering intuitive interfaces, zero-code notebooks, and scalable workflows.
Built for scientists 🧑🔬- no deep programming knowledge required! (2/7)
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🚀 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)
🔗 nature.com/articles/s41592-0…
#DeepLearning #BioimageAnalysis #BiaPy
ALT BiaPy logo, showing a depiction of a boat transporting a microscope.
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A team led by Ignacio Arganda (UPV/EHU, Ikerbasque, DIPC, IBF) and Arrate Muñoz-Barrutia (@uc3m, @info_iisgm) has developed BiaPy, an open-code #AI platform that facilitates the analysis of biomedical images using deep learning techniques. 👇
tinyurl.com/4rf97xpv
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and 4⃣, on Friday at 10:45am (Sala Toledo), I will be presenting the history and current state of @BiaPyX with my talk "BiaPy: Bioimage Analysis workflows for all audiences", see you all there! 😊
ALT Title slide of the presentation by Ignacio Arganda-Carreras at SPAOM 2024, entitled "BiaPy: Bioimage Analysis workflows for all audiences".
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BiaPy ⛴️ will be at SPAOM24 in Toledo twice! We'll lead a community workshop (Day 2) and @IgnacioArganda will give an invited talk (Day 3) about our library and application ☺️ See you all there! #SPAOM2024
And we made it to the news: europapress.es/castilla-lama….
We can't wait to see you next week! See you in Toledo.
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🆕 We have updated our preprint in @biorxivpreprint 📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it!
"BiaPy: Accessible deep learning on bioimages" biorxiv.org/content/10.1101/…
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🚀 For a fast overview on how to reuse models from the @bioimageio zoo 🦒in our notebooks 📒 (including exporting them too), check our video
"BiaPy: Import & Export BioImage Model Zoo models in Notebooks" youtu.be/R0Li3tZ7Ryc?si=qsHC… via @YouTube by @IgnacioArganda
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Would you like to use a model from the @bioimageio zoo 🦒 as core model of your BiaPy ⛴️ workflow? No worries! You can easily do that either 👇
1⃣ from the GUI 🖥️, specially if you follow the instructions of our friendly wizard 🪄🧙♀️
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📒 Our code-free notebooks are designed to be self-explainable and (hopefully 🤞) easy to use and follow. Nevertheless, in case you feel overwhelmed by them, you can have a look at our walkthrough video on BiaPy Notebooks youtu.be/KEqfio-EnYw?si=jvSx… via @YouTube by @IgnacioArganda
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🎃 Happy Halloween BiaPy-ers!!! 👻 Are you a novice user scared 😱 of using #BiaPy's GUI for the first time? Fear no more! 🤗 Here you have a full video with a complete walkthrough on BiaPy's graphical user interface 🖥️⛴️🚶youtu.be/vY7aBh5FUNk?si=pLlx… via @YouTube by @danifranco93
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