BiaPy

BiaPy: accessible deep learning workflows YouTube video by I2K Conference

Did you miss our workshop on 💫 Halfway to I2K 2025 💫(www.i2kconference.org)? Worry no more! The video is finally out 👇

youtu.be/dFLtKHWlYdQ?...

Check it out and learn about BiaPy and its latest news 🤗 with @iarganda.bsky.social and @danifranco93.bsky.social 🤩

This is a new step for accessible, FAIR bioimage AI 🚀

Try the tool 👉 imaging.usegalaxy.eu?tool_id=tool...

Contribute your models 🧑‍🔬 And join the community making bioimage analysis open & reproducible!

#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging

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🤝 And there’s more! Thanks to this integration, you can also tap into the 🦒 BioImage Model Zoo 🧬.

Pretrained models can now be run straight through Galaxy with BiaPy, bringing community AI models to your data in just a few clicks.

#BioImageModelZoo #OpenScience

🛠️ We wrapped BiaPy as a Galaxy tool with a ✨ wizard-style interface (just like BiaPy’s GUI).

That means:
✔️ Step-by-step experiment setup
✔️ Launch training / inference jobs with BiaPy under the hood
✔️ Share & reproduce pipelines the Galaxy way 🌌

🚀 Big news: BiaPy meets @galaxyproject.bsky.social! ⛴️🤝🌌

You can now run BiaPy directly inside Galaxy, making deep learning for bioimage analysis easier, reproducible & accessible to everyone.

👉 imaging.usegalaxy.eu?tool_id=tool...

#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging

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So, one more time, 💫 thanks everybody 💫 for making this happen: from our developers 🛠️ to our users 👥.

Huge thanks and keep it up! 💪

In 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 🤓

We fixed many issues ⚠️ and bugs 🐛 reported by our community 📩. You don't know how happy that makes us 😍

As an example, we can now reuse the predictions of a workflow and execute only the post-processing step with different parameters, which is much faster ⏩

biapy.readthedocs.io/en/latest/ge...

Development of Open-Source Deep Learning Tools for Bioimage Analysis

Special kudos to our fantastic summer intern Ibai Mayoral 👨‍🎓 from the @dipcehu.bsky.social who has made an incredible job at implementing all those methods now within BiaPy's core code 🤩

dipc.ehu.eus/en/career/in...

We have removed ✂️ our dependency to the unmaintained 'imgaug' library for data augmentation methods, which means we can now easily execute all our workflows in Google Colab without restarting 🔄 the session, yay! 🤗

bsky.app/profile/biap...

So no more this 👇

⛴️ 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 👇

Yay! Well done @danifranco93.bsky.social 🤗 and long life to @ai4life.bsky.social 🤩

By democratizing bioimage analysis, BiaPy is paving the way for faster, more inclusive scientific breakthroughs, bringing us closer to understanding the building blocks of life.

https://mappingignorance.org/2025/05/15/biapy-analising-bioimages-made-easy/

So happy to see #BiaPy in action! 🤗

Thanks a lot @jwpylvanainen.bsky.social 🤩

Right! That was one of our first options 🤗 However, since we need to extend many methods to 3D images, it seems more reasonable for us to write our own code and reduce the number of dependencies we already have 😇

Sure! We believe it is imgaug and its dependencies, which have not been updated in a while (5 years). So we're trying to get rid of it by writing our own code for the data augmentation methods we use from that library.

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Kudos to you, my captain! 🦸‍♂️

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Yay! 🥰

Thank you! 😊

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We're working on eliminating those dependencies 😅

The big deal is numpy. Some of the dependencies of BiaPy cannot work with numpy 2.*, so we have to remove the Colab's version of numpy and install numpy==1.26.*. And doing this, we're forced to restart the runtime for the changes to take effect 😬

BiaPy: accessible deep learning on bioimages - Nature Methods Nature Methods - BiaPy: accessible deep learning on bioimages

🙏 Thanks to
@naturemethods.bsky.social, @ritastrack.bsky.social, the reviewers, and the awesome bioimage analysis community.
We can't wait to see what you build with BiaPy! 🚀🧠
🔗 www.nature.com/articles/s41...
#BiaPy #BioimageAnalysis #DeepLearning

🔗 Want to try BiaPy?
Check out the full documentation and tutorials here:
👉 biapy.readthedocs.io
👉 www.youtube.com/@BiaPyX
Contribute, test, and join the community — BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI

🧬 BiaPy was built by an international collaboration between researchers from @upvehu.bsky.social, @dipcehu.bsky.social , @uc3m.es and others — led by
@iarganda.bsky.social and @arratemunoz.bsky.social.
A huge thanks to everyone who contributed! 🌟 (5/7)

💡 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 @BioImageModelZoo for easy model sharing and reuse!
#DeepLearning (4/7)

⚙️ 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)

🔍 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)
#AI #Bioimaging

BiaPy: accessible deep learning on bioimages - Nature Methods Nature Methods - BiaPy: accessible deep learning on bioimages

🚀 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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We understand this is not ideal and we're working 🛠️ on updating BiaPy's ⛴️ dependencies so we can avoid restarting the notebooks in the near future. We'll keep you posted 📮, thanks for your patience!

You need to run that cell and completely wait until it has finished, since it will restart 🔄 the notebook. You will see the message "Your session crashed for an unknown reason." Keep calm and carry on 🤓 You can execute the rest of the notebook as usual 👍