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BiaPy @biapyx.bsky.social · Jul 15

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

Huge thanks and keep it up! 💪

a man in a black and white sweater is standing in a living room and says `` seriously thanks so much '' .

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BiaPy @biapyx.bsky.social · Jul 15

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 🤓

BioImage.IO - Model Zoo

BioImage Model Zoo - A community-driven, open resource for sharing standardized AI models for bioimage analysis

bioimage.io

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BiaPy @biapyx.bsky.social · Jul 15

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...

Release Version 3.6.0 · BiaPyX/BiaPy

Major: Transition to numpy 2 (#134) Update notebooks by removing the cell that restarts the kernel, as it is no longer necessary after the transition to NumPy 2. Changing default normalization to ...

github.com

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BiaPy @biapyx.bsky.social · Jul 15

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...

Development of Open-Source Deep Learning Tools for Bioimage Analysis

dipc.ehu.eus

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BiaPy @biapyx.bsky.social · Jul 15

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 @biapyx.bsky.social · Mar 28

🆕 Did you experience troubles ⚠️ while installing BiaPy in our Google Colab notebooks? We did too! This is due to some updates in the default libraries of Colab. As a temporary solution, we have now included a new cell in the notebooks to reinstall the conflicting libraries 👇

Screenshot of BiaPy notebook showing the installation section. The first part of section reads "Play to reinstall Colab libraries so they are compatible wiht BiaPy. ⚠️ Wait until this cell is fully executed to run the next one ⚠️ This will make the notebook restart. Do not worry and continue executing the next cell once this one is finished."

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BiaPy @biapyx.bsky.social · Jul 15

⛴️ 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 👇

Release Version 3.6.1 · BiaPyX/BiaPy

Minor: Disable painting matching instances by default as it takes a lot of time, i.e. TEST.MATCHING_STATS_THS_COLORED_IMG to [] (#135) Refine DA notebook Update notebooks to install BiaPy v3.6.0 ...

github.com

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BiaPy @biapyx.bsky.social · May 28

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

AI4Life @ai4life.bsky.social · May 27

🧠 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!

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Reposted by BiaPy

Mapping Ignorance @mappingignorance.org · May 16

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/

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BiaPy @biapyx.bsky.social · May 15

So happy to see #BiaPy in action! 🤗

Thanks a lot @jwpylvanainen.bsky.social 🤩

Arrate Munoz-Barrutia @arratemunoz.bsky.social · May 15

No words needed! #neubiaspasteur2025 @iarganda.bsky.social @danifranco93.bsky.social @biapyx.bsky.social Thank you @jwpylvanainen.bsky.social

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BiaPy @biapyx.bsky.social · May 2

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 😇

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BiaPy @biapyx.bsky.social · Apr 30

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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BiaPy @biapyx.bsky.social · Apr 30

Kudos to you, my captain! 🦸‍♂️

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BiaPy @biapyx.bsky.social · Apr 30

Yay! 🥰

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BiaPy @biapyx.bsky.social · Apr 30

Thank you! 😊

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BiaPy @biapyx.bsky.social · Apr 30

We're working on eliminating those dependencies 😅

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BiaPy @biapyx.bsky.social · Apr 30

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 😬

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BiaPy @biapyx.bsky.social · Apr 29

🙏 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

BiaPy: accessible deep learning on bioimages - Nature Methods

Nature Methods - BiaPy: accessible deep learning on bioimages

www.nature.com

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BiaPy @biapyx.bsky.social · Apr 29

🔗 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: Accessible deep learning on bioimages — BiaPy documentation

biapy.readthedocs.io

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BiaPy @biapyx.bsky.social · Apr 29

🧬 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)

Screenshot of the BiaPy site showing the developing 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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BiaPy @biapyx.bsky.social · Apr 29

💡 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)

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).

Screenshot of the new BioImage.IO site, showing BiaPy as one of the available tools and community partners.

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BiaPy @biapyx.bsky.social · Apr 29

⚙️ 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)

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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BiaPy @biapyx.bsky.social · Apr 29

🔍 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

Animated gif showing an overview of BiaPy's features: its community inspiration, the diverse input data and analysis tasks, and its backend (PyTorch) and multiple frontends (GUI, notebooks, library).

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BiaPy @biapyx.bsky.social · Apr 29

🚀 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

BiaPy: accessible deep learning on bioimages - Nature Methods

Nature Methods - BiaPy: accessible deep learning on bioimages

www.nature.com

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BiaPy @biapyx.bsky.social · Mar 28

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!

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BiaPy @biapyx.bsky.social · Mar 28

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 👍

Screenshot of a BiaPy notebook showing the "Play to reinstall Colab libraries so they are compatible with BiaPy" cell. The cell has been executed and Colab shows a message stating "Your session crashed for an unknown reason."

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