#BiaPy
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biapyx.bsky.social
🚀 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
April 29, 2025 at 9:33 AM
biapyx.bsky.social
🙏 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
April 29, 2025 at 9:33 AM
biapyx.bsky.social
🆕 Now that the bugs have been fixed 🙃, we have a new video 📹 tutorial on how to import pretrained models from the BioImage Model Zoo 🦒 into your #BiaPy workflow using our friendly GUI 🖥️, by @iarganda.bsky.social:

youtu.be/Zq50Ew1s8ag
BiaPy GUI: Import models from the BioImage Model Zoo
YouTube video by BiaPy
youtu.be
January 25, 2025 at 2:18 PM
iarganda.eurosky.social
3️⃣ Tomorrow after lunch (16.15h – 17.15h, Workshop rooms), @arratemunoz.bsky.social, Lenka Backová, @aaitorg.bsky.social and I will give a community workshop on @biapyx.bsky.social, our deep learning library and application for #BioImageAnalysis #SPAOM2024
Outline of the community workshop on BiaPy at the SPAOM 2024. It reads: 16:15-17:15: Introduction to BiaPy What is a workflow Deep learning recap What is (and what’s not) BiaPy BiaPy workflows Use case: 2D instance segmentation Top-down vs Bottom-up approaches Demo with BiaPy notebook Helpers: Lenka Backová Aitor González-Marfil Arrate Muñoz-Barrutia
November 20, 2024 at 3:12 PM
biapyx.bsky.social
⛴️ 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
July 15, 2025 at 2:58 PM
iarganda.eurosky.social
🆕 We have updated our preprint in @biorxivpreprint.bsky.social
📰 It explains better the current state of #BiaPy ⛴️ while describing as well its limitations 🤗 Hope you like it!

"BiaPy: Accessible deep learning on bioimages"
www.biorxiv.org/content/10.1...
BiaPy: Accessible deep learning on bioimages
BiaPy is an open-source library and application that streamlines the use of common deep learning approaches for bioimage analysis. Designed to simplify technical complexities, it offers an intuitive i...
www.biorxiv.org
November 16, 2024 at 9:57 AM
mappingignorance.org
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/
May 15, 2025 at 7:05 PM
biapyx.bsky.social
🚀 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
Galaxy
Galaxy is a community-driven web-based analysis platform for life science research.
imaging.usegalaxy.eu
October 20, 2025 at 2:11 PM
natmethods.nature.com
Please check out BiaPy from Muñoz-Barrutia, Arganda-Carreras, and colleagues for user-friendly deployment of deep learning tools for bioimage analysis. www.nature.com/articles/s41...
April 29, 2025 at 7:55 PM
biapyx.bsky.social
🔗 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
April 29, 2025 at 9:33 AM
mappingignorance.org
BiaPy is a groundbreaking open-source platform that’s making bioimage analysis accessible to researchers, regardless of their coding expertise. 

https://mappingignorance.org/2025/05/15/biapy-analising-bioimages-made-easy/
May 16, 2025 at 12:05 AM
danifranco93.bsky.social
Finally 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🧵👇
biapyx.bsky.social 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
April 29, 2025 at 9:47 AM
iarganda.eurosky.social
Tomorrow I will be in Leioa (UPV/EHU campus) given a seminar at @achucarro.bsky.social about @biapyx.bsky.social Come by if you are interested in bioimage analysis for all audiences! ⛴️📉🖥️🧪🔬

www.achucarro.org/seminar/2025...
BiaPy: Accessible deep learning for bioimages - Achucarro Basque Center for Neuroscience
BiaPy stands as a versatile and open-source bioimage analysis library designed to meet the diverse needs of users and developers in the field of computational neuroscience. With an intuitive interface...
www.achucarro.org
March 13, 2025 at 12:59 PM
biapyx.bsky.social
👋 Hi everybody! We have a new release of ⛴️ BiaPy's GUI 🖥️ (v1.1.5) with plenty of new features ✨ and bug 🐞 fixes! Let me show you some of the novelties 👇

github.com/BiaPyX/BiaPy...
Release Version 1.1.5 · BiaPyX/BiaPy-GUI
Major: Move to PySide6 Add splash screen Enforce the light theme with pyqtdarktheme to prevent the automatic macOS white font change Add initial GUI tour window Update container download process: ...
github.com
January 23, 2025 at 1:42 PM
kemos.bsky.social
Beyond the 2D Bounding Box: Why Bioimage Deep Learning Is a Completely Different Beast and How BiaPy Tames It

[latexpage]https://github.com/lynchaos/biapy-hubht...

https://kemal.yaylali.uk/beyond-the-2d-bounding-box-why-bioimage-deep-learning-is-a-completely-different-beast-and-how-biapy-tames-it/
Beyond the 2D Bounding Box: Why Bioimage Deep Learning Is a Completely Different Beast and How BiaPy Tames It
[latexpage]https://github.com/lynchaos/biapy-hubhttps://lynchaos-biapy-hub-app-hlcmfj.streamlit.app/ If you have spent your machine learning career optimizing ResNets or YOLO on ImageNet and COCO, here is an inconvenient truth: standard computer vision has spoiled you. In standard computer vision, a batch is usually an RGB triplet $(B, 3, H, W)$ where $H, W \le 1024$. The pixels are isotropic, the spatial coordinates...
kemal.yaylali.uk
August 24, 2026 at 11:15 AM
biapyx.bsky.social
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 🤩
BiaPy: accessible deep learning workflows
YouTube video by I2K Conference
youtu.be
December 26, 2025 at 11:39 AM
iarganda.eurosky.social
and 4️⃣, on Friday at 10:45am (Sala Toledo), I will be presenting the history and current state of @biapyx.bsky.social with my talk "BiaPy: Bioimage Analysis workflows for all audiences", see you all there! 😊 #SPAOM2024
Title slide of the presentation by Ignacio Arganda-Carreras at SPAOM 2024, entitled "BiaPy: Bioimage Analysis workflows for all audiences".
November 20, 2024 at 3:12 PM
biapyx.bsky.social
🆕 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."
March 28, 2025 at 1:11 PM
arratemunoz.bsky.social
After tons of fun and work! BiaPy is out!
April 29, 2025 at 10:06 AM
biapyx.bsky.social
🧬 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
April 29, 2025 at 9:33 AM
katedra.eus
BiaPy is a groundbreaking open-source platform that’s making bioimage analysis accessible to researchers, regardless of their coding expertise. 

https://mappingignorance.org/2025/05/15/biapy-analising-bioimages-made-easy/
May 15, 2025 at 5:15 PM
danifranco93.bsky.social
📄 Preprint: figshare.com/s/83137b554b...
🔗 BiaPy: biapyx.github.io
📦 Models will be open at : bioimage.io 🦒🦒

👀 Stay tuned for Phase 2 results — they might surprise a few popular tools. (3/3)

#bioimaging #imageanalysis #instancesegmentation #representations #biapy
June 30, 2026 at 12:30 PM
biapyx.bsky.social
💡 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.
April 29, 2025 at 9:33 AM
biapyx.bsky.social
🔍 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).
April 29, 2025 at 9:33 AM
biapyx.bsky.social
🛠️ 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 🌌
Screenshot of the Galaxy application in a browser, showing the BiaPy tool selected and its parameter selection options.
October 20, 2025 at 2:11 PM