iiinova — where your digital self keeps evolving

BiaPy @biapyx.bsky.social · 26/12/2025

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 🤩

youtu.be

BiaPy: accessible deep learning workflows

YouTube video by I2K Conference

041

BiaPy @biapyx.bsky.social · 20/10/2025

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

imaging.usegalaxy.eu

Galaxy

Galaxy is a community-driven web-based analysis platform for life science research.

040

BiaPy @biapyx.bsky.social · 20/10/2025

🤝 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

media.tenor.com

a giraffe standing in front of a brick building that says headlife.camorange on the bottom

ALT: a giraffe standing in front of a brick building that says headlife.camorange on the bottom

130

BiaPy @biapyx.bsky.social · 20/10/2025

🛠️ 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.

120

BiaPy @biapyx.bsky.social · 20/10/2025

🚀 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

imaging.usegalaxy.eu

Galaxy

Galaxy is a community-driven web-based analysis platform for life science research.

191

BiaPy @biapyx.bsky.social · 15/07/2025

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

BioImage.IO - Model Zoo

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

153

BiaPy @biapyx.bsky.social · 15/07/2025

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...

github.com

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 ...

120

BiaPy @biapyx.bsky.social · 15/07/2025

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...

dipc.ehu.eus

Development of Open-Source Deep Learning Tools for Bioimage Analysis

120

BiaPy @biapyx.bsky.social · 15/07/2025

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 👇

240

BiaPy @biapyx.bsky.social · 15/07/2025

⛴️ 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 👇

github.com

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 ...

173

Reposted by BiaPy

Mapping Ignorance @mappingignorance.org · 16/05/2025

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. mappingignorance.org/2025/05/15/bia…

023

BiaPy @biapyx.bsky.social · 15/05/2025

So happy to see #BiaPy in action! 🤗 Thanks a lot @jwpylvanainen.bsky.social 🤩

020

BiaPy @biapyx.bsky.social · 02/05/2025

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 😇

010

BiaPy @biapyx.bsky.social · 30/04/2025

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.

120

BiaPy @biapyx.bsky.social · 30/04/2025

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 😬

210

BiaPy @biapyx.bsky.social · 29/04/2025

🙏 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

nature.com

BiaPy: accessible deep learning on bioimages - Nature Methods

Nature Methods - BiaPy: accessible deep learning on bioimages

0205

BiaPy @biapyx.bsky.social · 29/04/2025

🔗 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.readthedocs.io

BiaPy: Accessible deep learning on bioimages — BiaPy documentation

142

BiaPy @biapyx.bsky.social · 29/04/2025

🧬 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

151

BiaPy @biapyx.bsky.social · 29/04/2025

💡 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.

131

BiaPy @biapyx.bsky.social · 29/04/2025

⚙️ 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.

131

BiaPy @biapyx.bsky.social · 29/04/2025

🔍 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).

141

BiaPy @biapyx.bsky.social · 29/04/2025

🚀 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

nature.com

BiaPy: accessible deep learning on bioimages - Nature Methods

Nature Methods - BiaPy: accessible deep learning on bioimages

13113

BiaPy @biapyx.bsky.social · 28/03/2025

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!

media.tenor.com

a cartoon opossum is standing on a dirt road and saying `` thank you '' .

ALT: a cartoon opossum is standing on a dirt road and saying `` thank you '' .

020

BiaPy @biapyx.bsky.social · 28/03/2025

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."

120

BiaPy @biapyx.bsky.social · 28/03/2025

🆕 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."

252

BiaPy @biapyx.bsky.social · 25/01/2025

🆕 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

youtu.be

BiaPy GUI: Import models from the BioImage Model Zoo

YouTube video by BiaPy

0127

BiaPy @biapyx.bsky.social · 23/01/2025

Finally, we have solved many usability-related issues ⚠️ and, more importantly, an ugly 🫣 bug that was causing problems after checking for available models from the BioImage Model Zoo 🦒 and Torchvision with our friendly Wizard 🪄:

Screenshot of BiaPy's GUI showing the Wizard window but partially occluded by a "Available pretrained models" dialog showing a model from the BioImage Model Zoo and a model from Torchvision.

130

BiaPy @biapyx.bsky.social · 23/01/2025

Thanks to the feedback from our users we have updated the Docker container download ⬇️ process to provide more real-time information ℹ️ in the log panel and avoid a false impression of halt 🛑 that was occurring in some systems:

Screenshot of BiaPy's GUI in macOS, showing the Docker container downloading process. On the top part, a progress bar shows the downloaded percentage, while in the bottom, a black log window displays the text outputs of the process.

120

BiaPy @biapyx.bsky.social · 23/01/2025

➡️ Next, you'll get our new tour window, with a short set of explanations for 🆕 newbies, including the full list of currently available workflows and the novelties from the latest release. Of course, you can desactivate it 😇

Screenshot showing BiaPy's GUI and, on top of it, the initial page of the initial tour window.

Screenshot showing BiaPy's GUI and, on top of it, the second page of the new tour window displaying a brief description of the main panel of the GUI.

Screenshot showing BiaPy's GUI and, on top of it, the third page of the new tour window displaying the list of available workflows.

Screenshot showing BiaPy's GUI and, on top of it, the last page of the new tour window with the text and links for further help. The "Do not show this message again" chekbox is marked on purpose.

110

BiaPy @biapyx.bsky.social · 23/01/2025

The first thing you will notice is the splash 💫 screen we have added so you don't stay wondering ⏳ if BiaPy has started after clicking on it...

110

BiaPy @biapyx.bsky.social · 23/01/2025

👋 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...

github.com

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: ...

182

BiaPy @biapyx.bsky.social · 27/11/2024

More videos! 📽️ BiaPy's code-free notebooks 📓 are easy to use in either Google Colab ☁️ or locally 🏠. Here you have a full walkthrough video describing how to navigate and use BiaPy's notebooks by @iarganda.bsky.social Enjoy and let us know your thoughts! 🙏 youtu.be/KEqfio-EnYw?...

youtu.be

BiaPy Notebooks walkthrough

YouTube video by BiaPy

020

BiaPy @biapyx.bsky.social · 22/11/2024

Did you like what you heard about BiaPy at #SPAOM2024? 🔬 Are you interested in giving its GUI a try? 🖥️🧙 Search no more! Here you have our walkthrough video tutorial on BiaPy's GUI by @danifranco93.bsky.social 🤗 Let us know your thoughts, all feedback is welcome! 🤩 youtu.be/vY7aBh5FUNk?...

youtu.be

BiaPy graphical user interface walkthrough

YouTube video by BiaPy

022

Reposted by BiaPy

Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

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".

061

Reposted by BiaPy

Ignacio Arganda-Carreras @iarganda.eurosky.social · 20/11/2024

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

1103

BiaPy @biapyx.bsky.social · 19/11/2024

BiaPy ⛴️ will be at SPAOM24 in Toledo twice! We'll lead a community workshop (Day 2) and @iarganda.bsky.social will give an invited talk (Day 3) about our library and application ☺️ See you all there! #SPAOM2024

021

BiaPy @biapyx.bsky.social · 19/11/2024

Hello #BioImageAnalysis world! Is the sky bluer here? 🦋

270