BiaPy

BiaPy: Accessible deep learning on bioimages

[BiaPy @BiaPyX]

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

Try the tool 👉 https://t.co/PTedoLZXKX

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

#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging

[BiaPy @BiaPyX]

🚀 Big news: BiaPy meets Galaxy! ⛴️🤝🌌

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

👉 https://t.co/PTedoLZXKX

#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging

[BiaPy @BiaPyX]

🤝 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

[BiaPy @BiaPyX]

🙏 Thanks to @naturemethods, @rita_strack , the reviewers, and the awesome bioimage analysis community.
We can't wait to see what you build with BiaPy! 🚀🧠
🔗 https://t.co/DRH6yVEyuJ
#BiaPy #BioimageAnalysis #DeepLearning (7/7)

[BiaPy @BiaPyX]

🚀 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)
🔗 https://t.co/DRH6yVEyuJ
#DeepLearning #BioimageAnalysis #BiaPy

[BiaPy @BiaPyX]

🔗 Want to try BiaPy?
Check out the full documentation and tutorials here:
👉 https://t.co/rP2C6o5II6
👉 https://t.co/WTQSfAPIrz
Contribute, test, and join the community — BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI

[Ignacio Arganda-Carreras @IgnacioArganda]

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! 😊

[Ignacio Arganda-Carreras @IgnacioArganda]

3⃣ Tomorrow after lunch (16.15h – 17.15h, Workshop rooms), @ArrateMunoz @Lenka_Backova @AAitorG and I will give a community workshop on @BiaPyX , our deep learning library and application for #BioImageAnalysis
#SPAOM2024
https://t.co/WxJhUDzkRY

[BiaPy @BiaPyX]

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

[SPAOM @SPAOM5]

And we made it to the news: https://t.co/CesJFh3aWg.

We can't wait to see you next week! See you in Toledo.

[BiaPy @BiaPyX]

🆕 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" https://t.co/nAJ5159xVs

[BiaPy @BiaPyX]

🚀 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" https://t.co/UuvRPSvWl2 via @YouTube by @IgnacioArganda

[BiaPy @BiaPyX]

3⃣ and of course, programmatically 🤓 by editing the YAML configuration file.

We have a dedicated page in the documentation 📚 that explains the whole process in all three cases:
https://t.co/swlWduOtp6

[BiaPy @BiaPyX]

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 🪄🧙‍♀️

[BiaPy @BiaPyX]

2⃣ from the notebooks, by listing 📒 all available models compatible with your task, then selecting the 🦒 zoo as model source, and finally introducing the nickname of the model that best fits your needs:

[BiaPy @BiaPyX]

📒 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 https://t.co/dUYLOdjMkH via @YouTube by @IgnacioArganda