BiaPy: Accessible deep learning on bioimages
Donostia-San Sebastián, Spain
Joined January 2024
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🚀 Big news: BiaPy meets Galaxy! ⛴️🤝🌌
You can now run BiaPy directly inside Galaxy, making deep learning for bioimage analysis easier, reproducible & accessible to everyone.
👉 imaging.usegalaxy.eu/?tool_i…
#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging
🤝 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
This is a new step for accessible, FAIR bioimage AI 🚀
Try the tool 👉 imaging.usegalaxy.eu/?tool_i…
Contribute your models 🧑🔬 And join the community making bioimage analysis open & reproducible!
#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging
🚀 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)
🔗 nature.com/articles/s41592-0…
#DeepLearning #BioimageAnalysis #BiaPy
ALT BiaPy logo, showing a depiction of a boat transporting a microscope.
🔗 Want to try BiaPy?
Check out the full documentation and tutorials here:
👉 biapy.readthedocs.io/
👉 youtube.com/@BiaPyX
Contribute, test, and join the community — BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
🙏 Thanks to @naturemethods, @rita_strack , the reviewers, and the awesome bioimage analysis community.
We can't wait to see what you build with BiaPy! 🚀🧠
🔗 nature.com/articles/s41592-0…
#BiaPy #BioimageAnalysis #DeepLearning (7/7)
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
And we made it to the news: europapress.es/castilla-lama….
We can't wait to see you next week! See you in Toledo.
🆕 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" biorxiv.org/content/10.1101/…
🚀 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" youtu.be/R0Li3tZ7Ryc?si=qsHC… via @YouTube by @IgnacioArganda
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 🪄🧙♀️
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:
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:
biapy.readthedocs.io/en/late…
📒 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 youtu.be/KEqfio-EnYw?si=jvSx… via @YouTube by @IgnacioArganda
Nice news from our friends of @brain_globe 🤩🧠🔬🖥️
BrainGlobe has a new atlas, the prairie vole!
For more details see the blog: brainglobe.info/blog/prairie…
Original paper: doi.org/10.7554/eLife.87029.…
🎃 Happy Halloween BiaPy-ers!!! 👻 Are you a novice user scared 😱 of using #BiaPy's GUI for the first time? Fear no more! 🤗 Here you have a full video with a complete walkthrough on BiaPy's graphical user interface 🖥️⛴️🚶youtu.be/vY7aBh5FUNk?si=pLlx… via @YouTube by @danifranco93
