BiaPy: Accessible deep learning on bioimages
Joined January 2024
- Tweets 78
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35 Photos and videos
π Big news: BiaPy meets Galaxy! β΄οΈπ€π
You can now run BiaPy directly inside Galaxy, making deep learning for bioimage analysis easier, reproducible & accessible to everyone.
π imaging.usegalaxy.eu/?tool_iβ¦
#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging
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π€ And thereβs more! Thanks to this integration, you can also tap into the π¦ BioImage Model Zoo π§¬.
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
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This is a new step for accessible, FAIR bioimage AI π
Try the tool π imaging.usegalaxy.eu/?tool_iβ¦
Contribute your models π§βπ¬ And join the community making bioimage analysis open & reproducible!
#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging
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π 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. π(1/7)
π nature.com/articles/s41592-0β¦
#DeepLearning #BioimageAnalysis #BiaPy
ALT BiaPy logo, showing a depiction of a boat transporting a microscope.
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π Want to try BiaPy?
Check out the full documentation and tutorials here:
π biapy.readthedocs.io/
π youtube.com/@BiaPyX
Contribute, test, and join the community β BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
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π Thanks to @naturemethods, @rita_strack , the reviewers, and the awesome bioimage analysis community.
We can't wait to see what you build with BiaPy! ππ§
π nature.com/articles/s41592-0β¦
#BiaPy #BioimageAnalysis #DeepLearning (7/7)
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BiaPy retweeted
20 Nov 2024
and 4β£, 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! π
ALT Title slide of the presentation by Ignacio Arganda-Carreras at SPAOM 2024, entitled "BiaPy: Bioimage Analysis workflows for all audiences".
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BiaPy retweeted
20 Nov 2024
3β£ Tomorrow after lunch (16.15h β 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
x.com/SPAOM5/status/18309220β¦
The SPAOM 2024 Community Workshops are here! π Join us for hands-on sessions with experts, cutting-edge techniques, and the latest in optical microscopy and imaging. π¬
π Learn more and register: SPAOM2024.org
Don't miss out on this incredible opportunity #SPAOM2024
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BiaPy β΄οΈ 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 βΊοΈ See you all there! #SPAOM2024
And we made it to the news: europapress.es/castilla-lamaβ¦.
We can't wait to see you next week! See you in Toledo.
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π We have updated our preprint in @biorxivpreprint π° It explains better the current state of #BiaPy β΄οΈ while describing as well its limitations π€ Hope you like it!
"BiaPy: Accessible deep learning on bioimages" biorxiv.org/content/10.1101/β¦
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π For a fast overview on how to reuse models from the @bioimageio zoo π¦in our notebooks π (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
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Would you like to use a model from the @bioimageio zoo π¦ as core model of your BiaPy β΄οΈ workflow? No worries! You can easily do that either π
1β£ from the GUI π₯οΈ, specially if you follow the instructions of our friendly wizard πͺπ§ββοΈ
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3β£ and of course, programmatically π€ by editing the YAML configuration file.
We have a dedicated page in the documentation π that explains the whole process in all three cases:
biapy.readthedocs.io/en/lateβ¦
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π Our code-free notebooks are designed to be self-explainable and (hopefully π€) 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=jvSxβ¦ via @YouTube by @IgnacioArganda
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