BiaPy
@biapyx.bsky.social
Accessible deep learning on bioimages
Site: https://biapyx.github.io/
Doc: https://biapy.readthedocs.io/en/latest/
Code: https://github.com/BiaPyX/BiaPy
Site: https://biapyx.github.io/
Doc: https://biapy.readthedocs.io/en/latest/
Code: https://github.com/BiaPyX/BiaPy
Did you miss our workshop on π« Halfway to I2K 2025 π«(www.i2kconference.org)? Worry no more! The video is finally out π
youtu.be/dFLtKHWlYdQ?...
Check it out and learn about BiaPy and its latest news π€ with @iarganda.bsky.social and @danifranco93.bsky.social π€©
youtu.be/dFLtKHWlYdQ?...
Check it out and learn about BiaPy and its latest news π€ with @iarganda.bsky.social and @danifranco93.bsky.social π€©
BiaPy: accessible deep learning workflows
YouTube video by I2K Conference
youtu.be
December 26, 2025 at 11:39 AM
Did you miss our workshop on π« Halfway to I2K 2025 π«(www.i2kconference.org)? Worry no more! The video is finally out π
youtu.be/dFLtKHWlYdQ?...
Check it out and learn about BiaPy and its latest news π€ with @iarganda.bsky.social and @danifranco93.bsky.social π€©
youtu.be/dFLtKHWlYdQ?...
Check it out and learn about BiaPy and its latest news π€ with @iarganda.bsky.social and @danifranco93.bsky.social π€©
This is a new step for accessible, FAIR bioimage AI π
Try the tool π imaging.usegalaxy.eu?tool_id=tool...
Contribute your models π§βπ¬ And join the community making bioimage analysis open & reproducible!
#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging
Try the tool π imaging.usegalaxy.eu?tool_id=tool...
Contribute your models π§βπ¬ And join the community making bioimage analysis open & reproducible!
#BiaPy #GalaxyProject #BioImageAnalysis #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
This is a new step for accessible, FAIR bioimage AI π
Try the tool π imaging.usegalaxy.eu?tool_id=tool...
Contribute your models π§βπ¬ And join the community making bioimage analysis open & reproducible!
#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging
Try the tool π imaging.usegalaxy.eu?tool_id=tool...
Contribute your models π§βπ¬ And join the community making bioimage analysis open & reproducible!
#BiaPy #GalaxyProject #BioImageAnalysis #Bioimaging
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
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
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
media.tenor.com
October 20, 2025 at 2:11 PM
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
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
π οΈ We wrapped BiaPy as a Galaxy tool with a β¨ wizard-style interface (just like BiaPyβs GUI).
That means:
βοΈ Step-by-step experiment setup
βοΈ Launch training / inference jobs with BiaPy under the hood
βοΈ Share & reproduce pipelines the Galaxy way π
That means:
βοΈ Step-by-step experiment setup
βοΈ Launch training / inference jobs with BiaPy under the hood
βοΈ Share & reproduce pipelines the Galaxy way π
October 20, 2025 at 2:11 PM
π οΈ We wrapped BiaPy as a Galaxy tool with a β¨ wizard-style interface (just like BiaPyβs GUI).
That means:
βοΈ Step-by-step experiment setup
βοΈ Launch training / inference jobs with BiaPy under the hood
βοΈ Share & reproduce pipelines the Galaxy way π
That means:
βοΈ Step-by-step experiment setup
βοΈ Launch training / inference jobs with BiaPy under the hood
βοΈ Share & reproduce pipelines the Galaxy way π
π Big news: BiaPy meets @galaxyproject.bsky.social! 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_id=tool...
#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging
You can now run BiaPy directly inside Galaxy, making deep learning for bioimage analysis easier, reproducible & accessible to everyone.
π 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
π Big news: BiaPy meets @galaxyproject.bsky.social! 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_id=tool...
#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging
You can now run BiaPy directly inside Galaxy, making deep learning for bioimage analysis easier, reproducible & accessible to everyone.
π imaging.usegalaxy.eu?tool_id=tool...
#BioImageAnalysis #GalaxyProject #AI4Life #Bioimaging
So, one more time, π« thanks everybody π« for making this happen: from our developers π οΈ to our users π₯.
Huge thanks and keep it up! πͺ
Huge thanks and keep it up! πͺ
a man in a black and white sweater is standing in a living room and says `` seriously thanks so much '' .
ALT: a man in a black and white sweater is standing in a living room and says `` seriously thanks so much '' .
media.tenor.com
July 15, 2025 at 2:58 PM
So, one more time, π« thanks everybody π« for making this happen: from our developers π οΈ to our users π₯.
Huge thanks and keep it up! πͺ
Huge thanks and keep it up! πͺ
In the meantime, we have more than 46 pretrained models from β΄οΈ BiaPy available now in the π¦ Bioimage Model Zoo π«Ά @ai4life.bsky.social
π Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI π₯οΈ, Colab notebooks π and our API π€
π Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI π₯οΈ, Colab notebooks π and our API π€
BioImage.IO - Model Zoo
BioImage Model Zoo - A community-driven, open resource for sharing standardized AI models for bioimage analysis
bioimage.io
July 15, 2025 at 2:58 PM
In the meantime, we have more than 46 pretrained models from β΄οΈ BiaPy available now in the π¦ Bioimage Model Zoo π«Ά @ai4life.bsky.social
π Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI π₯οΈ, Colab notebooks π and our API π€
π Have a look at: bioimage.io#/models
As usual, they are accesible from BiaPy's GUI π₯οΈ, Colab notebooks π and our API π€
We fixed many issues β οΈ and bugs π reported by our community π©. You don't know how happy that makes us π
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 β©
biapy.readthedocs.io/en/latest/ge...
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 β©
biapy.readthedocs.io/en/latest/ge...
Release Version 3.6.0 Β· 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 ...
github.com
July 15, 2025 at 2:58 PM
We fixed many issues β οΈ and bugs π reported by our community π©. You don't know how happy that makes us π
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 β©
biapy.readthedocs.io/en/latest/ge...
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 β©
biapy.readthedocs.io/en/latest/ge...
Special kudos to our fantastic summer intern Ibai Mayoral π¨βπ from the @dipcehu.bsky.social who has made an incredible job at implementing all those methods now within BiaPy's core code π€©
dipc.ehu.eus/en/career/in...
dipc.ehu.eus/en/career/in...
Development of Open-Source Deep Learning Tools for Bioimage Analysis
dipc.ehu.eus
July 15, 2025 at 2:58 PM
Special kudos to our fantastic summer intern Ibai Mayoral π¨βπ from the @dipcehu.bsky.social who has made an incredible job at implementing all those methods now within BiaPy's core code π€©
dipc.ehu.eus/en/career/in...
dipc.ehu.eus/en/career/in...
We have removed βοΈ 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 π the session, yay! π€
bsky.app/profile/biap...
So no more this π
bsky.app/profile/biap...
So no more this π
π Did you experience troubles β οΈ 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 π
July 15, 2025 at 2:58 PM
We have removed βοΈ 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 π the session, yay! π€
bsky.app/profile/biap...
So no more this π
bsky.app/profile/biap...
So no more this π
β΄οΈ BiaPy just reached version 3.6.1 π« (latest release)!
github.com/BiaPyX/BiaPy...
β‘οΈ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs π
Let me tell you a bit about what's new π
github.com/BiaPyX/BiaPy...
β‘οΈ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs π
Let me tell you a bit about what's new π
Release Version 3.6.1 Β· 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
β΄οΈ BiaPy just reached version 3.6.1 π« (latest release)!
github.com/BiaPyX/BiaPy...
β‘οΈ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs π
Let me tell you a bit about what's new π
github.com/BiaPyX/BiaPy...
β‘οΈ v3.6.1 came right after (the more dense) v3.6.0 to fix some small bugs π
Let me tell you a bit about what's new π
Yay! Well done @danifranco93.bsky.social π€ and long life to @ai4life.bsky.social π€©
π§ AI4Life wouldnβt be the same without the amazing BioImage.IO community partners!
Now showcasing real-world tools from our partners: DeepIcy, @biapyx.bsky.social, SpotMAX and QuPath.
Huge thanks to our collaborators!
Now showcasing real-world tools from our partners: DeepIcy, @biapyx.bsky.social, SpotMAX and QuPath.
Huge thanks to our collaborators!
May 28, 2025 at 9:14 AM
Yay! Well done @danifranco93.bsky.social π€ and long life to @ai4life.bsky.social π€©
Reposted by BiaPy
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/
https://mappingignorance.org/2025/05/15/biapy-analising-bioimages-made-easy/
May 16, 2025 at 4:05 AM
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/
https://mappingignorance.org/2025/05/15/biapy-analising-bioimages-made-easy/
No words needed! #neubiaspasteur2025 @iarganda.bsky.social @danifranco93.bsky.social @biapyx.bsky.social Thank you @jwpylvanainen.bsky.social
May 15, 2025 at 10:58 AM
Right! That was one of our first options π€ 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 π
May 2, 2025 at 9:24 AM
Right! That was one of our first options π€ 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 π
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.
April 30, 2025 at 6:30 AM
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.
Kudos to you, my captain! π¦ΈββοΈ
a man with dreadlocks and a beard is wearing a pirate hat and pointing at something .
ALT: a man with dreadlocks and a beard is wearing a pirate hat and pointing at something .
media.tenor.com
April 30, 2025 at 6:18 AM
Kudos to you, my captain! π¦ΈββοΈ
We're working on eliminating those dependencies π
a black cat is sitting in front of a laptop computer .
ALT: a black cat is sitting in front of a laptop computer .
media.tenor.com
April 30, 2025 at 6:12 AM
We're working on eliminating those dependencies π
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 π¬
April 30, 2025 at 6:11 AM
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 π¬
π 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! ππ§
π www.nature.com/articles/s41...
#BiaPy #BioimageAnalysis #DeepLearning
@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! ππ§
π 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
π 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! ππ§
π www.nature.com/articles/s41...
#BiaPy #BioimageAnalysis #DeepLearning
@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! ππ§
π www.nature.com/articles/s41...
#BiaPy #BioimageAnalysis #DeepLearning
π Want to try BiaPy?
Check out the full documentation and tutorials here:
π biapy.readthedocs.io
π www.youtube.com/@BiaPyX
Contribute, test, and join the community β BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
Check out the full documentation and tutorials here:
π biapy.readthedocs.io
π www.youtube.com/@BiaPyX
Contribute, test, and join the community β BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
BiaPy: Accessible deep learning on bioimages β BiaPy documentation
biapy.readthedocs.io
April 29, 2025 at 9:33 AM
π Want to try BiaPy?
Check out the full documentation and tutorials here:
π biapy.readthedocs.io
π www.youtube.com/@BiaPyX
Contribute, test, and join the community β BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
Check out the full documentation and tutorials here:
π biapy.readthedocs.io
π www.youtube.com/@BiaPyX
Contribute, test, and join the community β BiaPy is open source! (6/7)
#OpenScience #Microscopy #AI
𧬠BiaPy was built by an international collaboration between researchers from @upvehu.bsky.social, @dipcehu.bsky.social , @uc3m.es and others β led by
@iarganda.bsky.social and @arratemunoz.bsky.social.
A huge thanks to everyone who contributed! π (5/7)
@iarganda.bsky.social and @arratemunoz.bsky.social.
A huge thanks to everyone who contributed! π (5/7)
April 29, 2025 at 9:33 AM
𧬠BiaPy was built by an international collaboration between researchers from @upvehu.bsky.social, @dipcehu.bsky.social , @uc3m.es and others β led by
@iarganda.bsky.social and @arratemunoz.bsky.social.
A huge thanks to everyone who contributed! π (5/7)
@iarganda.bsky.social and @arratemunoz.bsky.social.
A huge thanks to everyone who contributed! π (5/7)
π‘ How is BiaPy different?
β’ Full multi-GPU support for training and inference
β’ Efficient memory management for very large datasets (MBs β TBs)
β’ Single-container installation via Docker
β’ Integration with @BioImageModelZoo for easy model sharing and reuse!
#DeepLearning (4/7)
β’ Full multi-GPU support for training and inference
β’ Efficient memory management for very large datasets (MBs β TBs)
β’ Single-container installation via Docker
β’ Integration with @BioImageModelZoo for easy model sharing and reuse!
#DeepLearning (4/7)
April 29, 2025 at 9:33 AM
π‘ How is BiaPy different?
β’ Full multi-GPU support for training and inference
β’ Efficient memory management for very large datasets (MBs β TBs)
β’ Single-container installation via Docker
β’ Integration with @BioImageModelZoo for easy model sharing and reuse!
#DeepLearning (4/7)
β’ Full multi-GPU support for training and inference
β’ Efficient memory management for very large datasets (MBs β TBs)
β’ Single-container installation via Docker
β’ Integration with @BioImageModelZoo for easy model sharing and reuse!
#DeepLearning (4/7)