#QuPath + Imglib2 and #BDV ❤️
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
October 7, 2025 at 8:34 PM
#QuPath + Imglib2 and #BDV ❤️
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
Promising start!
(Mainly Léo and Pete's work github.com/qupath/qupat... + a small addition)
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3)
forum.image.sc/t/qupath-ext...
forum.image.sc/t/qupath-ext...
QuPath extension Spotiflow is now available
Hello @qupath team & users, We are pleased to announce a new qupath-spotiflow-extension to handle spotiflow in QuPath 🎉 ! This extension reproduces the logic behind the qupath-extension-cellpose to ...
forum.image.sc
August 12, 2025 at 3:10 PM
A new extension! Rémy made a wrapper of @albertdm.bsky.social + @maweigert.bsky.social 's Spotiflow (2/3)
forum.image.sc/t/qupath-ext...
forum.image.sc/t/qupath-ext...
We've updated our BIOP extensions to QuPath 0.6! 🎉
forum.image.sc/t/qupath-bio...
One-click extension installs are her! ABBA, Warpy, Cellpose, and the last one? chef's kiss 👌(1/3)
forum.image.sc/t/qupath-bio...
One-click extension installs are her! ABBA, Warpy, Cellpose, and the last one? chef's kiss 👌(1/3)
QuPath-BIOP catalog is out
Hello @qupath team & users, We are pleased to announce the changes to our extensions that come with the release of QuPath 0.6.0. QuPath BIOP catalog Starting from v0.6.x, QuPath now handles extensio...
forum.image.sc
August 12, 2025 at 3:10 PM
We've updated our BIOP extensions to QuPath 0.6! 🎉
forum.image.sc/t/qupath-bio...
One-click extension installs are her! ABBA, Warpy, Cellpose, and the last one? chef's kiss 👌(1/3)
forum.image.sc/t/qupath-bio...
One-click extension installs are her! ABBA, Warpy, Cellpose, and the last one? chef's kiss 👌(1/3)
Videos are now available from the 2025 QuPath Training Course, from @iamichaelnelson.bsky.social, @zmikulski.bsky.social, and myself.
Watch for multiplex tutorials! For image analysis inspiration! Or just watch to hear me speak like an overcaffeinated squirrel!
www.youtube.com/playlist?lis...
Watch for multiplex tutorials! For image analysis inspiration! Or just watch to hear me speak like an overcaffeinated squirrel!
www.youtube.com/playlist?lis...
February 3, 2026 at 11:22 PM
Videos are now available from the 2025 QuPath Training Course, from @iamichaelnelson.bsky.social, @zmikulski.bsky.social, and myself.
Watch for multiplex tutorials! For image analysis inspiration! Or just watch to hear me speak like an overcaffeinated squirrel!
www.youtube.com/playlist?lis...
Watch for multiplex tutorials! For image analysis inspiration! Or just watch to hear me speak like an overcaffeinated squirrel!
www.youtube.com/playlist?lis...
📢Announcing a QuPath Workshop 📢
February 24-25, 2025, in San Diego, CA, at the La Jolla Institute for Immunology.
This year’s event will be all about Multiplex Immunofluorescence Analysis.
The workshop will be followed by an 🎉 Advanced QuPath User’s Meeting 🎉- February 26, 2025.
February 24-25, 2025, in San Diego, CA, at the La Jolla Institute for Immunology.
This year’s event will be all about Multiplex Immunofluorescence Analysis.
The workshop will be followed by an 🎉 Advanced QuPath User’s Meeting 🎉- February 26, 2025.
December 10, 2024 at 6:04 PM
📢Announcing a QuPath Workshop 📢
February 24-25, 2025, in San Diego, CA, at the La Jolla Institute for Immunology.
This year’s event will be all about Multiplex Immunofluorescence Analysis.
The workshop will be followed by an 🎉 Advanced QuPath User’s Meeting 🎉- February 26, 2025.
February 24-25, 2025, in San Diego, CA, at the La Jolla Institute for Immunology.
This year’s event will be all about Multiplex Immunofluorescence Analysis.
The workshop will be followed by an 🎉 Advanced QuPath User’s Meeting 🎉- February 26, 2025.
@ahklemm.bsky.social shows pipelines developed by the SciLife bioimage analysis core facility.
Here are some training videos for QuPath #CBIAS2024
Here are some training videos for QuPath #CBIAS2024
November 26, 2024 at 12:49 PM
@ahklemm.bsky.social shows pipelines developed by the SciLife bioimage analysis core facility.
Here are some training videos for QuPath #CBIAS2024
Here are some training videos for QuPath #CBIAS2024
3rd day of the #NEUBIASpasteur2025 with a introduction lecture to OMICS by Florian Muller, followed by a full day of #qupath by Thierry Pecot and #ome-zarr / #dask by @m-albert.bsky.social
May 14, 2025 at 10:22 AM
3rd day of the #NEUBIASpasteur2025 with a introduction lecture to OMICS by Florian Muller, followed by a full day of #qupath by Thierry Pecot and #ome-zarr / #dask by @m-albert.bsky.social
Qupath training course by @microscopy.bsky.social @lji.org ** learn from the experts in 🔬 and image analysis firsthand
2025 QuPath Training Course: From Samples to Knowledge
Turn your multiplexed tissue images into useful biological data!
www.eventbrite.com
January 20, 2025 at 5:16 AM
Qupath training course by @microscopy.bsky.social @lji.org ** learn from the experts in 🔬 and image analysis firsthand
Hehe, finally had time to revamp a bit Warpy. It's now possible to concatenate a series of transformed sections in a 3D stack for #QuPath. Computed on the fly and with reasonable performance (image and transform field caching).
May 2, 2025 at 1:23 PM
Hehe, finally had time to revamp a bit Warpy. It's now possible to concatenate a series of transformed sections in a 3D stack for #QuPath. Computed on the fly and with reasonable performance (image and transform field caching).
❗ Interested in quantifiying and displaying histological data? Check out our recent python package operating downstream of histological alignement and segmentation pipelines (eg ABBA, QuPath) to calculate and illustrate various metrics, including exquisite tutorials!
joss.theoj.org/papers/10.21...
joss.theoj.org/papers/10.21...
cuisto: A Python package to quantify neurohistological data from QuPath and ABBA
Le Goc et al., (2025). cuisto: A Python package to quantify neurohistological data from QuPath and ABBA. Journal of Open Source Software, 10(111), 7906, https://doi.org/10.21105/joss.07906
joss.theoj.org
July 18, 2025 at 11:34 AM
❗ Interested in quantifiying and displaying histological data? Check out our recent python package operating downstream of histological alignement and segmentation pipelines (eg ABBA, QuPath) to calculate and illustrate various metrics, including exquisite tutorials!
joss.theoj.org/papers/10.21...
joss.theoj.org/papers/10.21...
🧠 AI4Life wouldn’t 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 27, 2025 at 9:05 AM
🧠 AI4Life wouldn’t 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!
📢 Learn #QuPath across 🇵🇹!
The 4th edition of our Intro to QuPath course is happening:
🗓️ May 21–23, 2025
📍 PPBI Nodes across Portugal
🔹 Register by May 11
📝 Info & registration: see comments
The 4th edition of our Intro to QuPath course is happening:
🗓️ May 21–23, 2025
📍 PPBI Nodes across Portugal
🔹 Register by May 11
📝 Info & registration: see comments
April 23, 2025 at 5:01 PM
📢 Learn #QuPath across 🇵🇹!
The 4th edition of our Intro to QuPath course is happening:
🗓️ May 21–23, 2025
📍 PPBI Nodes across Portugal
🔹 Register by May 11
📝 Info & registration: see comments
The 4th edition of our Intro to QuPath course is happening:
🗓️ May 21–23, 2025
📍 PPBI Nodes across Portugal
🔹 Register by May 11
📝 Info & registration: see comments
Registration is OPEN for the 2025 QuPath Training Course on Feb 24-25 and an Advanced Users Meeting on Feb 26 at @lji.org .
The year, the focus will be on Multiplex Immunofluorescence analysis. Hosted by Zbigniew Mikulski, @iamichaelnelson.bsky.social , and myself.
The year, the focus will be on Multiplex Immunofluorescence analysis. Hosted by Zbigniew Mikulski, @iamichaelnelson.bsky.social , and myself.
January 14, 2025 at 12:04 AM
Registration is OPEN for the 2025 QuPath Training Course on Feb 24-25 and an Advanced Users Meeting on Feb 26 at @lji.org .
The year, the focus will be on Multiplex Immunofluorescence analysis. Hosted by Zbigniew Mikulski, @iamichaelnelson.bsky.social , and myself.
The year, the focus will be on Multiplex Immunofluorescence analysis. Hosted by Zbigniew Mikulski, @iamichaelnelson.bsky.social , and myself.
Day 3 for the ECI track at #neubiaspasteur2025!
Photo: Thierry Pécot introducing the wonders of #QuPath to very attentive students
Photo: Thierry Pécot introducing the wonders of #QuPath to very attentive students
May 14, 2025 at 9:43 AM
Day 3 for the ECI track at #neubiaspasteur2025!
Photo: Thierry Pécot introducing the wonders of #QuPath to very attentive students
Photo: Thierry Pécot introducing the wonders of #QuPath to very attentive students
Running our first QuPath workshop today with @pradeepr.bsky.social, who doesn't love multiplex slide analysis on a Friday?
October 19, 2023 at 7:52 PM
Running our first QuPath workshop today with @pradeepr.bsky.social, who doesn't love multiplex slide analysis on a Friday?
Registration is now open for the Cochin #QuPath training course for the manipulation of Fluo or color pyramid images, #histology or #microscopy, with the application of #deeplearning
November 5, 2025
November 12, 2025
@institutcochin.bsky.social
institutcochin.fr/formation-co...
November 5, 2025
November 12, 2025
@institutcochin.bsky.social
institutcochin.fr/formation-co...
October 6, 2025 at 3:01 PM
Registration is now open for the Cochin #QuPath training course for the manipulation of Fluo or color pyramid images, #histology or #microscopy, with the application of #deeplearning
November 5, 2025
November 12, 2025
@institutcochin.bsky.social
institutcochin.fr/formation-co...
November 5, 2025
November 12, 2025
@institutcochin.bsky.social
institutcochin.fr/formation-co...
Followed by a very interesting presentation from Stephan Fisher on the Bioinformatics analysis part of the spatial omics pipeline, and a great improvised session of retraining Cellpose in QuPath using SAM annotation by Thierry Pecot
May 15, 2025 at 3:53 PM
Followed by a very interesting presentation from Stephan Fisher on the Bioinformatics analysis part of the spatial omics pipeline, and a great improvised session of retraining Cellpose in QuPath using SAM annotation by Thierry Pecot
Martin Schatz @schatzcz.bsky.social giving an intro to QuPath to students of Instituto Mexicano del Seguro Social research units as part of his @embl.org @globalbioimaging.bsky.social job shadowing program.
September 17, 2025 at 5:33 PM
Martin Schatz @schatzcz.bsky.social giving an intro to QuPath to students of Instituto Mexicano del Seguro Social research units as part of his @embl.org @globalbioimaging.bsky.social job shadowing program.
🧠Today we’re enjoying a packed afternoon of talks: current PhDs on their findings so far; exploring image analysis tools and techniques including QuPath (qupath.github.io) and a keynote lecture from @tomgillingwater.bsky.social ‘Reframing spinal muscular atrophy as a developmental disease’ 🧠
January 28, 2025 at 2:41 PM
🧠Today we’re enjoying a packed afternoon of talks: current PhDs on their findings so far; exploring image analysis tools and techniques including QuPath (qupath.github.io) and a keynote lecture from @tomgillingwater.bsky.social ‘Reframing spinal muscular atrophy as a developmental disease’ 🧠
2/5
- QuPath: used for data def and cell detection
- BioFormats: reading native multiresolution file without conversion
- BigDataViewer: interactive display of potentially massive dataset
- BigWarp: interactive non-linear transformation by @bogovicj.bsky.social / @herrsaalfeld.bsky.social
- QuPath: used for data def and cell detection
- BioFormats: reading native multiresolution file without conversion
- BigDataViewer: interactive display of potentially massive dataset
- BigWarp: interactive non-linear transformation by @bogovicj.bsky.social / @herrsaalfeld.bsky.social
July 24, 2025 at 10:04 AM
2/5
- QuPath: used for data def and cell detection
- BioFormats: reading native multiresolution file without conversion
- BigDataViewer: interactive display of potentially massive dataset
- BigWarp: interactive non-linear transformation by @bogovicj.bsky.social / @herrsaalfeld.bsky.social
- QuPath: used for data def and cell detection
- BioFormats: reading native multiresolution file without conversion
- BigDataViewer: interactive display of potentially massive dataset
- BigWarp: interactive non-linear transformation by @bogovicj.bsky.social / @herrsaalfeld.bsky.social
Congratulations to Mark Arends, Peter Bankhead & the QuPath Team who won The Royal College of Pathologists (RCPath) Team Award for Innovation, Technology or Development of AI.
QuPath is one of the world’s most widely used image analysis platforms for digital pathology. Read more:
QuPath is one of the world’s most widely used image analysis platforms for digital pathology. Read more:
QuPath
QuPath is cross-platform, user-friendly open source software for digital pathology and whole slide image analysis, written using JavaFX. QuPath has also been designed to be developer-friendly, and…
qupath.github.io
June 29, 2026 at 9:01 AM
Congratulations to Mark Arends, Peter Bankhead & the QuPath Team who won The Royal College of Pathologists (RCPath) Team Award for Innovation, Technology or Development of AI.
QuPath is one of the world’s most widely used image analysis platforms for digital pathology. Read more:
QuPath is one of the world’s most widely used image analysis platforms for digital pathology. Read more:
Our QuPath course is back!
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.
📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.
📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...
January 16, 2025 at 2:19 PM
Our QuPath course is back!
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.
📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.
📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...
Thrilled to be teaching this course again this semester!
Join us in Boston for an exciting day of learning image analysis, cell detection & classification, spatial analysis and so much more using QuPath.
Registration: tinyurl.com/iac-qupath-2...
Join us in Boston for an exciting day of learning image analysis, cell detection & classification, spatial analysis and so much more using QuPath.
Registration: tinyurl.com/iac-qupath-2...
Our QuPath course is back!
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.
📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...
Join us this semester to learn QuPath with a combination of lectures and hands-on exercises inspired by real research collaborations we worked on.
📌 Introduction to Bioimage Analysis using QuPath
📆 Date: Feb 10, 2025
🔗 tinyurl.com/iac-qupath-2...
January 16, 2025 at 2:28 PM
Thrilled to be teaching this course again this semester!
Join us in Boston for an exciting day of learning image analysis, cell detection & classification, spatial analysis and so much more using QuPath.
Registration: tinyurl.com/iac-qupath-2...
Join us in Boston for an exciting day of learning image analysis, cell detection & classification, spatial analysis and so much more using QuPath.
Registration: tinyurl.com/iac-qupath-2...
Explore whole slide images and run powerful tissue analysis directly in your browser with the QuPath-Galaxy interactive tool.
https://galaxyproject.org/news/2025-06-24-qupath-post/
##UseGalaxy ##GalaxyProject ##EOSC
https://galaxyproject.org/news/2025-06-24-qupath-post/
##UseGalaxy ##GalaxyProject ##EOSC
ð¬ QuPath-Galaxy: Bringing digital pathology image analysis to your br
Explore whole slide images and run powerful tissue analysis directly in your browser with the QuPath-Galaxy interactive tool.
galaxyproject.org
June 28, 2025 at 6:22 PM
Explore whole slide images and run powerful tissue analysis directly in your browser with the QuPath-Galaxy interactive tool.
https://galaxyproject.org/news/2025-06-24-qupath-post/
##UseGalaxy ##GalaxyProject ##EOSC
https://galaxyproject.org/news/2025-06-24-qupath-post/
##UseGalaxy ##GalaxyProject ##EOSC