QuPath is an open, powerful, flexible, extensible software platform for whole slide image analysis.

September 2020: New updates released

QuPath v0.2.3 is available here.

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This is a minor release focused on fixing bugs; see the changelog for details.

June 2020: QuPath v0.2.0 now available!

The first Edinburgh release of QuPath is available here.

More than three years since v0.1.2 and a lot has changed.
Highlights include:

• Entirely new pixel classifier (link)
• Rewritten object classifiers (link)
• New methods of thresholding images (link)
• New & improved tools to create & adjust annotations (link)
• Much more support for multiplexed images (link)
• Updated object hierarchy (link)
• Bigger, better, smarter projects (link)
• Export images & annotations, including pyramidal OME-TIFFs (link)
• Many bug fixes, performance improvements… and a lot more (link)

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Find the full documentation at https://qupath.readthedocs.io

Important! It is not recommended to mix different version of QuPath for analysis. If you started a project in v0.1.2, it is probably best to continue with that version - or start again with v0.2.0.

Other news

April 2020: QuPath webinar at NEUBIAS Academy

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The QuPath webinar at NEUBIAS Academy is now on YouTube.

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April 2020: From Samples to Knowledge workshop online

Videos from the recent QuPath workshop held at the La Jolla Institute for Immunology are now on YouTube

Please remember to cite the QuPath paper if you use it in your work!

Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017). https://doi.org/10.1038/s41598-017-17204-5

QuPath is developed at the University of Edinburgh.

The software was originally created at the Centre for Cancer Research & Cell Biology at Queen’s University Belfast, as part of research projects funded by Invest Northern Ireland and Cancer Research UK.