QuPath

QuPath is an open, powerful, flexible, extensible software platform for bioimage analysis.

September 2021: New QuPath API docs

To coincide with the release of v0.3.0, QuPath’s API docs are finally online at http://qupath.github.io/javadoc/docs.

These give an overview of all the public methods in the main QuPath code, and may be useful for anyone writing custom scripts or extensions.

September 2021: QuPath v0.3.0 now available!

Release highlights

New ‘Create density map’ command to visualize hotspots & generate annotations based on object densities
Many code fixes & major performance improvements - especially for pixel classification
Revised code structure, with non-core features now separated out as optional extensions
Rotate images in the viewer 360°
Easier OpenCV scripting with many new methods in OpenCVTools
New build scripts, now with continuous integration via GitHub Actions
Groundwork for new features coming soon…

Download QuPath v0.3.0 here!

QuPath screenshots

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

March 2021: We need your help!

It’s grant application time again – which means planning for the future and trying to convince funding bodies that QuPath is important.

Please help us by completing our QuPath User Survey!

By participating, you not only help us to establish QuPath’s continued existence, but also to shape our priorities. This isn’t just about adding new software features and improving the existing ones: we’d really appreciate your views on training opportunities, support models, research collaborations, and community events as we aim to make the software as useful as possible for researchers worldwide.

Thanks!

September 2020: New updates released

QuPath v0.2.3 is available here.

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)

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

The QuPath webinar at NEUBIAS Academy is now on YouTube.

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

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.