QuPath: New open source software using OpenSlide

Pete Bankhead pete.bankhead at gmail.com
Thu Oct 6 02:41:04 EDT 2016

Dear OpenSliders,

I’m happy to announce a new open source software application using OpenSlide, QuPath:
https://qupath.github.io <https://qupath.github.io/>

QuPath has been developed at Queen’s University Belfast, with the aim of providing a cross-platform desktop application for whole slide image analysis in digital pathology that is both user- and developer-friendly.

Features include:
- A new, multi-threaded whole slide image viewer, with many extra features e.g. color transforms, support for touchscreens / 3D mice / graphics tablets
- Tools for manual image evaluation, including annotation and counting tools
- A collection of novel algorithms, e.g. for cell segmentation, dearraying Tissue Microarrays
- A hierarchical, object-based data model to support working with many hundreds of thousands of image objects quickly and efficiently
- Interactive machine learning for object classification, e.g. using cell features or region textures
- Ability to combine steps into workflows for a wide range of applications, which can then be automated
- Support for high-throughput Tissue Microarray scoring, including basic survival analysis based upon biomarker scores
- Powerful scripting using Groovy (or, alternatively, Jython or Javascript)
- Ability to exchange data interactively with other software, e.g. ImageJ and MATLAB
- Extensible design, enabling developers to add features to help share new algorithms and ideas

QuPath is available under GPL v3.  Over the next few weeks I plan to extend the documentation and stabilize the main parts of the API, however binaries are already provided for an initial 'beta’ version, which I hope you may find interesting and useful.

Finally, I’d like to say thanks to the OpenSlide developers for making their work available.  It has been an enormous help in my own battles with analyzing huge images, and in creating QuPath.

Best wishes,

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