QuPath
Open source desktop software for pathology and microscopy image analysis on Windows, macOS and Linux, with cell segmentation and machine learning.
QuPath is a free, open source desktop application for researchers analyzing whole slide pathology and microscopy images on their own computers. It combines image viewing and annotation with cell segmentation and interactive machine learning, so researchers can examine tissue and classify what they find within the same application. It runs on Windows, macOS and Linux.
Its analysis workflows cover both brightfield and fluorescence images. Researchers can annotate regions, segment cells, and train classifiers to distinguish objects or pixels. For tissue microarray studies, it includes tools to identify and separate the individual tissue cores for analysis.
QuPath pairs these visual tools with scripting for researchers who need to customize an analysis or apply it across a batch of images. Scripts also support querying analysis data. This makes it relevant to work that starts with close inspection of individual slides and then needs the same methods applied to a larger collection.
ImageJ integration connects QuPath with another established image analysis tool. Its extensible design lets developers add capabilities, while the application uses Java and JavaFX for its desktop interface.
QuPath is intended for research use only. It is available under the GNU General Public License v3.0 (GPL-3.0), which allows researchers to inspect its source code and modify the software.
