qupath/qupath

What it solves

QuPath is designed for bioimage analysis, specifically for large-scale images such as whole slide images and microscopy images. It provides tools to annotate, view, and analyze these images to extract quantitative data from biological samples.

How it works

The software provides a suite of tools for both brightfield and fluorescence image analysis. It uses algorithms for common biological imaging tasks like cell segmentation and tissue microarray dearraying. It also incorporates interactive machine learning for classifying pixels and objects, allowing researchers to perform quantitative pathology.

Who it’s for

It is primarily intended for academic researchers and scientists working in bioimage analysis and quantitative pathology.

Highlights

• Interactive machine learning for object and pixel classification.
• Support for whole slide and microscopy images.
• Support for both brightfield and fluorescence workflows.
• Scripting capabilities for customization, batch-processing, and data interrogation.
• Integration with other tools like ImageJ.