🔬 QuPath-Galaxy: Bringing digital pathology image analysis to your browser.

QuPath is a powerful, open-source software application for bioimage analysis, designed especially for whole slide images and digital pathology.

QuPath-Galaxy integrates this functionality into Galaxy as an interactive tool, enabling users to run complex image analysis directly from their browser — no installation needed.

With QuPath-Galaxy, users can explore large histological images, draw regions of interest, detect and classify cells, and run advanced tissue analysis workflows, all in an interactive, user-friendly environment.

• Based on the official QuPath application, ensuring full compatibility with existing workflows and features.
• Packaged in a Docker container maintained by the Galaxy Europe team for reproducible and portable deployment.
• Fully integrated into Galaxy’s ecosystem of tools, histories, and data management.

In this example, a cardiac tissue section stained by immunofluorescence is visualized using QuPath-Galaxy. DAPI (blue) highlights the nuclei, while F-CHP (green, 5-FAM conjugate) reveals areas of denatured collagen.

A cardiac tissue section stained with DAPI (blue) and F-CHP (green), visualized in the QuPath-Galaxy interactive tool.