QuPath is an open source software for whole slide imaging brightfield analysis of H&E and colorimetric immunohistochemistry (IHC), as well as fluorescence based IHC.

Qupath is aimed at digital pathology where high throughput biomarker analysis in IHC stained Tissue Microarrays (TMAs) for example for cancer research, can detect cells versus tumor with machine learning. It even incorporates survival analysis tools to link this analysis back to clinical data to help quickly uncover the prognostic and predictive roles for each biomarker.

QuPath provides analysis for :

  • both colorimetric IHC and H&E
  • cell segmentation
    • manually drawing regions and counting structures
    • automatically detecting (machine learning) and interactively classifying cells (adaptive machine learning)
  • Tissue microarray dearraying
  • cell and texture classification


It is

  • an object-based hierarchical data model, with scripting support
  • Extensible to add new features or support for different image sources
  • easily integration with other tools, e.g. MATLAB and ImageJ


The program can be downloaded here, and there is a helpful QuPath Wiki.


QuPath tutorial #1 - Getting started

QuPath tutorial #2 - IHC analysis


From Samples to Knowledge 2020

Files for the workshop (warning 11Gb):