QuPath: Open source software for digital pathology image analysis

Sci Rep. 2017 Dec 4;7(1):16878. doi: 10.1038/s41598-017-17204-5.


QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor identification and high-throughput biomarker evaluation tools, QuPath provides researchers with powerful batch-processing and scripting functionality, and an extensible platform with which to develop and share new algorithms to analyze complex tissue images. Furthermore, QuPath's flexible design makes it suitable for a wide range of additional image analysis applications across biomedical research.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Biomarkers, Tumor / metabolism
  • Colonic Neoplasms / mortality
  • Colonic Neoplasms / pathology
  • Humans
  • Image Interpretation, Computer-Assisted
  • Kaplan-Meier Estimate
  • Programmed Cell Death 1 Ligand 2 Protein / metabolism
  • User-Computer Interface*


  • Biomarkers, Tumor
  • Programmed Cell Death 1 Ligand 2 Protein