QuPath: Open source software for digital pathology image analysis

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.


Batch processing scripts
This file contains batch processing scripts used in the analysis described in Bankhead et al. 'QuPath: Open source software for digital pathology image analysis'.
It is not intended that these scripts would be used directly for other projects with similar goals (e.g. scoring CD3 or PD-L1 in tissue microarrays), since differences in antibodies, staining and scanning mean that the parameters required for each dataset may be quite different. Nevertheless, the scripts may be used as a template for how similar analysis may be performed using QuPath.
The majority of the scripts here were generated automatically from QuPath's 'Command history' while interactively analyzing an image, with minor editing afterwards to remove any unnecessary steps applied when running commands multiple times to tune parameters.
Further documentation describing how to work with QuPath is provided at https://github.com/qupath/qupath/wiki After export, tissue microarray results can be viewed with QuPath's 'TMA data viewer' or imported into other software.

CD3 & CD8 scripts
These scripts calculate positive cell counts and densities for CD3 and CD8 Tissue Microarrays, as described in Bankhead et al. 'QuPath: Open source software for digital pathology image analysis'.
Each script automates applying the results of running the following commands: * 'Analyze -> Preprocessing -> Estimate stain vectors' * 'Analyze -> Preprocessing -> Simple tissue detection' * 'Analyze -> Cell analysis -> Fast cell counts (brightfield)' * 'File -> Export TMA data' For the first three, it is strongly advised to apply these commands directly to a representative image in order to determine appropriate parameters, which will depend upon the specific scanner and staining used.
QuPath logs the parameters that were used, and can generate the appropriate lines of code to use within the script.

PD-L1 scripts
These scripts were used to score PD-L1 within tissue microarrays (TMAs), as described in Bankhead et al. 'QuPath: Open source software for digital pathology image analysis'.
The process is as follows: