Liver Micrometastases area quantification using QuPath and pixel classifier

Sample: Mouse (NSG) liver slices with human colorectal cancer cells metastases, stained with Hematoxylin & Eosin. 

Image Acquisition: Images were acquired on an Olympus VS120 Whole Slide Scanner, using a 20x objective (UPLSAPO, N.A. 0.75) and a color camera (Pike F505 Color) with an image pixel size of 0.345 microns.

Image Processing and Analysis: Obtained images were analyzed using the software QuPath [1] (version 0.3.2) using groovy scripts, making use of a pixel classifier to segment and measure cancer cell clusters.

Files :

Detailed_worflow.pdf : contains a detailed description of how pixel classifier was created

images_for_classifier_training.zip : contains all the vsi file obtained from the microscope and used for the training

project_for_classifier_training.zip : contains the QuPath project, with Training Image, annotations, classifiers and scripts for analysis

PythonCode.txt : code ran to transform output results from QuPath to final results

[1] Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017). https://doi.org/10.1038/s41598-017-17204-5