Abstract
Brain metastases (BrM) occur when malignant cells spread from a primary tumor located in other parts of the body to the brain. BrM is a deadly complication for cancer patients and currently lacks effective therapies. Due to the limited access to patient samples, preclinical models remain a valuable tool for studying metastasis development, progression, and response to therapy. Thus, reliable methods for quantifying metastatic burden in these models are crucial. Here, we describe step by step a new semi-automatic machine-learning approach to quantify metastatic burden on mouse whole-brain stereomicroscope images while preserving tissue integrity. This protocol utilizes the open-source, user-friendly image analysis software QuPath. The method is fast, reproducible, unbiased, and provides access to data points not always obtainable with other existing strategies.