AQSA—Algorithm for Automatic Quantification of Spheres Derived from Cancer Cells in Microfluidic Devices

Sphere formation assay is an accepted cancer stem cell (CSC) enrichment method. CSCs play a crucial role in chemoresistance and cancer recurrence. Therefore, CSC growth is studied in plates and microdevices to develop prediction chemotherapy assays in cancer. As counting spheres cultured in devices is laborious, time-consuming, and operator-dependent, a computational program called the Automatic Quantification of Spheres Algorithm (ASQA) that detects, identifies, counts, and measures spheres automatically was developed. The algorithm and manual counts were compared, and there was no statistically significant difference (<i>p</i> = 0.167). The performance of the AQSA is better when the input image has a uniform background, whereas, with a nonuniform background, artifacts can be interpreted as spheres according to image characteristics. The areas of spheres derived from LN229 cells and CSCs from primary cultures were measured. For images with one sphere, area measurements obtained with the AQSA and SpheroidJ were compared, and there was no statistically significant difference between them (<i>p</i> = 0.173). Notably, the AQSA detects more than one sphere, compared to other approaches available in the literature, and computes the sphere area automatically, which enables the observation of treatment response in the sphere derived from the human glioblastoma LN229 cell line. In addition, the algorithm identifies spheres with numbers to identify each one over time. The AQSA analyzes many images in 0.3 s per image with a low computational cost, enabling laboratories from developing countries to perform sphere counts and area measurements without needing a powerful computer. Consequently, it can be a useful tool for automated CSC quantification from cancer cell lines, and it can be adjusted to quantify CSCs from primary culture cells. CSC-derived sphere detection is highly relevant as it avoids expensive treatments and unnecessary toxicity.