Measuring Nuclear/Cytoplasmic Intensity with CellProfiler

Detailed walk-through of a CellProfiler pipeline to quantify nuclear localization of a protein from microscope images. I discuss the pros and cons of using the whole cytoplasm versus the perinuclear ring region and the importance of log transforming the ratio.
Labels used here were Hoechst (DNA and nuclear segmentation) and anti-YAP/TAZ (subcellular localization and cell segmentation).