DNA labeling in vivo using nucleoside analogues is a current experimental approach to determine cell proliferation rates in cell cultures and tissues. It has also been successfully used to localize adult stem cell niches through the identification of nucleoside label-retaining cells (LRC) in long-term experiments. A major hindrance of this methodology relies on the selection of adequate procedures to quantify the nucleoside analogue content from image data files. Here we propose a simple procedure using Fiji image processing software to accurately calculate nucleoside analogue retaining chromatin/total chromatin (LRC/DAPI) signal ratios in the well-known mouse hair follicle stem cell niche.