The adult mammalian testis is filled with seminiferous tubules, which contain somatic Sertoli cells along with germ cells undergoing all phases of spermatogenesis. During spermatogenesis in postnatal mice, male germ cells undergo at least 17 different nomenclature changes as they proceed through mitosis as spermatogonia (=8), meiosis as spermatocytes (=6), and spermiogenesis as spermatids (=3). Adding to this complexity, combinations of germ cells at each of these stages of development are clumped together along the length of the seminiferous tubules. Due to this, considerable expertise is required for investigators to accurately analyze changes in spermatogenesis in animals that have spontaneous mutations, have been genetically modified (transgenic or knockout/knockin), or have been treated with pharmacologic agents. Here, we leverage our laboratory's expertise in spermatogenesis to optimize the open-source "Quantitative Pathology & Bioimage Analysis" software platform for automated analyses of germ and somatic cell populations in both the developing and adult mammalian testis.