Immunofluorescence microscopy is a widely adopted method for studying meiotic prophase in the nematode model organism, Caenorhabditis elegans . An in-depth examination of specific meiotic processes requires the quantitative analysis of immunofluorescence images, which often involves the segmentation of individual cells or nuclei. Here, we introduce our image analysis pipeline to automate significant portions of this task. This pipeline relies on the powerful deep learning model Cellpose 2.0 …