Tools to analyze the organization and formation of the germline cyst in zebrafish oogenesis.

Oocytes develop in a cellular organization called the germline cyst, in which germ cells are tightly interconnected and surrounded by somatic cells. The cyst produces oocytes for follicle formation and is a hub for essential processes in meiosis and oocyte differentiation. However, the formation and organization of the cyst, and their contribution to oocyte production in vertebrates remain unclear. Here, we provide tools for three-dimensional and functional in-vivo analyses of the germline cyst in the zebrafish ovary. We describe the use of serial block face - scanning electron microscopy (SBF-SEM) to resolve the three-dimensional architecture of cells and organelles in the cyst at ultrastructure resolution. We present a deep learning-based pipeline for high throughput quantitative analysis of three-dimensional confocal datasets of cysts in vivo. We provide a method for laser-ablation of cellular components for manipulating cyst cells in ovaries. These methods will facilitate the investigation of the cyst cellular organization, expand the toolkit for the study of the zebrafish ovary, and advance our understanding of female developmental reproduction. They can be further applied for the investigation of other developmental systems.