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The ovary is a unique organ containing both germline and somatic tissues which are essential for the reproductive function. It is also characterized by an important rearrangement process during the female life cycle and oogenesis. In the medaka Oryzias latipes, as in other teleost fishes, the ovary has been extensively described in qualitative terms, but the mechanisms of oogenesis have rarely been explored in a global tissue context. As a result, there is little understanding about oogenesis dynamics, its regulation and their implication in fertility control, especially in species with short spawning intervals and a protracted reproductive period such as medaka. To shed new light on ovarian dynamics, a comprehensive analysis method was developed by combining tissue transparency, 3D confocal microscopy and open source deep-learning algorithms allowing the extraction of quantitative, spatial and morphological data from whole ovaries at different stages of development. Through the analysis of these data, different follicular reserves were identified during female maturation, as well as major stages of follicle recruitment towards primary and secondary growth in reproductively active adults. The importance of these recruitments for the formation of the spawning batch and the control of normal fecundity rate has been highlighted by the study of a transgenic line with reduced fecundity (miR-202-KO). Furthermore, the precise identification of deregulations in miR-202-KO females seems to indicate a role of this microRNA in the regulation of follicular recruitment.