Understanding ovarian function requires a clear and detailed picture of biological processes that take place deep inside the body, within a narrow window of time. Essential progress is being held back by the limited experimental approaches currently available to study the ovarian cycle in real time. We recently developed a model system to study ovulation live using high-resolution microscopy. We adapted a long-term membrane-based culture system of isolated mouse follicles for use with advanced quantitative live imaging. In brief, antral follicles are mechanically isolated from whole mouse ovaries and cultured in medium containing hormone combinations that mimic late folliculogenesis and ovulation. This enabled us to, for the first time, resolve the entire 12-hour-long ovulatory process at cellular resolution. To follow the behaviour of individual cells, we used transgenic mice expressing a membrane (Myr-tdTomato) and a histone (H2B-GFP) marker. Using confocal microscopy, we were able to follow the dynamic behaviour of cells and the oocyte inside the follicle. We were also able to use two-photon microscopy and 3D reconstructions to measure follicle volume and shape changes during ovulation. This generated robust quantitative measurements of the process. The major advantage of our method is the introduction of multiple imaging modalities and perturbations, allowing for the detailed visualisation and manipulation of ovarian function in real time. In this protocol, we describe the procedures for follicle isolation, culture, imaging.