The organization of microtubules in spindles is complex and not fully understood. Here we report on current advances in generating 3D reconstructions of staged spindles by serial-section electron tomography, exemplified by the first mitotic spindle in early Caenorhabditis elegans embryo. We then review how advances in correlative light microscopy and quantitative electron tomography enable the development of theory and stochastic simulations, which describe how the microtubule organization in spindles emerges from their dynamics. We show how theory and simulations can be used to address long-standing questions in cell division research, advancing the field beyond a pure structural description of microtubules in spindles.