Cryogenic electron microscopy (cryo-EM) can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. We have developed a general method for the localized three-dimensional reconstruction of such subunits earlier (Ilca et al. 2015 Nature Commununications). In this project we implemented Localized Reconstruction as a plugin (Locarec) for Scipion (Abrishami et al. 2020 Progress in Biophysics & Molecular Biology).