Welcome to the protomo website. Protomo is a software package used in electron tomography for marker-free alignment and 3D reconstruction of tilt series. The marker-free alignment is based on cross-correlation methods and projection matching. It also includes the refinement of geometric parameters of the tilt series. 3D reconstruction is carried out by weighted backprojection with general weighting functions that allow varying tilt angle increments. The software was originally developed for thin sections of insect flight muscle and paracrystalline protein arrays, but has since been successfully applied to various specimens in cyro-electron tomography.