NovaCTF is a freeware for 3D-CTF correction for electron microscopy, as described in this publication:

Turoňová, B., Schur, F.K.M, Wan, W. and Briggs, J.A.G. Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å.
(doi.org/10.1016/j.jsb.2017.07.007) doi.org/10.1016/j.jsb.2017.07.007

The source code for NovaCTF is distributed under an GPL v.3 license.