Code outputs and figures from "Efficient high-resolution refinement in cryo-EM with stochastic gradient descent"

Code outputs and figures for the numerical experiments on preconditioned SGD for cryo-EM reconstruction for reproducing the results in the article: Efficient high-resolution refinement in cryo-EM with stochastic gradient descent. Bogdan Toader, Marcus A. Brubaker, Roy R. Lederman Acta Crystallographica Section D, 2025 The outputs are obtained by running the Jupyter notebooks in the notebooks/preconditioned_sgd directory in the GitHub repository (release v0.2): https://github.com/bogdantoader/simplecryoem The particle images used for these experiments can be downloaded from EMPIAR-10076 and require inverting the contrast. The file containing the pose variables and CTF parameters is the particles_file/my_particles_8.star file in the attached archive.