Published June 24, 2025
| Version v2
Dataset
Open
Code outputs and figures from "Efficient high-resolution refinement in cryo-EM with stochastic gradient descent"
-
1.
York University
-
2.
Yale University
Description
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):
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.
Files
Files
(8.3 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:8a8348a8782f4db84d33e7878adfee35
|
37.5 MB | Download |
|
md5:a9eb319d0fb7e2c874ae527efdc584c3
|
8.3 GB | Download |
Additional details
Related works
- Is supplement to
- Journal article: 10.1107/S205979832500511X (DOI)
Dates
- Available
-
2025-06-24
Software
- Repository URL
- https://github.com/bogdantoader/simplecryoem
- Programming language
- Python
- Development Status
- Active