Python programs for electron microscopy
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pyem Call stack for parallel pdistdq. Feb 14, 2019
.gitignore Added ipynb, eman2 logs to .gitignore Dec 17, 2017
LICENSE Licensing, documentation and enhanced feature completeness. Aug 5, 2016 Updated for Dec 12, 2016
activate activate script for EMAN2 virtualenv Aug 30, 2016 Aug 30, 2016 rudimentary changelog Sep 17, 2018 output merge key Sep 22, 2018 Added final mask argument in Dec 25, 2018 Refactor --base-map and --overlap to work as expected Aug 23, 2018 option for cisTEM Relion imports Oct 16, 2018 Most of (no plots, untested). Dec 5, 2018 phase flipping support Sep 8, 2018 Move util.convert and util.quat to new geom package. Nov 20, 2018 Code cleanup inspections (minor). Feb 13, 2019 Let relion compute apix if none provided Sep 30, 2017
requirements.txt healpy is required Feb 3, 2019 added healpy to Feb 3, 2019 Added for projection matching/sorting May 13, 2018 Sep 18, 2018 Fix for single merge-field. Feb 13, 2019 added --class Jul 23, 2018 Code cleanup inspections (minor). Feb 13, 2019 maintenance. Dec 5, 2018 Corrected Dec 5, 2018


UCSF PyEM is a collection of Python modules and command-line utilities for electron microscopy of biological samples.

The entire collection is licensed under the terms of the GNU Public License, version 3 (GPLv3).

Copyright information is listed within each individual file. Current copyright holders include:

  • Eugene Palovcak (UCSF)
  • Daniel Asarnow (UCSF)

Documentation for the programs can be found in their usage text, comments in code, and in the Wiki of this repository.


  1. - Perform projection subtraction using per-particle FRC normalization.
  • - Recenter particles on the center-of-mass of corresponding 2D class-averages.
  • - Graph angular distributions on polar scatter plots. Supports particle subset selection.
  • pyem/ - Alter .star files. Supports dropping arbitrary fields, Euler angles, etc.
  • - Project a map according to .star file entries (angles, CTF, etc.).
  • - Convert Cryosparc metadata files to Relion .star format.

Library modules

  1. pyem/ - Simple, standalone MRC I/O functions.
  • pyem/ - Parse and write .star files. Uses pandas.DataFrame as a backend.

Other files

  1. activate - Place in EMAN2/bin to turn EMAN2 into a Python virtual environment.

(C) 2016 Daniel Asarnow
University of California, San Francisco