DE_process_frames.py

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Current version: 3.0.0

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Description

Processes raw frames generated by direct detection cameras. Available features include:

  • Flat-field (dark/gain) correction,
  • Motion correction of whole frames,
  • Motion correction of subregions from frames,
  • Motion correction of individually boxed particles,
  • Extraction of boxed regions-of-interest,
  • Damage compensation (radiation damage filtering),
  • Generation of various sums of individual frames,
  • Bad row/column correction,
  • Filtering of “hot” pixels,
  • Typical processing steps such as edge-normalization, inversion, oversampling, etc.

Requirements

This program requires EMAN2 (Tang et al., J Struct Biol 157 (2007), pp. 38-46). EMAN2 is freely available from: http://blake.bcm.edu/emanwiki/EMAN2.

Usage

Run this program from the command line. Specify command line options (see below), the output directory, and a list of input directories (or image stacks if –input_type=stacks is specified). Input directories should be the directories automatically saved by a Direct Electron camera (e.g., the input directories should contain files such as “info.txt”, “FinalImage.tif”, “RawImage_0.tif”, etc.) Alternatively, input stacks should be MRC stacks of direct detection camera frames.

Usage is:

DE_process_frames.py [options] <output directory> <input directories>

A complete list of command line options are available by typing:

DE_process_frames.py --help

Configuration

Parameters for the script can be specified either through command-line options or by using a configuration file (named DE_process_frames.cfg, in the working directory).
If you choose to use a configuration file, you can generate a file containing all the default parameters by running:

DE_process_frames.py --config_makefile