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This version (2018/06/20 13:12) is a draft.
Approvals: 0/1

sxpipe reboxing

Reboxing: Generate coordinates files and micrograph selection text file based on information stored in the image headers of SPHIRE particle stack file, by extracting coordinates from the input stack, then center them according to projection parameters in the header and user-provided 3D shift.


Usage in command line  reboxing  input_stack_path  output_directory  --box_size=BOX_SIZE  --shift3d_x=SHIFT3D_X  --shift3d_y=SHIFT3D_Y  --shift3d_z=SHIFT3D_Z

Typical usage

sxpipe reboxing does not support MPI. reboxing 'bdb:outdir_window#data' 'outdir_pipe_reboxing'  --box_size=352  --shift3d_z=15


Main Parameters

Input image stack: Specify path to input particle stack. (default required string)
Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)
Particle box size [Pixels]: The x and y dimensions of square area to be windowed. (default 0)
3D x-shift [Pixels]: User-provided 3D x-shift corresponding to shifting the 3D volume along x-axis. (default 0)
3D y-shift [Pixels]: User-provided 3D y-shift corresponding to shifting the 3D volume along y-axis. (default 0)
3D z-shift [Pixels]: User-provided 3D z-shift corresponding to shifting the 3D volume along z-axis. (default 0)

Advanced Parameters


List of output Files

File Name Discription
original/${MICROGRAPH_ROOTNAME} The list of original coordinates stored in the headers of particle images in the stack. These files can be used as inputs of sxwindow
centered/${MICROGRAPH_ROOTNAME} The list of centered (or transformed) coordinates. . These files can be used as inputs of sxwindow
micrographs.txt Micrograph selection text file containing the list of extracted micrograph basenames. This file can be used as micrograph selection text file for sxcter, sxgui_cter, sxwindow, sxpipe organize_micrographs, and e2bdb


This command executes the following processes:

  1. Extract the following information stored in the header of each particle image.
    • source micrograph path.
    • box center coordinates within the micrograph.
    • projection parameters.
  2. Convert the center coordinates to EMAN1 box coordinates format, and then save the results to output files.
  3. Transform the coordinates based on the projection parameters and user-provided 3D shift, and then save the results to output files.
  4. Save the list of extracted micrograph names to an output file.



Developer Notes

2018/02/21 Toshio Moriya

Wish list:

  • Add --proj_params to use the projection parameter files stored in a text file instead of image headers.
  • Setting --box_size to zero (default value) should save the coordinates file in SPHIRE format
  • Save adjusted shifts to files
  • Save projection parameters
  • Save CTF parameters

Author / Maintainer

Christos Gatsogiannis and Toshio Moriya





See also


Alpha:: Under development.


There are no known bugs so far.

pipeline/meridien/sxpipe_reboxing.txt ยท Last modified: 2018/06/20 13:12 (external edit)