batchboxer

This program is used for offline boxing of micrographs (MRC format ONLY!)

batchboxer [refimg=<filespec>] Input reference projection image [dbbox=<filespec>] [i [auto[=<refs>,<thr1>,<thr2>,<thr3>]] [xform=<dx>,<dy>,<da>] [scale=<mult>] [newsize=<size>] [input=<filespec>] [output=<filespec>] [ctfout=<filespec>] [dbout=<filespec>] [invert]

Parameters:


[refimg=<filespec>] Input reference projection image[refimg=<filespec>] Input reference projection images
[dbbox=<filespec>]Input box database
[iRead box database from particle image set headers
[auto[=<refs>,<thr1>,<thr2>,<thr3>]]Autobox with defined thresholds
[xform=<dx>,<dy>,<da>]Rotate and translate the box database before output (see alignhuge)
[scale=<mult>]Scale the box locations, useful if the micrograph has been resized
[newsize=<size>]New box size for all boxes (center preserved)
[input=<filespec>]Image to be boxed (MRC format only!!!)
[output=<filespec>]Output file for boxed images
[ctfout=<filespec>]File to put CTF curves into (if input is focal pair merged)
[dbout=<filespec>]Output box database file
[invert]Invert the particle image before output

Usage:

batchboxer dbbox=jj0441.box input=jj0441.mrc output=0441.hed

Description

This program does offline boxing of particles using a box database or an automatic boxing routine. Please note that it will work only on MRC images.


EMAN Manual page, generated Tue Oct 8 21:38:47 2002