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

== Usage ==
 batchboxer [input=<filespec>] [dbbox=<filespec>] [imgbox=<filespec>] [refimg=<filespec>] [auto[=<thr1>,<thr2>,<thr3>]] [mindist=<pixels>] [xform=<dx>,<dy>,<da>] [scale=<mult>] [newsize=<size>] [output=<filespec>] [ctfout=<filespec>] [dbout=<filespec>] [invert] [adjust=<filespec>] [insideonly]

=== Parameters ===
 ||[input=<filespec>]||Image to be boxed (MRC format only!!!)||
 ||[dbbox=<filespec>]||Input box database||
 ||[imgbox=<filespec>]||Read box database from particle image set headers||
 ||[refimg=<filespec>]||Reference particle images for autoboxing||
 ||[auto[=<thr1>,<thr2>,<thr3>]]||Autobox with defined thresholds||
 ||[mindist=<pixels>]||Remove boxes whose centers are within <pixels> of each other||
 ||[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)||
 ||[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||
 ||[adjust=<filespec>]||If images were from a focal pair, this will try to center the particles properly||
 ||[insideonly]||This will not box particles that extend outside the micrograph||
 Typical 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.

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EMAN Manual page, generated Mon Jan  8 17:35:59 2007