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


  • 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]


  • [input=<filespec>]

    Image to be boxed (MRC format only!!!)


    Input box database


    Read box database from particle image set headers


    Reference particle images for autoboxing


    Autobox with defined thresholds


    Remove boxes whose centers are within <pixels> of each other


    Rotate and translate the box database before output (see alignhuge)


    Scale the box locations, useful if the micrograph has been resized


    New box size for all boxes (center preserved)


    Output file for boxed images


    File to put CTF curves into (if input is focal pair merged)


    Output box database file


    Invert the particle image before output


    If images were from a focal pair, this will try to center the particles properly


    This will not box particles that extend outside the micrograph

    Typical usage: batchboxer input=jj0441.mrc output=0441.hed


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 Mon Jan 8 17:35:59 2007

EMAN1/Programs/BatchBoxer (last edited 2008-11-26 04:42:30 by localhost)