Wiki Page Content

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.


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

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