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