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!!!) | ||
| [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
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