[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 |
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.