snrboxer

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

snrboxer [input=<filespec>] [dbbox=<filespec>] [imgbox=<filespec>] [refimg=<filespec>] [auto[=<thr1>,<thr2>,<thr3>]] [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
[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

Usage:

snrboxer input=jj0441.mrc output=0441.hed dbout=0441.box auto=0.005,1,6 refimg=refs.hed

Description

This program does offline boxing of particles using using an automatic boxing routine. (Please note that it will work only on MRC images.) This program is meant as an alternative to the batchboxer program, with slightly different thresholds: (1) the first threshold uses a minimum estimated SNR to find all candidate particles, (2) the second eliminates boxes with high residual noise energy, and (3) the third eliminates boxes with high spectral variation in the residual noise. The second and third have similar purposes, but one may be more effective in particular cases. It is strongly recommended that the user specify an accurate set of references (in particular, accounting for the CTF if possible).


EMAN Manual page, generated Wed Feb 18 10:33:43 2009