Q: Boxer - How can I use boxer to evaluate and clean up the automatically selected particles from batchboxer ?
A: This is best done using a shell script. You can get boxer to preload a micrograph and a box database as it starts, for example:
boxer image.mrc box=image.box bright=0 contrast=0.2
So, you just write a shell script which calls boxer sequentially with each pair of image files and box databases. After saving the results within boxer, just quit, and the shell script will load the next image. Since boxer remembers window positions, everything should pop up pretty much like you left it.
Note that boxer (and most other EMAN programs) append new images to existing files. That is, if you already have a file called img123.hed, and select this as a file to write particles to in boxer, it will append the new particles to the existing file rather than create a new one. For this reason, my approach is to:
Run batchboxer on all images (using a shell script), but only output the box database, not the selected particles
Run boxer on all images (using a shell script), again, only save the box database (this will be overwritten, not appended)
When all of my box databases are good, then run batchboxer again to extract the particles, but don't have it autobox, just have it use the existing box database files.
My own shell script (I use zsh) for the second step above looks like this (assumes .mrc extension on the micrographs): {{{foreach i (*box) boxer ${i%.box}.mrc box=$i bright=0 contrast=.15}}}