usage: prog [options] stack1.hdf stack2.mrcs ...

	Program to erase gold fiducials and other high-density features from images, such as frames in DDD movies or images in tiltseries. Requires scipy.

Option Type Description
--version None show program's version number and exit
--apix float Override Apix in image header.
--lowpass float Multiply lowpass filter frequency by this constant when filtering noise image. Default is 1.11.
--coords str Specify box file with x and y gold coordinates. Must follow standard box file format (x<tab>y<tab>xsize<ysize>) although box sizes are ignored.
--keepdust None Do not remove 'dust' from mask (include objects smaller than gold fiducials).
--goldsize float Diameter (in pixels) of gold fiducials to erase.
--oversample int Oversample noise image to smooth transitions from regions with different noise.
--boxsize int Box size to use when computing local noise.
--debug None Save noise and mask/masked image(s).
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--ppid int Set the PID of the parent process, used for cross platform PPID
--parallel str Default=None (not used). Parallelism. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel
--subset int Default=0 (not used). Apply algorithm to only a subset of images in each stack file.
--nsigmas float Default=3.0. Number of standard deviations above the mean to determine pixels to mask out (erase).