
| <input file> | Source file |
| <output file> | Destination file |
| [watershed[=<lp>[,<hp>]] | Apply simplistic watershed segmentation instead of the default (k-means), with an optional pre-filter |
| [nseg=<n seg>] | Number of segments to split map into |
| [ampw] | Apply a straight line integral amplitude weight to the distance parameter |
| [thr=<val>] | Only segment voxels above the given threshold |
| [split] | Separate out the individual segments |
| [maxit=<n>] | Specify maximum iterations before giving up on convergence |
| [itxp=<n>] | After the segmentation, iteratively extend the segments into regions below threshold, n is the number of voxels of expansion |
| [vector=<outfile>] | Write segment centers to a text file x,y,z,dx,dy,dz |
| [apix=<apix>] | A/pix for chimera output |
| [chimeraout=<outfile.cmm>] | Write segment centers to a chimera marker file |
| [pdb=<outfile>] | Write segment centers to a PDB file |
| [gaussmod=<mrc out>] | Construct a 3d model from Gaussians centered at the group centers. |
| [randomize] | This will randomize the gaussians by rotating them randomly with a fixed radius |
| [stats] | Produce a file containing mean density values in each segment |
| [segmaxv] | Instead of an integer segmap, writes the 'max' value for the segment |
| [resegbystats=<thr>] | Merge segments with mean densities above or below the threshold value |
| [sym=<sym>] | Insure a symmetric segmentation |
segment3d threed.1a.mrc seg.mrc 12 thr=1
This program will take a 3D map and that map into 'segments'.
That is, every voxel in the map will be assigned to one of Note that using the 'watershed' option combined with 'nseg=' will not produce
a true 'watershed' segmentation of the image. Instead, it will produce nseg segments
then will 'flood fill' the remaining areas above the threshold.
EMAN Manual page, generated Tue May 25 14:15:52 2004