Split a 3d map into several pieces.
segment3d <input file> <output file> [watershed[=<lp>[,<hp>]] [nseg=<n seg>] [morph=<vector file>] [ampw] [thr=<val>] [split] [maxit=<n>] [itxp=<n>] [vector=<outfile>] [apix=<apix>] [chimeraout=<outfile.cmm>] [pdb=<outfile>] [gaussmod=<mrc out>] [randomize] [stats] [segmaxv] [resegbystats=<thr>] [sym=<sym>]
| <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 | ||
| [morph=<vector file>] | Takes the result of a previous segmentation and uses it to seed a new segmentation | ||
| [ampw] | Apply a straight line integral amplitude weight to the distance parameter | ||
| [thr=<val>] | Only segment voxels above the given threshold, neg values use sigma multipliers | ||
| [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 |
Typical usage: segment3d threed.1a.mrc seg.mrc 12 thr=1 Description
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 segments. The assignment is performed in such a way that high density regions will be grouped together.
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 Mon Jan 8 17:35:59 2007