= segment3d =
 ''Split a 3d map into several pieces.''

== Usage ==
 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>]

=== Parameters ===
 || <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

== 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