celegans_straighten.wiki

Check out location

	svn co https://svn.janelia.org/penglab/projects/vaa3d_tools/released_plugins/v3d_plugins/celegans_straighten

Usage

func

cst
help

   Usage : v3d -x straighten -f cst -i <inimg_file> <marker_file> -o <outimg_file> 
               -p <refchannel> <ratio> <ctnum> <ocradius> <xy_factor> <xz_factor> <cpradius>

     inimg_file    file name of input image
     marker_file   file name of input marker
     outimg_file   file name of output image
     refchannel    channel number, r: 0, g: 1, b: 2, all: 9, default 1
     ratio         downsampling ratio, default 4.0
     ctnum         number of control points, default 10
     ocradius      radius of openclosing, default 0
     xy_factor     xy fg thresh factor, default 3.0
     xz_factor     xz fg thresh factor, default 0.0
     cpradius      cutting plane radius, default 100

   e.g. v3d -x straighten -f cst -i input.raw marker_file.marker -o output.raw -p 1 4.0 10 0 3.0 0.0 100