Surface Documentation

Detects three-dimensional surface points in a stack of images that represent optical sections of an object. A 3-D viewer is provided to render detected surface points for visualization purposes.

Licensed under Creative Commons BY-NC-SA 3.0.

Questions or comments? Contact Joseph Schlecht.

usage: surface OPTIONS [img-%d num_imgs | img-1 ... img-n]
where OPTIONS is one or more of the following:
 -h, --help              Prints program usage.
 -v, --version           Prints program version.
 -n, --named             Indicates that the images to read are fully named and
                         listed in sequence on the command line. The default is
                         to read the images as numbered by a printf-formatted
                         name.
 -c, --colored-out=ARG   Original images with surface colored. Use a printf
                         formatted name to output the images in a numbered
                         sequence.
 -m, --map-out=ARG       Bi-level image surface map. Use a printf formatted name
                         to output the images in a numbered sequence.
 -p, --pts-out=ARG       ASCII formatted surface points.
 -b, --begin-thresh=ARG  Hysterisis starting threshold.
 -e, --end-thresh=ARG    Hysterisis stopping threshold.
 -s, --sigma=ARG         Gaussian smoothing sigma.
 -r, --sample-rate=ARG   Surface point sampling rate.
 -w, --grad-weight=ARG   Weights for each direction of the gradient. Format for
                         the argument is 'img,row,col'. They all must be
                         non-negative and sum to > 0.
 -w, --resolution=ARG    Down-sampling resolution for the input image stack.
                         Format for the argument is 'img,row,col'. They all
                         must be in (0,1]. 

usage: surface-viewer OPTIONS surface_points
where OPTIONS is one or more of the following:
 -h, --help                   Program usage
 -v, --version                Program version.
     --size=ARG               Window size with format width,height. Default is
                              600,600.
     --glasses=ARG            Type of colored glasses for anaglyph mode in the
                              interactive window. Possible left-right filter
                              types include include red-blue, red-green,
                              red-cyan, blue-red, green-red, cyan-red. Default
                              is cyan-red.
     --capture=ARG            View capture name in the interactive mode.
     --surf-scale=ARG         Number of world units per image pixel. Has format
                              x,y,z.
     --sample-rate=ARG        Surface point sampling rate.
     --patch-size=ARG         Surface patch size. Must be > 0.