preNAD(1)                                                            preNAD(1)



NAME
       preNAD - 2D anisotropic diffusion filter for tilt projections

SYNOPSIS
       preNAD [options]

DESCRIPTION
       preNAD is an anisotropic diffusion pre-reconstruction filtering program
       that aims to improve image quality for electron microscopy tilt projec-
       tion images. The aim of the preNAD program is to improve the image
       quality of reconstructed volumes by improving the quality of each tilt
       projection.

       Specifically, a family of Non-Linear Anisotropic Diffusion (NAD) fil-
       ters parametrized by the tilt angle is implemented.  The stopping cri-
       terion for iteration in the preNAD filter is based on the Masked Vari-
       ance Difference. However, in addition to options to control the algo-
       rithm itself, this version provides the automatic selection of the
       Masked Variance Difference using the -MinIterations and -MaxIterations
       options.

       For a more detailed description of the algorithm used in this code, see
       Mauro Maiorca, Eric Hanssen, Edmund Kazmierczak, Bohumil Maco, Misha
       Kudryashev, Richard Hall, Harry Quiney and Leann Tilley, "Improving the
       quality of electron tomography image volumes using pre-reconstruction
       filtering", Journal of Structural Biology, (2012) 180: 132-142.  Please
       reference this article if you use the filter.


OPTIONS
       preNAD uses the PIP package for input (see the manual page for pip).
       Options can be specified either as command line arguments (with the -)
       or one per line in a command file (without the -).  Options can be
       abbreviated to unique letters; the currently valid abbreviations for
       short names are shown in parentheses.

       -input (-i) OR -InputStack     File name
              Input image file with tilt projections. PreNAD algorithm will be
              applied to this image.

       -output (-o) OR -OutputFileName     File name
              Output filtered image file

       -angles (-a) OR -AnglesFile    File name
              File with tilt angles, one per line. This file has usually a
              .tlt extension.

       -MVD (-MV) OR -MaskedVarianceDifference       Floating point
              User-defined Masked Variance Difference (MVD). MVD is an image-
              dependent parameter which defines a stopping condition for pre-
              NAD. The user-defined MVD is optional. However, generic users
              are suggested to ignore this parameter and use MinItera-
              tions/MaxIterations for an automatic estimation of the MVD.

       -s OR -sigma    Floating point
              Initial sigma for smoothing the structure tensor (in pixels).
              Default initial sigma is 1 pixel.

       -minite (-mi) OR -MinIterations     Integer
              Minimum Number of Iterations allowed for each tilt projection.

       -maxite (-ma) OR -MaxIterations     Integer
              Maximum Number of Iterations allowed for each tilt projection.

       -views (-v) OR -ViewsToProcess      List of integer ranges
              List of views to process from input file, numbered from 1. List
              should be in the form 1,3-6,9,19.  Other views will be copied to
              the output file, unchanged.

       -help (-h) OR -usage
              Print help output

       -StandardInput
              Read parameter entries from standard input

AUTHOR
       Mauro Maiorca

SEE ALSO
       nad_eed_3d

BUGS
       Email bug reports to mast at colorado dot edu.




IMOD                                 4.9.5                           preNAD(1)