preNID(1)                   General Commands Manual                  preNID(1)

       preNID - 2D non-linear isotropic diffusion filter for tilt projections

       preNID [options]

       preNID is a pre-reconstruction non-conservative non-linear isotropic
       diffusion (NID) filter that automatically identifies and reduces local
       irregularities in the tilt projections (see Maiorca M., Millet C.,
       Hanssen E., Abbey B., Kazmierczak E., Tilley L., J Struct Biol. 2014
       Apr;186(1):28-37). In particular, the filter targets highly electron
       dense regions, such as gold nanoparticles, that can hide proximal bio-
       logical structures and degrade the overall quality of the reconstructed

       Notes from David Mastronarde: The names of the options below correspond
       to the various factors referred to in the paper: sigma for initial
       Gaussian smoothing, alpha as a scaling factor of sigma for smoothing a
       difference between initially smoothed and original images, tau as a
       threshold for a normalized gradient value, beta as a sigma for Gaussian
       smoothing of areas above threshold during diffusion iterations.  The
       effectiveness of sigma, alpha, and tau for selecting the gold versus
       other regions can be assessed by outputting a mask file with the -mask
       option and comparing it to the original data.

       With the unbinned IMOD tutorial data set, most gold can be masked with
       a sigma of 5, alpha of 0.5, tau of 0.1 - 0.12, beta of 5 to 8, and 10
       to 15 iterations.  Failure to mask the gold at high angles leaves some
       streaking artifacts around the gold.  There is some slight masking of
       the basal body microtubules near zero tilt.

       The options for entering sigma, alpha, beta, tau, and iterations all
       allow multiple values to be entered, which is why they are shown as
       "array" entries.  The same number of values must be entered for each.
       Consult the source code or experiment to see what effect these multiple
       entries would have.

       preNID 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 (-in) OR -InputStack    File name
              Input image file.

       -output (-o) OR -OutputFileName     File name
              Output image file, the filtered image or a mask image

       -angles (-an) OR -AnglesFile   File name
              Tilt angles file, one angle per line.

       -s OR -Sigma    Multiple floats
              Sigma (in pixels) for initial Gaussian smoothing, typically
              approximately the same as the radius of the gold particles.
              This entry is required.

       -a OR -Alpha    Multiple floats
              Alpha, the fraction of the initial sigma used as the sigma of a
              Gaussian for smoothing the difference between the initially
              smoothed and original image.  Typical values are 0.2 to 0.5;
              default is 0.5.

       -b OR -Beta     Multiple floats
              Sigma beta (in pixels) for Gaussian smoothing of regions above
              threshold during diffusion iterations.  Typical values are from
              0.5 to 8; the default is 0.5 and not very useful.

       -t OR -Tau      Multiple floats
              Tau, the threshold fraction of the maximum gradient for regions
              to be smoothed.  Typical values are from 0.1 to 0.2; the default
              is 0.1.

       -ite (-it) OR -Iterations      Multiple integers
              Number of iterations in the smoothing process, irrelevant if the
              -mask option is used.  The default is 1, which is not very use-
              ful; typical values are 3 to 20.

       -im OR -InputMask    File name
              Input image file with mask to apply, defining areas to be

       -mask (-m) OR -MaskOutput
              Produce a binary mask as output

       -views (-v) OR -ViewsToProcess      List of integer ranges
              List of views to process (not implemented)

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

              Read parameter entries from standard input

       Mauro Maiorca

       preNAD, nad_eed_3d

       Email bug reports to mast at colorado dot edu.

IMOD                                4.9.10                           preNID(1)