preNID(1) General Commands Manual preNID(1)
NAME
preNID - 2D non-linear isotropic diffusion filter for tilt projections
SYNOPSIS
preNID [options]
DESCRIPTION
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
tomograms.
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.
OPTIONS
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
smoothed
-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
-StandardInput
Read parameter entries from standard input
AUTHOR
Mauro Maiorca
SEE ALSO
preNAD, nad_eed_3d
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 preNID(1)