sumdensity(1) General Commands Manual sumdensity(1)
NAME
sumdensity - adds densities above a threshold for pixels within con-
tours
SYNOPSIS
sumdensity [options] image_file model_file output_file
DESCRIPTION
Sumdensity will sum the density within contours of selected IMOD model
objects. Pixels within a specified distance of the boundary contour
can be excluded. A threshold can be set so that only pixels above
threshold are summed, and the threshold value is subtracted from the
pixel values in the sum. Data are reported by surface if there are
surfaces defined in the model contours.
The threshold density must be specified in one of three ways. It can
be entered as an absolute density value, such as one would view in the
Pixel View window in 3dmod. If you do not want to apply a threshold at
all you could specify the minimum density in the file, or zero, which-
ever is less. The second way to enter the density is as a contrast
setting. Load the data into 3dmod without any intensity scaling (i.e.,
without using "-s"). Bring the black and white sliders together and
adjust until structures of interest are selected by the threshold. The
slider value would be entered with the "-contrast" option. Finally,
one can draw contours around reference areas that contain the desired
baseline density. The mean of density within these contours will be
taken as the threshold density. All of these contours should be in a
single object specified with "-reference".
The output of the program consists of a summary table with the follow-
ing columns: object number, surface number or ALL for the entire
object, the number of pixels within the contour (after excluding the
border region), the number of pixels above the threshold, the percent
of pixels above threshold, and the sum, average, and standard deviation
of the densities above threshold. If a pixel model is being produced
then the number of points selected for the model appears in a final
column; this value can be less than the points above threshold if adja-
cent points are required. These values are reported for each surface
in an object, then for the sum of all surfaces. With the "-verbose"
option, values are reported for each contour.
The program will detect contours that are nested inside other contours
and exclude pixels that are inside or with a border distance of inner
contours. There can be any number of levels of nested contours, and in
the general case the program will exclude pixels that are inside an
even-level contour but not inside an odd-level contour contained within
it (where the outermost contour is considered level 1).
OPTIONS
Sumdensity uses the PIP package for input exclusively (see the manual
page for pip). The following options can be specified either as
command line arguments (with the -) or one per line in a command file
or parameter file (without the -). Options can be abbreviated to
unique letters; the currently valid abbreviations for short names are
shown in parentheses.
-image (-im) OR -ImageFile File name
Input image file with densities to be summed. If this option is
not entered, the first non-option argument will be used for this
input file.
-model (-m) OR -ModelFile File name
Input model file with contours delimiting areas to be summed.
If this option is not entered, the second non-option argument
will be used for this input file.
-output (-ou) OR -OutputFile File name
Output file for results. If this option is not entered, the
third non-option argument will be used for this output file. If
no output file is entered, results will be printed to standard
output.
-pixel (-pi) OR -PixelModel File name
Output file for model with added scattered-point objects con-
taining points on the pixels that were included in the sum.
-adjacent (-ad) OR -AdjacentRequired Integer
Number of adjacent points above threshold required to include a
given point in the output model. All points above threshold
will be counted in the density sums, but only those that meet
this requirement will be marked in the model.
-diagonals (-d) OR -DiagonalsCount
Count all 8 neighboring pixels,incuding ones on diagonals, when
determining whether a point is adjacent to the required number
above threshold.
-objects (-ob) OR -ObjectsToDo List of integer ranges
A list of objects containing boundary contours within which to
compute sums. The default is to do all closed contour objects.
-border (-b) OR -BorderSize Floating point
Distance from contour within which to exclude pixels from con-
sideration. For example, if the contours are drawn on the cen-
ters of membranes, this entry can be used to exclude pixels in
the membrane as well as within a certain distance of the mem-
brane. The default is to include all pixels within the contour.
-inside (-in) OR -InsideBorder Floating point
Distance from interior contours within which to exclude pixels
from consideration. All pixels inside of interior contours will
be excluded, so this entry governs the border outside those con-
tours. The default is to use the BorderSize value.
-absolute (-ab) OR -AbsoluteThreshold Floating point
Threshold value in absolute units of the image file density
-contrast (-c) OR -ContrastThreshold Integer
Relative threshold in units of black/white contrast settings
after loading the data into 3dmod with the default scaling.
This value should be in the range 0-255.
-reference (-ref) OR -ReferenceObject Integer
Object enclosing areas from which to measure threshold. Multi-
ple contours can be used to sample several areas for setting the
threshold.
-reverse (-rev) OR -ReversePolarity
Count and sum pixels lower than the threshold instead of higher.
The densities to be summed can have either positive or negative
contrast; use this option in the latter case.
-verbose (-v) OR -VerboseOutput
Output counts and densities for every contour
-param (-pa) OR -ParameterFile Parameter file
Read parameter entries from file
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 sumdensity(1)