Version = 1.0
Pip = 1
[Field = TomogramFile]
short = tomo
type = FNM
usage = Name of image file to analyze
tooltip =
manpage = Name of image file to analyze. At least one image file must be
entered either with this option or as a non-option argument. All non-option
arguments are taken to be tomograms for analysis.
[Field = SurfaceModel]
short = surface
type = FN
usage = File name for output of surface model for flattening
tooltip =
manpage = File name for output of a surface model that can be used for
flattening in Flattenwarp(1).
[Field = TomoPitchModel]
short = pitch
type = FN
usage = File name for output of boundary model for use with Tomopitch
tooltip =
manpage = File name for output of boundary model for use with Tomopitch(1). Such
a model will have two straight lines at each sample position. If multiple
tomograms are analyzed, each is assumed to be a separate sample, and there
will be a pair of lines for each sample, with the contours assigned to times
corresponding to the sample number. If there is only a single tomogram,
then the \fB-samples\fR option must be entered to indicate how many regions in
Y to sample.
[Field = SeparatePitchLineFits]
short = separate
type = B
usage = Fit each surface separately in making lines for Tomopitch output
tooltip =
manpage = When making a model of paired lines for use in Tomopitch(1), the
default is to fit a pair of parallel lines to the top and bottom surfaces.
With this option, lines will be fit separately to points on each surface.
This method would be suitable if every sample has material across a wide
enough area so that the fit will not be thrown off by a few aberrant points.
[Field = NumberOfSamples]
short = samples
type = I
usage = Number of positions to sample in a single tomogram for pitch lines
tooltip =
manpage = Number of positions to sample in a single tomogram to obtain lines
for Tomopitch(1). The position and spacing between these samples is
determined by their number, the sample extent, and the total number of
blocks of analyzed boxes in Y.
[Field = SampleExtentInY]
short = extent
type = I
usage = Approximate extent in Y to use at each sample position, in unbinned
pixels
tooltip =
manpage = Approximate extent in Y analyzed at sampled positions from a single
tomogram, in unbinned pixels. Since a surface position is estimated only for
each block of boxes, spanning 100 unbinned pixels by default, the actual
extent included in the analysis will be based on an integral number of blocks.
The default is to analyze one block at each sample position. When multiple
tomogram samples are analyzed, all of the available positions will be used.
[Field = HighSDboxCriterion]
short = high
type = F
usage = Criterion for using high SD boxes to define extent for Tomopitch output
tooltip =
manpage = Determine sample extent and orientation from boxes with SD values that are
the given criterion number of MADNs above the edge median.
[Field = BeadModelFile]
short = bead
type = FN
usage = Name of model file with positions to use when finding extent with high SD
tooltip =
manpage = When finding extent and orientation from boxes with high SD values,
a set of fiducial positions will also be taken into account if this option is
entered with a model file containing bead positions.
[Field = BeadDiameter]
short = diameter
type = F
usage = Diameter of beads to assume when considering bead extent (default 5)
tooltip =
manpage = Diameter of beads to assume when including bead positions in the
analysis. Half the diameter will be subtracted or added to the lower or upper
position based on beads, respectively. The default is 5.
[Field = BoostHighSDThickness]
short = boost
type = F
usage = Fraction by which to increase thickness from high SD analysis
tooltip =
manpage = Fraction by which to increase the thickness from the analysis of high SD.
The lower and upper boundaries from this analysis will each be moved by half of
this amount, or less if that brings one of them to the edge of the volume. If
bead positions are being considered also, limits based on them are applied
after this increase.
[Field = LowestSDforEdges]
short = lowest
type = B
usage = Find Z planes with lowest SD and use to measure edge statistics
tooltip =
manpage = Scan through Z planes for the ones with the lowest SD values and use
these to measure the statistics of the edge, instead of using planes atthe
surfaces of the volume.
[Field = NumberOfDefaultScales]
short = scales
type = I
usage = Number of default, isotropic binnings to analyze
tooltip =
manpage = This option can be used to specify how many default binnings to
analyze, instead of entering each one with the \fB-binning\fR option. These
binnings are isotropic (the same in each dimension). The default binnings
available are 1, 2, 3, 4, 6, 8, 12, 16, 24, 32, 48, and 64. The default is to
do a single scale at binning 1.
[Field = BinningInXYZ]
short = binning
type = ITM
usage = Binning in X, Y, and Z for each scale to analyze
tooltip =
manpage = Binning in X, Y, and Z for each scale to analyze. Multiple binning
entries should be in order by increased binning. This option
cannot be entered with \fB-scale\fR.
[Field = SizeOfBoxesInXYZ]
short = size
type = ITM
usage = Size in X, Y, and Z of boxes in which to measure mean and SD
tooltip =
manpage = Size in X, Y, and Z of boxes in which to measure mean and SD, in
binned pixels. This option can be entered multiple times, up to once
per each scaling, but one entry seems to be sufficient. For scalings past the
last one for which a size was entered, the size in each dimension will be set
to span about the same extent in unbinned pixels as for the last binning
for which size was entered. The entry is required.
[Field = SpacingInXYZ]
short = spacing
type = ITM
usage = Spacing in X, Y, and Z between boxes, in binned pixels
tooltip =
manpage = Spacing in X, Y, and Z between boxes, in binned pixels. This option
can be entered multiple times, only once, or not at all; the default is to
set the spacing to half of the size. For scalings past the last one for which
a spacing was entered, the spacing in each dimension will be set to give the
same overlap between boxes as for the last binning for which a spacing was
entered.
[Field = BlockSize]
short = block
type = I
usage = Size of block in which to consolidate analyzed boxes (unbinned pixels)
tooltip =
manpage = Size of block in which to consolidate the boxes for further
analysis, in unbinned pixels. If this option is not entered, the program will start
with a size of 100 pixels, or 200 if making a surface model, and then increase
the size to get an equivalent area if there are too few boxes in one direction
(specifically, when using multiple tomogram samples, the size generally gets
increased to ~300). If the option is entered, the number is used as is,
without such an adjustment.
[Field = XMinAndMax]
short = xminmax
type = IP
usage = Minimum and maximum X coordinate to include in analysis
tooltip =
manpage = Minimum and maximum X coordinate to include in the analysis. The
default is to trim off 2.5% of the extent on each end when outputting a
surface model, otherwise 5%.
[Field = YMinAndMax]
short = yminmax
type = IP
usage = Minimum and maximum Y coordinate to include in analysis
tooltip =
manpage = Minimum and maximum Y coordinate to include in the analysis.
If Y is the thickness dimension, the default is to use the whole extent;
otherwise the default is to trim off either 2.5% or 5% of the
extent on each end, depending on whether a surface model is being made.
[Field = ZMinAndMax]
short = zminmax
type = IP
usage = Minimum and maximum Z coordinate to include in analysis
tooltip =
manpage = Minimum and maximum Z coordinate to include in the analysis.
If Z is the thickness dimension, the default is to use the whole extent;
otherwise the default is to trim off either 2.5% or 5% of the
extent on each end, depending on whether a surface model is being made.
[Field = ThickDimensionIsY]
short = flipped
type = I
usage = 0 or 1 if the thickness dimension of the reconstruction is Z or Y
tooltip =
manpage = This option can be used to specify which axis of a single tomogram
is the thickness dimension, if necessary. The default is to assume that the
shortest dimension of Y or Z is the thickness dimension. Multiple tomograms
are assumed to be samples as built by Tilt(1) and must have their thickness in
Y.
[Field = AxisRotationAngle]
short = axis
type = F
usage = Rotation angle from Y axis to tilt axis in raw tilt series
tooltip =
manpage = Rotation angle from Y axis to tilt axis in the raw tilt series,
counterclockwise positive. With this entry, the program will avoid analyzing
regions outside the area that can be well-reconstructed from the
original images. However, the correct region is identified only if the
aligned stack and reconstruction were centered on the original tilt series.
[Field = TiltSeriesSizeXY]
short = tilt
type = IP
usage = (Binned) size in X and Y of raw tilt series
tooltip =
manpage = Size in X and Y of raw tilt series for volume being analyzed,
divided by the binning applied to make its aligned stack. When \fB-axis\fR
option is entered, this option should be entered if this size differs from
that of the reconstruction.
[Field = EdgeExtentInXYZ]
short = edge
type = IT
usage = Approximate # of pixels in X, Y, and Z to use for edge statistics
tooltip =
manpage = Approximate # of pixels in X, Y, and Z to use for getting statistics
about the edge of the volume in the thickness dimension. The default is to
use 2.5% of the extent in the thickness dimension and 50% of the extent in the
other two dimensions.
[Field = CenterExtentInXYZ]
short = center
type = IT
usage = Approximate # of pixels in X, Y, and Z to use for center statistics
tooltip =
manpage = Approximate # of pixels in X, Y, and Z to use for getting statistics
about the center of the volume. The default is to use 10% of the extent in
the thickness dimension and 33% of the extent in the other two dimensions.
[Field = ControlValue]
short = control
type = FPM
usage = Parameter number and value for setting algorithm control parameters
tooltip =
manpage = Parameter number and value for setting algorithm control parameters.
Parameters and their numbers (and default values in parentheses) are:
^ 1: Minimum # of points for using robust fit to get pitch line on one
surface (6)
^ 21: Fraction that the difference between distinguishability of center from
edge points must improve to adopt a higher scaling for analysis (0.33)
^ 22: Threshold weight from robust fit for including a point in the final
smoothing fit (0.2)
^ 23: Threshold weight from robust fit for counting a point as "good" (0.6)
^ 27: Fraction of depth extent to use for center samples (0.1, or 0.4 if
analyzing high SD)
^ 30: Take square root of SD values if > 0 (0, or 1 when analyzing high SD)
^ Parameters for finding midpoint
^ 3: Number of edge MADN's above edge median that maximum value must be to
proceed (2.)
^ 4: Fraction of maximum - edge difference to achieve (0.5)
^ 5: Number of edge MADNs above edge to achieve as well (3.)
^ 6: Number of box medians that need to be above those criteria (3)
^ Parameters for fitting boundaries of columns
^ 7: Number of center MADN's below the center median for inside median to be
too low (5.)
^ 8: Fraction of inside - edge median difference that it must fall toward
edge median (0.3)
^ 9, 10: Low and high limits of range of fractions of inside - edge median
difference to fit (0.2 and 0.8)
^ 11: Fraction of inside - edge median difference at which to save boundary
(0.5)
^ 12: Fraction of difference at which to estimate extra boundary distance for
pitch output (0.25)
^ 13: Minimum fraction of boxes in column that must yield boundaries (0.5)
^ Parameters for checking block thickness
^ 14: Criterion fraction of median thickness for considering block too thin
(0.5)
^ 15: Drop a boundary if it is this much farther from local mean than other
boundary is (2.)
^ 16: Drop a boundary if its difference from the mean is this fraction of
median thickness (0.35)
^ Robust fitting parameters
^ 17: K-factor for the weighting function (4.68)
^ 18: Maximum change in weights for terminatiom (0.02)
^ 19: Maximum change in weights for terminating on an oscillation (0.05)
^ 20: Maximum iterations (30)
^ Parameters for estimate of Z limits for combine with Autopatchfit
^ 24: Fraction for percentile of positions included in the limits (0.10)
^ 25: Fraction for lower percentile of positions that can be partly outside
the limits (0.01)
^ 26: Number of pixels outside the limits the latter positions can be (20)
^ Parameters for analysis of high SD
^ 28: Fraction of extreme beads to exclude when finding orientation that
gives minimum spread (0.04)
^ 29: Basic amount to weight bead separation in the measure of spread; they
will also be weighted less if they occupy less lateral area (0.33)
^ 31: Type of data to use for analyzing projections of SD at each layer in
depth; 1: mean, 2: median, 3: 75th percentile, 4: fraction of boxes above
criterion (0)
^ 32: Fraction of the way from baseline to peak for finding rising point of
layer projections (0.1)
^ 33: Use extrapolation to baseline rather than point where layer projection
crosses the criterion (0)
^ 34: Use second or fourth moment (1 or 2) of layer projection values as
measure of spread (0)
^ 35: Fraction of extreme beads to exclude when determining low and high
boundaries (0.01)
[Field = VolumeRootname]
short = volume
type = CH
usage = Root name for output of mean and SD volumes at each scale
tooltip =
manpage = Root name for output of mean and SD volumes at each scale. Each
pixel in such volumes corresponds to an individual box within which mean and
SD were measured. The volumes names will have the form
"rootname#-scale#.means" and "rootname#-scale#.SDs", where the first # is the
tomogram number and the second is the scale index (both numbered from 0).
[Field = PointRootname]
short = point
type = CH
usage = Root name for output of models with raw and smoothed points
tooltip =
manpage = Root name for output of models with raw positions along
the surfaces of the section, and with points after smoothing the surface.
The models will be named
"rootname#-colbound.mod" and "rootname#-smooth.mod", respectively, where # is
the tomogram number. There will be two scattered point objects, one for each
surface.
[Field = DebugOutput]
short = debug
type = I
usage = 1 or 2 for debugging output
tooltip =
manpage = 1 or 2 for debugging output; 2 gives output about individual
smoothing fits.
[Field = usage]
short = help
type = B
usage = Print help output
tooltip =
manpage =