Version=1.0
Pip=1
[Field = InputFile]
short = input
type = FN
usage = Input file with image volume
tooltip =
manpage =
[Field = OutputFile]
short = output
type = FN
usage = Output file for model of correlation peaks
tooltip =
manpage =
[Field = CandidateModel]
short = candidate
type = FN
usage =
tooltip =
manpage =
[Field = BeadSize]
short = size
type = F
usage = Size of beads in pixels
tooltip =
manpage = Diameter of beads in pixels, a required entry. If the volume is
binned, this size can be entered in unbinned pixels and the -binning entry
used to specify the binning.
[Field = BinningOfVolume]
short = binning
type = I
usage = The current binning of the image volume, used to scale bead size
tooltip =
manpage = The current binning of the image volume. The entered bead size is
divided by this binning to obtain the actual size of the beads in the volume.
[Field = XMinAndMax]
short = xminmax
type = IP
usage = Starting and ending X coordinates of region to find beads in
tooltip =
manpage = Starting and ending X coordinates of region in which to find beads.
X, Y, and Z coordinates are numbered from 1. The default is to search the
whole volume.
[Field = YMinAndMax]
short = yminmax
type = IP
usage = Starting and ending Y coordinates of region to find beads in
tooltip =
manpage =
[Field = ZMinAndMax]
short = zminmax
type = IP
usage = Starting and ending Z coordinates of region to find beads in
tooltip =
manpage =
[Field = LightBeads]
short = light
type = B
usage = Beads are light on dark background
tooltip =
manpage =
[Field = AngleRange]
short = angle
type = FP
usage = Starting and ending tilt angles, for computing elongation factor
tooltip =
manpage = Starting and ending tilt angles, for computing the elongation factor
due to the missing wedge in single-axis tomograpy. The elongation is computed
using a formula in Radermacher (1988), with the maximum tilt angle for that
formula taken as the mean of the absolute values of the minimum and maximum
angles of the series. The elongation will be capped at 2.5, and the program
will exit with an error if it exceeds 5.
[Field = TiltFile]
short = tilt
type = FN
usage = File with tilt angles, for computing elongation factor
tooltip =
manpage = File with tilt angles, for computing elongation factor from the
minimum and maximum tilt angle, as just described. Only one of -angle and
-tilt may be entered.
[Field = YAxisElongated]
short = ylong
type = B
usage = Features are elongated along the Y instead of Z axis
tooltip =
manpage = Features are elongated by the missing wedge along the Y axis instead
of the Z axis. This entry is needed when analyzing a tomogram as produced by
Tilt(1) with Z slices along the tilt axis and Y perpendicular to the plane of
the specimen.
[Field = MinRelativeStrength]
short = peakmin
type = F
usage = Minimum relative peak strength for retaining peak in analysis
tooltip =
manpage = Minimum relative peak strength for
keeping a peak in the analysis. The square root of the
specified value is used for comparing with the square root of peak strength,
for compatibility with existing command files.
The default is 0.05, which corresponds to a relative square root peak strength of
0.22. Too many weak peaks can prevent a dip from
showing up in the smoothed histogram of strengths. If
the program fails to find a histogram dip, one strategy is to try raising this
value.
[Field = ThresholdForAveraging]
short = threshold
type = F
usage = Threshold relative peak strength or number of beads for averaging
tooltip =
manpage = Threshold relative peak strength or number of beads for averaging.
With a non-zero entry, selected beads from the first round of peak finding and
integral measurement are averaged to produce a reference for a second round. If a
negative value is entered, the program will analyze the histogram of peak
strengths and find the dip indicating the best boundary between actual and
false beads. The value has 4 different meanings depending on the range:
^ Greater than 1: an absolute number of beads with the strongest peaks
^ Between 0 and 1: minimum relative square root of peak strength
^ Between 0 and -1: negative of strongest fraction of peaks above histogram
dip (e.g., -0.33 for the strongest 1/3 of the peaks above the dip)
^ -2: 1/4 of way from histogram dip to histogram peak (the default)
[Field = StorageThreshold]
short = store
type = F
usage = Threshold relative peak strength for storing peaks in model
tooltip =
manpage = Threshold relative peak strength for storing peaks in model. With a
value of 0 (the default), the program will find the dip in the histogram of
peak strengths, find the mean and SD of the strengths above the dip, and store
all of the beads above the dip plus additional ones below the dip. The latter
will be up to the 5 SD's below the mean or up to the number of ones above the
dip. Enter a number between 0 and 1 to specify a relative square root
strength above which peaks will be stored. Enter a negative number to specify
the number to store as a fraction of the number above the histogram dip (e.g.,
-1 for all points above the dip, -0.33 for the strongest 1/3 above the dip,
-1.33 for all above plus 1/3 that many below the dip.) If you use the
default, or a number below -1, then you must examine the points in 3dmod,
adjust the threshold if necessary, and delete points below the threshold.
[Field = FallbackThresholds]
short = fallback
type = FP
usage = Thresholds for averaging and storage if no histogram dip is found
tooltip =
manpage = Thresholds to use as fallbacks when no histogram dip is found. The
first number is a threshold to use for averaging when no dip is detected in
the histogram of peak strengths in the first round. It can be between 0 and 1
to specify a relative peak strength, or a number greater than 1 to specify a
number of beads. The second number is a threshold relative strength for peaks
to store, between 0 and 1, when no dip is found in the histogram of
second-round peak strengths. If a fallback is desired for only one of these
two rounds, enter a zero for the other value.
[Field = MinSpacing]
short = spacing
type = F
usage = Minimum spacing between peaks as fraction of bead size (default 0.9)
tooltip =
manpage = Minimum spacing between peaks as a fraction of the bead size. When
two peaks are closer than this distance apart, the weaker one is eliminated
unless the -both option is entered.
The default is 0.9. A value less than 1 is helpful for picking both beads in
a pair.
[Field = EliminateBoth]
short = both
type = B
usage = Eliminate both peaks when their spacing is below the minimum spacing
tooltip =
manpage =
[Field = GuessNumBeads]
short = guess
type = I
usage = A guess for the number of beads, which can be an underestimate
tooltip =
manpage = A guess for the number of beads. This entry may
sometimes be required to help the program find a dip in the histogram,
especially if there are very few beads. The number can be an underestimate
and a very rough estimate. Use this entry if a histogram dip is found at a
rather high peak strength with few peaks above it.
[Field = MaxNumBeads]
short = max
type = I
usage = The maximum possible number of beads to look for
tooltip =
manpage = The maximum possible number of beads to look for. Only this number
of peaks will be retained and used for finding the histogram dip. If the
program fails to find a histogram dip, try entering a value that is at least
twice the estimated number of beads. The default is 50000.
[Field = VerboseOutput]
short=verbose
type=I
usage = 1 for diagnostics, 2 for peaks, 3 and 4 for histogram verbosity
tooltip=
manpage= Enter 1 for diagnostic output, 2 for listing of peaks, and 3 or 4 for
verbose output from the histogram routines
[Field = ParameterFile]
short=param
type=PF
usage=Read parameter entries from file
tooltip=
manpage=
[Field = usage]
short = help
type=B
usage=Print help output
tooltip=
manpage=