Version = 1.0
Pip = 1
[Field = TrackedModel]
short = tracked
type = FNM
usage = Name of tracked model file from one Beadtrack run
tooltip =
manpage = Name of tracked model file from one Beadtrack run. This entry is
needed for each run to be included in the analysis.
[Field = SurfaceFile]
short = surface
type = FNM
usage = Name of file with surface information from one Sortbeadsurfs run
tooltip =
manpage = Name of file with surface information from one Sortbeadsurfs run.
There must be the same number of surface file entries as tracked models.
[Field = ElongationFile]
short = resid
type = FNM
usage = Name of file with residual and elongation data from one Beadtrack run
tooltip =
manpage = Name of file with residual and elongation data from one Beadtrack run.
There must be the same number of elongation file entries as tracked models.
[Field = OutputSeedModel]
short = output
type = FN
usage = Name of final output model file
tooltip =
manpage =
[Field = AppendToSeedModel]
short = append
type = B
usage = Read in existing output seed model and add points to it
tooltip =
manpage = Read in existing output seed model and add points to it. All points
will be retained from this model. Candidate points that match these points
will be accepted before phase 1, then the regular sequence of phases will be
followed to reach the target number.
[Field = BeadSize]
short = size
type = F
usage = Diameter of beads in pixels in the images where beads were found
tooltip =
manpage =
[Field = ImageSizeXandY]
short = image
type = IP
usage = X and Y dimensions of image file used for finding and tracking beads
tooltip =
manpage =
[Field = BordersInXandY]
short = border
type = IP
usage = Number of pixels to exclude on each side in X and in Y
tooltip =
manpage =
[Field = MiddleZvalue]
short = middle
type = I
usage = Z value of middle section for tracking, numbered from 0
tooltip =
manpage =
[Field = TwoSurfaces]
short = two
type = B
usage = Try to find an equal number of beads on two surfaces
tooltip =
manpage = Try to sort beads onto two surfaces then select a seed model that
has equal numbers of beads on the two surfaces if possible.
[Field = BoundaryModel]
short = boundary
type = FN
usage = Model containing contours enclosing areas in which to use or exclude beads
tooltip =
manpage = Name of model file whose first object contains contours enclosing
areas in which to use or to exclude beads, depending on whether -exclude is
entered. If more than one contour is drawn on a view, points inside any one
of the contours will be considered inside the area. This program will
use only the contours on the view closest to the middle section for tracking.
[Field = ExcludeInsideAreas]
short = exclude
type = B
usage = Use the boundary model to exclude regions from analysis
tooltip =
manpage = Use the contours in the boundary model to define regions to exclude from
analysis rather than regions to include.
[Field = BoundaryForCounting]
short = counting
type = B
usage = Use the boundary model just for counting candidates inside and outside
tooltip =
manpage = Use the contours in the boundary model just for counting candidates
inside and outside the boundary when outputting a candidate model.
[Field = TargetNumberOfBeads]
short = number
type = I
usage = Desired total number of beads to choose for output seed model
tooltip =
manpage = Desired total number of beads to choose for output seed model. If
beads are on two surfaces, the program will seek to find half the target number
on each surface, then pick more beads on either surface to reach the target.
Either this option or -density must be entered.
[Field = TargetDensityOfBeads]
short = density
type = F
usage = Desired density of beads in final seed model per 1000 square pixels
tooltip =
manpage = Desired density of beads in final seed model per 1000 square pixels
of area, excluding the area outside boundary contours if any. This option
provides an alternative way of specifying the target that is independent of
data set size.
[Field = LimitMajorityToTarget]
short = nobeef
type = B
usage = Accept no more than half the number of target beads on majority surface
tooltip =
manpage = Do not increase the number of beads on the surface with more beads
to make up for a deficiency on the other surface. Autofidseed(1) uses this
option to limit the number of beads on the majority surface in response to its
-ratio option.
[Field = ElongatedPointsAllowed]
short = elongated
type = I
usage = 1-3 to include elongated beads
tooltip =
manpage = Enter 1, 2, or 3 to include
beads identified as elongated in up to 1/3, up to 2/3, or all of the Beadtrack
runs, respectively.
[Field = ClusteredPointsAllowed]
short = cluster
type = I
usage = 1 to include beads near others, 2-4 to include elongated beads also
tooltip =
manpage = Enter 1 to include clustered beads. i.e, ones that appear to be
located within 2 diameters of other beads, where foreshortening perpendicular
to the tilt axis is taken into account in computing this separation. Only one
of a pair of clustered points will be accepted. If -elongated is not entered,
2, 3, or 4 can be entered to also include beads identified as elongated in up
to 1/3, up to 2/3, or all of the Beadtrack runs, respectively.
[Field = LowerTargetForClustered]
short = lower
type = F
usage = Include clustered/elongated beads only if # is still below this target
tooltip =
manpage = Include clustered and elongated points as allowed by the -cluster
and -overlap options only when the total number of beads is still below the
reduced target given here. The value entered should be in the same form as
the regular target was specified, i.e, a number of beads if -number was
entered or a bead density if -density was entered.
[Field = RotationAngle]
short = rotation
type = F
usage = Angle of rotation of the tilt axis in the images
tooltip =
manpage = Angle of rotation of the tilt axis in the images; specifically, the
angle from the vertical to the tilt axis (counterclockwise positive).
[Field = HighestTiltAngle]
short = highest
type = F
usage = Absolute value of highest tilt angle
tooltip =
manpage =
[Field = WeightsForScore]
short = weights
type = FA
usage = Alternative weights for composing a score for each candidate bead
tooltip =
manpage = Alternative weights for composing a score for each candidate bead.
Enter 4 weights: for fraction of points missing in a track; for
fraction of Beadtrack runs from which the point is missing; for mean residual
during bead tracking; and for the mean deviation between the different tracks
of the same bead. The default weights are all 1.
[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; float
parameters have decimal points) are:
^ 1: Deviation between points as fraction of bead diameter for tracks to be
close (0.5)
^ 2: Multiple of target spacing at which to exclude points from further
searches (0.75)
^ 3: Width of rings for finding points when filling gaps, as fraction of
target spacing (0.25)
^ 4: Number of rings to search (4)
^ 5: Maximum # of bead diameters separation for points to be considered
clustered (2.0)
^ 6: Fraction of points that must be close in two tracks for them to be
considered same (0.6)
^ 7: Scaling factor for the two elongation criteria (parameters 12 and 16),
applied to the default or entered values (1.0).
^ 8: Maximum fraction of target density at which to add points in initial
phase (0.9)
^ 9: Higher fraction of target at which to add points in more desperate
searches (1.1)
^ 10: Scaling from desired spacing to H for kernel density computation (1.3)
^ 11: Scaling from desired spacing to density grid spacing (0.2)
^ 12: Criterion for edge SD values or elongations to be considered outliers (2.24)
^ 13: Ratio of minority to majority for using higher density factor (0.65)
^ 14: Fraction of nominal spacing allowed for initial addition of points (0.85)
^ 15: Fraction of spacing for adding best half of points on next phase (0.7)
^ 16: Absolute threshold for elongation to be considered overlap (2.5)
^ 17: Option flags: the sum of 1 for fitting elongation measures versus bead
integral and replacing measures with the residual of the fit (which does not
help), and 2 for analyzing the elongation measure in successive groups of at
least 50 values, when values are arranged in order by bead integral (which
does not help)
^ 18: Angle to rotate plot of mean of edge SD versus SD of edge SD to obtain
an adjusted edge SD (-59.0 degrees, the mean from 7 data sets)
^ 19: Angle to rotate plot of mean versus SD of elongation measure to obtain
an adjusted elongation measure (-67.0 degrees, the mean of 8 data sets)
^ 20: Angle to rotate plot of adjusted elongation measure versus adjusted edge
SD to obtain the final elongation measure to analyze for outliers (45.0 degrees,
corresponds to simply averaging the two adjusted values)
^ 21: Maximum number of MADNs above the median score allowed to accept a
candidate point in phases 1-4 (8.0).
^ 22: Maximum number of MADNs above the median score allowed to accept a
clustered or elongated candidate point in phases 5-8 (12.0).
[Field = PhaseOutput]
short = phase
type = B
usage = Color output points by phase they were added in as well as by surface
tooltip =
manpage = Color output points by the phase in which they were added as well as
by their surface. Available colors in order are green, magenta, yellow, cyan,
red, solid blue, orange, purple, dark blue, salmon, dark red. One or two
colors will be used for each phase, depending on whether beads are sorted into
two surfaces. If more than 10 colors are needed the 9 after green are reused.
[Field = DensityOutputRootname]
short = root
type = CH
usage = Root name for output of density maps in gnuplot format
tooltip =
manpage =
[Field = CandidateModel]
short = candidate
type = FN
usage = Name of output model with all candidates sorted by cluster/elongation
tooltip =
manpage = Filename for an output model with all candidates beads sorted by
clustering and elongation scores. Points will be assigned to up to 8
model surfaces. Surface numbers 0 to 3 are for non-clustered points with elongation
values of 0 to 3, and are colored dark green, magenta, bright green, and yellow,
respectively. Numbers 4 to 7 are for clustered points with elongation values
of 0 to 3, and are colored mustard green, red, light blue, and orange. Open
the Surface/Contour/Point dialog in 3dmod (Edit-Surface-Go To) to navigate to
contours within and between surfaces and to see labels for the surfaces.
[Field = VerboseOutput]
short = verbose
type = I
usage = 1 for verbose output, 2 for very verbose output
tooltip =
manpage = 1 for verbose output including lists of candidates and their
properties; 2 for more verbose output from addPointsInGaps routine.
[Field = usage]
short = help
type = B
usage = Print help output
tooltip =
manpage =