Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
FIBERPITCH(1) FIBERPITCH(1)
NAME
fiberpitch - measure pitch of fibers and position relative to an axis
SYNOPSIS
fiberpitch
DESCRIPTION
Fiberpitch measures the angle of fibers relative to a central axis
and their distance from the axis. The pitch is resolved into radial
and tangential components. Several fiber bundles in a model may be
analyzed separately by drawing contours around them. The central
axis may be specified by a model contour; otherwise it will be
assumed to be located at the centroid of the fibers and oriented
either vertically or along the average trajectory of the fibers.
Measurements can be made from fibers in a subset of the model
in Z. The program can analyze several models and output the results
to a single file.
To use the program, the fibers should be modeled as open contours in
an Imod model. These contours can be in more than one object. The
pitch for a fiber will be measured from the vector connecting the
starting and ending points of the contour. The position of the fiber
is characterized by a single point for the purposes of measuring the
distance from the central axis, resolving the pitch into radial
and tangential components, and determining whether a fiber is a
member of a bundle. This point can be either the starting point,
ending point, or middle of the contour; the same kind of point is
used for every contour in an object. If the middle is chosen, the
program finds the point in the contour that is halfway along the
length of the contour between the starting and ending points. If a
subset of Z is chosen for analysis, then the starting and ending
points for all of these purposes are the first and last points inside
the specified Z range, respectively.
If separate bundles are to be analyzed, include an object with
separate closed contours that surround the fibers in each bundle.
These contours should be drawn in an X/Y plane and may be drawn at
any desired Z-level. The X and Y coordinates of the characteristic
point for each contour are used to determine whether it is inside a
given boundary contour.
To define the central axes of bundles, include another object with
open contours that describe the trajectories of the axes. Only two
points are needed for each axis. The first point should be placed
at about the same Z level as the characteristic points for the
fibers. The direction in Z will affect the angles and should be
chosen appropriately (see below). If no central axis object is
used, or if there is no central axis contour inside the contour
specifying a particular bundle, then the program will assume that
the axis for that bundle is located at the centroid of the
characteristic points for all of the fibers in that bundle. You can
specify that such an axis will follow the mean trajectories of the
fibers; otherwise it will be made perpendicular to the X/Y plane.
The program includes in its output an identifying number for the
model (optional), the contour number of the boundary contour
(optional), the object and contour number of the fiber, the X and Y
coordinates of the characteristic point relative to the central axis
(in a coordinate system achieved after rotating the axis to
vertical), the distance from the axis to the characteristic point,
the angle between the fiber and axis, and the radial and tangential
components of the pitch. The coordinates and distance will be in
nanometers, or in pixels if there is no scale in the model header.
The overall angle varies from 0 to 180 degrees and will depend on
the direction of the central axis as well as that of the fiber. It
is greater than 90 degrees if the fiber forms an oblique angle with
the axis, with these directions taken into account. The radial
pitch varies from -180 to 180 degrees; it is positive if the fiber
is heading away from the axis and negative if the fiber is heading
toward it; its magnitude is greater than 90 the the angle to the
axis is oblique. The tangential pitch varies from -90 to 90 degrees
and is positive or negative depending on whether the fiber follows a
right-handed or lefted-handed screw thread around the axis. The
program allows options to invert the polarity of all the fibers in
an object, and to invert the polarity of the axis marker for a
particular object, so that these angles can all be made to come out
right even if fibers or the axis marker are not modeled in the right
polarity for a particular object. When an axis is derived from the
mean trajectory of fibers that have mixed polarities, the polarity
of the axis is determined by which polarity is predominant among the
fibers.
The first three entries to the program apply to the output for all
of the following models:
Name of output file, or Return to output to the terminal or log file.
1 to output an identifying number for each model, or 0 not to.
1 to output boundary contour numbers, or 0 not 0.
The following entries are made for each model to be processed:
Name of model file, or Return to exit the program.
IF you entered 1 above to output identifying numbers, then enter
the identifying number for this model; otherwise skip this entry.
Lower and upper Z levels within which to measure pitches, or 0,0
to have no constraints in Z.
List of objects with fibers to analyze. Ranges may be entered, e.g.,
1-3,5,8.
For each object to be analyzed, enter -1, 0, or 1 to take the
characteristic point for measuring fiber position to be at the start,
middle, or end of the contour, respectively.
For each object to be analyzed, enter 1 to invert the polarity of
fibers and compute their direction using the vector from the end to
the start, or 0 to use the normal polarity from start to end.
For each object to be analyzed, enter 1 to invert the polarity of
the central axis, or 0 not to.
Object number of object containing boundary contours around bundles
of fibers, or 0 to treat all fibers as belonging to one bundle.
Object number of object containing contours marking the central axes,
or 0 to use a vertical axis through the centroid of the fiber
positions in X and Y, or -1 to use an axis that follows the mean
trajectory of the fibers.
HISTORY
Written by David Mastronarde, 5/3/01