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.TH mtpairing 1 4.6.34 IMOD
.SH NAME
mtpairing - to analyze pairing between MTs
.SH SYNOPSIS
mtpairing [graph options]
.SH DESCRIPTION
Mtpairing calculates the length over which MTs are paired with each other in
3-D, and allows one to assign MTs to new objects based on these pairing
lengths. It can also assign polarities to MTs based on the positions of
their endpoints in Z, and allows one to assign MTs to new objects based on
these polarities. The program combines features of MTOVERLAP and GENHSTPLT.
It also has several exploratory features that are not documented because
they were not particularly useful.
.P
MTs are considered "paired" when they are within a certain distance of each
other in the X/Y plane. Typically, you would set this distance to be the
upper limit of the peak from a neighbor density analysis. The absolute
pairing length for a pair of MTs is the total length in Z over which they
are within that distance of each other. A fractional pairing length is also
computed; this is the pairing length divided by the length over which the
two MTs appear in the same sections.
.P
Before running the program, you must figure out how to specify which MT's
are in a bundle. If all of the MT's in a model belong to one bundle, then
this task is easy. If you have several bundles in one model, then you have
several alternatives. One is to determine the lower and upper X, Y and Z
coordinates of a box, such that the bundle consists of all MT's that contain
at least one point within the box. Another way is to make a model object
within the plane of one section to serve as a boundary contour. This
contour, together with a lower and upper Z coordinate, specifies a
"cylinder", and this program will include in the bundle any MT with at least
one point inside this cylinder. The most elaborate way is to make a series
of model objects for boundary contours in different sections. The program
will then include in the bundle any MT that is included within any one of
the contours.
.P
When you enter X, Y or Z coordinates for this purpose, they must be index
coordinates of the image file. That is, X and Y values must be in terms of
pixel coordinates, and Z values must be in units of the original section
numbers, before adjustment for tilt or scaling by section thickness.
.P
If the sections were significantly tilted during microscopy, the program can
adjust for these tilts given the proper information. Prepare a file in
which the first line shows the Z value and the tilt of the first tilted
section (or of the first section, if that one was tilted), and each
successive line shows the Z value and tilt for each section on which tilt
was changed. Z values should occur in ascending order.
.P
Mtpairing takes several standard command-line options about the graphics
window: \fB-s\fR followed by a window size in x and y, \fB-p\fR
followed by a window position in x and y, \fB-message\fR followed by a
message to be shown in a message box, \fB-tooltip\fR followed by a
tooltip for the graphics window, and \fB-nograph\fR to disable the
graphics window.
.P
When you start the program, you will have to make a standard series of
entries until you get the first display. From there, you can select a
number of options to loop back and change those entries. Initial entries in
order are:
.P
0 for plots in the graphics window, or 1 for plots only on the
terminal, or -1 for plots always in the graphics window. If you
enter -1, BSPLT will not ask about doing terminal plots. Note that
if you need to use terminal plots, you will need to specify that
option each time that you do a plot.
.P
Name of command file to take entries from, or Return to continue making
entries from the keyboard. The program can read entries from a file instead
of from the keyboard, then switch back to keyboard input if the file ends
with the appropriate entry.
.P
Number of bundles to read from model files, or 0 if the entries specifying
all of the bundles are in yet another file.
.P
IF you enter a positive number, then enter for each bundle:
.P
Name of model file with bundle in it, or Return to use same file as
previous bundle
.P
IF you enter the name of file, then make the following 3 entries:
.P
Name of file with information on tilt angles, or Return if there
is no such file (pictures taken at 0 tilt)
.P
Section thickness in nm, to scale Z coordinates to microns; or /
to leave Z values unscaled
.P
Magnification of negatives, and scale of digitization (the value
of microns/pixel), to scale the X/Y coordinates correctly; or /
to leave X/Y coordinates unscaled. This entry makes no
difference unless you choose to calculate one of the special
three-dimensional overlap factors.
.P
Number of limiting regions (boundary contours or rectangles defined
by X/Y coordinates) needed to specify the bundle, or 0 to take all
of the objects in the model.
.P
For each limiting region, then enter:
.P
The number of an object specifying a boundary contour, or 0 to
enter limiting X and Y coordinates of a box.
.P
IF you entered 0, next enter the lower and upper X index
coordinates and the lower and upper Y coordinates of the box,
or enter / to have no limit on the X and Y coordinates THEN
enter the lower and upper Z coordinates of the box (in units
of sections), or / to have no limits on Z coordinates
.P
IF you entered the number of a boundary object, next enter
lower and upper Z coordinates of the "cylinder", or / to set
those limiting coordinates to the Z coordinate of the boundary
contour. The latter is typical if one uses several contours in
different sections to specify the bundle.
.P
IF you entered 0 for the number of bundles, next enter instead the name of a
file. The first line of this file should have the number of bundles
specified there. The rest of the file should be all of the entries just
described for each bundle.
.P
Enter a list of numbers of the bundles to work with. Ranges may be entered,
e.g. 1-3,7-9.
.P
The lower and upper limits of Z within which to compute pairing.
.P
A minimum number of sections to assume as shared sections when the
fractional pairing is computed. This entry was intended to avoid
unreasonably large fractional pairing lengths when two MTs only appear
together in a few sections. A value of 4 may be useful.
.P
The number of kinds of pairs to compute pairing for. If you enter a
positive number, then each type in a pair will be treated as both reference
MTs and as neighbors MTs. If you enter a negative number, the first type in
a pair will be treated only as reference MTs and the second type only as
neighbors.
.P
Enter two types (object numbers) for each pair of types, the types of
"reference MTS" and "neighbor MTs" in the pairing calculations. Enter a 0
to include all types in a pairing. If you entered a positive number for the
previous entry, then entering, e.g., "1,2" is the same as entering
"1,2,2,1".
.P
Enter 1 for a simple pairing factor which is 1 for MTs within a certain
distance of each other and 0 beyond, or 2 or 3 for a pairing factor that
decays with distance in the X/Y plane, either as an inverse power or
exponentially.
.P
Enter the distance in the X/Y plane at and below which overlap will equal 1.
The distance should be in microns if you have scaled X/Y values, or in
pixels if you have not.
.P
IF you entered 2, next enter the power for the decay (e.g., with a power
of 2, overlap will decay as the inverse square of distance)
.P
IF you entered 3, enter instead the space constant for exponential decay.
Overlap will be 1/e less for MT's separated by 2 space constants than for
MT's separated by 1 space constant. Distance should be in microns if you
have scaled X/Y values, or in pixels if you have not.
.P
Minimum pairing length that a pair of MTs should have before its data will
be stored for examination. If there are not hundreds of MTs, a minimum of 0
will retain all data about MTs with any pairing.
.P
At this point, the program computes the pairings and gives information about
the lengths of the many pairs of MTs with no pairing. You are then at the
option point. Options are:
.P
1: to plot the pairing data about each MT. Columns available are:
1 = MT length
2 = absolute pairing length summed over all neighbors to the MT
3 = maximum pairing length achieved with one other MT
4 = fractional pairing length summed over all neighbors to the MT
5 = maximum fractional pairing length achieved with one other MT
6 = Z value of midpoint of MT.
.P
2: to plot the data about paired MTs. Columns available are:
1 = arithmetic mean of the lengths of the two MTs
2 = geometric mean of the lengths of the two MTs
3 = absolute pairing length of that pair
4 = fractional pairing length
9 = mean separation between MTs while they were paired
10 = SD of separation
11 = coefficient of variation = SD/mean of separation
.P
With either option 1 or 2, you must enter the numbers of the columns to be
plotted on the X or Y axes. Next, enter a number for the symbol type as
commonly referred to in Genhstplt(1) and other places. After this, you will
enter the BSPLT subroutine, whose entries are described in the manpage for
Bsplt(1).
.P
3: to loop back to the point where you specify which bundles to work with
and then enter other parameters of the pairing calculations.
.P
4: to loop back and read in new bundles, replacing existing ones.
.P
5: to loop back and read in new bundles, retaining existing ones.
.P
6/7: to plot the current Postscript file on the screen/printer
.P
8: to exit the program
.P
9: to output a model with MTs reassigned to new objects. After selecting
this option, you make an indefinite series of entries of the following form.
In one line, you enter the following information to select a set of MTs:
.P
New object # for MTs. Enter -1 here to terminate the series of
reassignments.
.P
Column to use to select MTs. The data about each MT are referred to
by positive column numbers (1 to 6 as described above); the data
about pairs are referred to by negative column numbers (-1 to -4 as
described above). An entry of 0 will use the "polarity" values
determined after using options 11 and 12.
.P
The lower and upper criterion limits to apply to values in that
column.
.P
0 to select MTs that are within the limits, or 1 to select ones
outside the limits.
.P
On the next line, enter a list of the original types (object
numbers) that MTs should have in order for them to be reassigned
according to these criteria, or Return to apply the criteria to MTs
of all types.
.P
In this way, you can assign each type of MT that meets a particular
criterion to a particular new object.
.P
After you have entered all of the selections, enter the name of the output
file in which to place the new model.
.P
10: to take commands from a file (next enter filename, or Return to
take input from the keyboard)
.P
11 will find clusters of mutually paired MTs (which can be all of the MTs in
a bundle), 12 will find polarities based on positions of the MTs in the
bundle or cluster, and 13 will graph the clusters. These features are not
documented here - consult the code.
.SH HISTORY
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Written by David Mastronarde, 1993
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.SH BUGS
Email bug reports to mast@colorado.edu.