```mtpairing(1)                General Commands Manual               mtpairing(1)

NAME
mtpairing - to analyze pairing between MTs

SYNOPSIS
mtpairing [graph options]

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.

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 pair-
ing length is also computed; this is the pairing length divided by the
length over which the two MTs appear in the same sections.

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 bun-
dle, 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.

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 sec-
tion thickness.

If the sections were significantly tilted during microscopy, the pro-
gram 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.

Mtpairing takes several standard command-line options about the graph-
ics window: -s followed by a window size in x and y, -p followed by a
window position in x and y, -message followed by a message to be shown
in a message box, -tooltip followed by a tooltip for the graphics win-
dow, and -nograph to disable the graphics window.

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:

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.

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.

Number of bundles to read from model files, or 0 if the entries speci-
fying all of the bundles are in yet another file.

IF you enter a positive number, then enter for each bundle:

Name of model file with bundle in it, or Return to use same file as
previous bundle

IF you enter the name of file, then make the following 3 entries:

Name of file with information on tilt angles, or Return if there
is no such file (pictures taken at 0 tilt)

Section thickness in nm, to scale Z coordinates to microns; or /
to leave Z values unscaled

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.

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.

For each limiting region, then enter:

The number of an object specifying a boundary contour, or 0 to
enter limiting X and Y coordinates of a box.

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

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.

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 bun-
dles specified there.  The rest of the file should be all of the
entries just described for each bundle.

Enter a list of numbers of the bundles to work with.  Ranges may be
entered, e.g. 1-3,7-9.

The lower and upper limits of Z within which to compute pairing.

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.

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 ref-
erence 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 sec-
ond type only as neighbors.

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 num-
ber for the previous entry, then entering, e.g., "1,2" is the same as
entering "1,2,2,1".

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.

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 val-
ues, or in pixels if you have not.

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)

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.

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.

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:

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.

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

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 and other places.  After
this, you will enter the BSPLT subroutine, whose entries are described
in the manpage for Bsplt.

3: to loop back to the point where you specify which bundles to work
with and then enter other parameters of the pairing calculations.

4: to loop back and read in new bundles, replacing existing ones.

5: to loop back and read in new bundles, retaining existing ones.

6/7: to plot the current Postscript file on the screen/printer

8: to exit the program

9: to output a model with MTs reassigned to new objects.  After select-
ing this option, you make an indefinite series of entries of the fol-
lowing form.  In one line, you enter the following information to
select a set of MTs:

New object # for MTs.  Enter -1 here to terminate the series of
reassignments.

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.

The lower and upper criterion limits to apply to values in that
column.

0 to select MTs that are within the limits, or 1 to select ones
outside the limits.

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.

In this way, you can assign each type of MT that meets a particular
criterion to a particular new object.

After you have entered all of the selections, enter the name of the
output file in which to place the new model.

10: to take commands from a file (next enter filename, or Return to
take input from the keyboard)

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 fea-
tures are not documented here - consult the code.

HISTORY
Written by David Mastronarde, 1993

BUGS
Email bug reports to mast at colorado dot edu.

IMOD                                4.10.22                       mtpairing(1)
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