mtrotlong(1) General Commands Manual mtrotlong(1)
NAME
mtrotlong - extract MTs rotated into longitudinal orientation
SYNOPSIS
mtrotlong
DESCRIPTION
Mtrotlong can be used to extract a series of subvolumes with fibrous
elements such as microtubules (MTs) rotated into a longitudinal orien-
tation, and with one end of the item in the center of the extracted
subvolume. To use it, model each fiber in 3dmod with a single open
contour along its axis. Then run Mtrotlong with entries indicating
which contours to analyze and how to orient them, and it will produce
an IMOD command file for extracting the subvolumes with Rotatevol.
This command file would then be run with "subm command_file". This
allows the rotation angles to be edited if necessary to produce a bet-
ter result, using angles found in the Slicer window.
The program will determine the orientation near the end of a fiber by
fitting to a specified number of points. It is thus desirable to have
different fibers modeled with points at roughly equivalent spacings.
For example, if some fibers are modeled very densely while others are
modeled with only a few points over a long distance, then the fit will
be over a very short distance in the former case and over a very long
distance in the latter if it is determined from the same number points
in each case. The orientation may be less than optimal in both cases.
Another way to avoid this problem is to enter different values for the
number of points to fit.
The program can produce subvolumes with double the sampling in the Z
dimension, i.e. half the pixel size. Do do this, it issues commands to
extract the volume twice, one with an odd Z size and once with an even
Z size, which results in a half-pixel offset. These files are then
combined by running Newstack with a file named "interleave", which
is also produced by Mtrotlong.
The program will extract a volume at either the starting or the ending
point of a contour. To have it do both, just make two entries for the
contour. Each subvolume will be named with a starting letter that
encodes the object number, the contour number, an ending letter that
encodes with it is from the start or end of a contour, and the exten-
sion .st. The program can also extract a subvolume centered on the
middle point of the contour, which would be useful if you are not
interested in either endpoint but just want to extract some fibrils.
Inputs to the program:
Name of input model file
Name of output command file
Name of input image file
1 if the volume has been flipped or rotated so that the X/Y planes are
the plane of the sample, or 0 if not (i.e. if it still needs to be
loaded into 3dmod with flipping)
1 for an isotropic volume, 2 for a volume with double sampling (half
the pixel size) in the Z dimension, or 0 for no command file output
X, Y and Z size of a single isotropic extracted volume. If the sam-
pling is doubled in Z, the final volume will have Z size 2 * NZ + 1
Single letter codes for each object; for example if object 1 has kine-
tochore and object 2 has nonkinetochire MTs, the entry could be "kn"
Two single letter codes for volumes extracted from contour starts and
ends, respectively.
A series of lines with the following format:
Object number; contour number; 0, 1, or -1 to extract from contour
start, end, or middle; 0 or 1 to rotate so that the fiber extends
upward or downward from the middle; and the number of points to fit
over. When extracting from middle, the number of points being consid-
ered is the minimum of the number being fit and the number in the par-
ticular contour. The middle point among that set of points will be
centered in the volume. If there is an even number of points the point
used will be that number divided by 2; i.e., it will be centered on
point 3 if there are either 5 or 6 points.
A line with 0,0,0,0,0 to end the series and exit the program
HISTORY
Written by David Mastronarde about 1996
Incorporated in IMOD 9/11/06
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 mtrotlong(1)