Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells
TOMOPITCH(1) TOMOPITCH(1)
NAME
tomopitch - Determines tomogram shift and angles from models of section
SYNOPSIS
tomopitch
DESCRIPTION
TOMOPITCH analyes simple models of the boundaries of the section in slices
from a tomogram and recommends how much to change tilt angles to make the
section flat, how much to shift the tilt axis in Z to produce centered
slices, and how thick to make the slices. It can also recommend how much
X-axis tilt is needed to make the section flat in the orthogonal direction
as well. It can also be used with a model drawn on a whole tomogram,
possibly binned down.
The typical use is with samples of the tomogram in separate files. For
each sample of the tomogram, make a model file with two contours in it.
Each contour should have two points, with the line between them lying
along the top or bottom surface of the section. The points do not have to
be entered in any particular order, and the lines do not need to be any
particular length (the program will extend them in X, if necessary, to
within 5% of each edge of the tomogram).
As an alternative to making a separate model file for each sample, you can
load all of the samples into 3dmod together and make a single model file,
creating a pair of contours at each different time index. Make this model
file be the sole entry to Tomopitch, and it will analyze each of the time
indexes separately, the same as if they were in separate files.
A third alternative is to make a model on an entire tomogram. Such a
model can take two forms. It can consist of any number of pairs of
horizontal lines, where each par is drawn predominantly in the X direction
along the top and bottom of the section. This can be done while viewing
the YZ planes of the tomogram, just as in the samples of YZ slices. The
lines can also be drawn while viewing the XY planes of the tomogram in the
Zap window, or they can be drawn in the Slicer window with the angles
adjusted to make a surface appear all at once in the window. These lines
do not need to be parallel to the X axis, but try to draw the two lines of
a pair at approximately the same location in Y. The program expects the
separation in Y between the two lines of a pair to be less than 0.3 times
the separation between successive pairs.
The second form for a model on a whole tomogram consists of a pair of
horizontal lines near the middle of the tomogram, and a pair of lines
oriented vertically (predominantly in the Y direction) along the top and
bottom of the tomogram. Only one pair of lines of each type is allowed.
With this input, the program will construct two more pairs of horizontal
lines by sliding the pair that were entered to the low Y and high Y ends
of the vertical lines. Analysis then proceeds with the three pairs of
horizontal lines.
If you make a model on an entire tomogram, you need not enter a value for
the spacing in Y. If the tomogram is binned down relative to the final
tomogram, enter the binning factor as a scale factor to get values
appropriate for the final tomogram.
The program analyzes each pair of horizontal lines separately. It
determines what rotation is required to make the section be flat. It
reports the upward shift needed to center the section in Y, and the slice
thickness needed to contain the section. These values are derived and
reported before and after the recommended rotation is applied. Thickness
values include an additional amount that you specify and are rounded up to
integers suitable for taking 3D FFTs. After all pairs of lines are
analyzed, the program makes the same analysis and report based on the data
from all of the files. It then computes an X-axis tilt and reports
thickness and rotation if that tilt is taken into account as well.
Tomopitch uses the PIP package for input (see the manual page for pip)
and can take input interactively for options that existed when it was
converted, to maintain compatibility with old command files. The
following options can be specified either as command line arguments (with
the -) or one per line in a command file or parameter file (without
the -):
-model OR -ModelFile File name
Model file with lines to analyze. If there are multiple model file
entries, they should be in order that they will be considered in the
program.
(Successive entries accumulate)
-extra OR -ExtraThickness Floating point
Additional pixels of thickness to add to both the top and the bottom of
the tomogram, beyond the region described by the model lines. Enter
values as unbinned pixels, i.e. pixels after the scaling factor has been
applied.
-spacing OR -SpacingInY Floating point
Spacing between tomogram samples (distance in Y in tilted views). If a
non-zero number is entered, the program will compute the tilt around the
X-axis that will make the tomogram be flat in its Z dimension.
-scale OR -ScaleFactor Floating point
Amount by which to scale the Z shift and thickness recommended by the
program. Use this entry if the model was drawn on binned-down samples or
a whole binned-down tomogram but you intend to make an unbinned tomogram.
The scale factor is the binning factor.
-angle OR -AngleOffsetOld Floating point
Angle offset in the alignment used to make the samples. If this entry is
present, the program will output the original, added, and total offset.
-zshift OR -ZShiftOld Floating point
Z shift value in the alignment used to make the samples, in unbinned
pixels. If this entry is present, the program will output the original,
added, and total Z shift.
-xtilt OR -XAxisTiltOld Floating point
X axis tilt applied when the samples were made. If this entry is present,
the program will output the original, added, and total X axis tilt.
-param OR -ParameterFile Parameter file
Read parameter entries as keyword-value pairs from a parameter file.
-help OR -usage
Print help output
-StandardInput
Read parameter entries from standard input.
If the program is started with no command line arguments, it reverts to
interactive input with the following entries:
Additional pixels of thickness to add to both the top and the bottom
of the tomogram, beyond the region described by the model lines.
Spacing between tomogram samples (the distance in Y in the tilt
images.) If a non-zero number is entered, the program will
compute the tilt around the X-axis that will make the tomogram be
flat in its Z dimension.
Number of model files to analyze
For each file, then enter the name of the file.
HISTORY
Written by David Mastronarde, January 2000
5/20/01: Added analysis of single file with multiple time indexes
11/13/03: Converted to PIP, added ability to draw lines in whole tomogram