findsection(1)                                                  findsection(1)

       findsection - Locates section boundaries in tomogram slices


       Findsection  analyes groups of slices from a tomogram, detects the
       boundaries of the section, 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.

       The program detects the section boundary at a certain position in the
       tomogram by measuring the standard deviation of image intensity at each
       value of Y in the tomogram slice.  It measures S.D. in a "patch" with a
       width in the X direction and extent in the Z direction specified by the
       user.  To find the bottom edge of the section, it takes the mean S.D.
       over several Y values at the bottom of the slice and over Y values just
       below the middle of the slice.  It finds the point where S.D. rises
       above halfway between these mean values and fits a line to the nearby
       S.D. values.  The Y values where this line crosses the halfway point
       and the mean at the bottom of the slice are estimates of the position
       of the middle and the end of the edge, respectively.  The mid-positions
       are fairly accurate and are used to determine the midpoint of the sec-
       tion in Y; the end positions are less accurate and are used just to
       obtain a more conservative measure of section thickness.  The same pro-
       cedure is used on the top of the section.

       This analysis is performed at a series of patch positions across the
       width of the tomogram.  It can be done over a set of files (each being
       a portion of the same tomogram), with the same patch positions being
       analyzed in each.  After analyzing a set of patches for one file, the
       program 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 either edge middles or edge
       ends.  These values are derived and reported before and after the rec-
       ommended rotation is applied.  Thickness values are rounded up to inte-
       gers suitable for taking 3D FFTs.  After all files 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.

       Entries to the program:

       Width of patch in X, number of patches to analyze across the width
          of the tomogram

       Number of points to average to get mean S.D. at the edge of the
          slice, number to average to get mean S.D. near the middle of the
          slice, and number of points to fit the line to.  Note that the
          within-section average is taken on one side of the middle, not
          across the center of the slice, so the number of points should be
          constrained accordingly.  Defaults are 3, 10, and 4.

       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 files to analyze

       For each file, first enter the name of the file.
       Then enter the starting and ending slices to analyze (/ for all in
          the file)
       Then enter a list of patches to drop from the analysis for that file,
          or Return to retain all patches.

       Written by David Mastronarde, November 1995
       2/18/99: added X axis tilt output

       Email bug reports to mast at colorado dot edu.

BL3DEMC                              4.7.3                      findsection(1)