Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

FINDSECTION(1)							 FINDSECTION(1)

NAME
	findsection - Locates section boundaries in tomogram slices

SYNOPSIS
	findsection

DESCRIPTION
	  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 section in Y; the end positions
	  are less accurate and are used just to obtain a more conservative
	  measure of section thickness.  The same procedure 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 recommended rotation is applied.  Thickness
	  values are rounded up to integers 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.


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