Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

MTDETECT(1)							   MTDETECT(1)

NAME
	mtdetect - detect circularly symmetric features

SYNOPSIS
	mtdetect

DESCRIPTION
  This program is a companion to MTTEACH, the interactive program for
  defining a discriminant analysis for feature detection.  On each
  section, it follows the procedures of that program: it looks at
  either single pixels or sums of pixels within circular windows,
  seeking points with values beyond a threshold value, then applies
  the discriminant function derived in MTTEACH to classify the points
  as features or non-features.  However, it also reads in the teaching
  points used by MTTEACH and uses them, as well as the points
  identified by the procedure just described, as a basis for searching
  from one section to the next for additional points.  On the first
  pass through the sections, it applies the procedure just described,
  then it examines the vicinity of known points on adjacent sections.
  For each such position, it looks for points within a specified
  radius that have values greater than a relaxed threshold, and forms
  discriminant scores for those points; if there are points with
  scores better than the criterion (which may be relaxed by a
  specified amount), then the best such point is taken as a new
  feature point. On a second pass through the sections, it does only
  the checking from section to section.  If the images being examined
  are unaligned but an alignment is available, one can enter a file of
  g transforms to improve the section-to-section correspondence for
  the search.
  
  ENTRIES to the program:
  
  Image file name
  Name of file of piece coordinates if image is a montage, otherwise
     Return
  Name of file of teaching points
  Name of output file for list of detected points
  Name of file of discriminant analysis parameters and solutions
     produced by MTTEACH
  Name of file of g transforms that align the whole data stack, or
     Return if none is available
  
  IF you enter a file of g transforms, enter 4 lines:
     0 if images are unaligned, or 1 if images are aligned via these
   	transforms
     0 if teaching points were picked on unaligned images, or 1 if
   	points were picked on aligned images
     0 to output points that would match unaligned images, or 1 to
   	output points that match aligned images
     X and Y center coordinates of the transforms, or / to take the
        default of the center coordinates of the image file
  
  Minimum distance between centers of adjacent features

  Radius to search around the position of a feature for features in
     adjacent sections

  Amount to relax criterion discriminant score for the search in
     adjacent sections.  This is expressed as the number of standard
     deviations of the scores for true features; the program will first
     print out what the criterion is already in terms of the number of
     S.D.'s below the mean score for true features.
  
  Amount to relax threshold for choosing peaks in the search for
     features in adjacent sections.  Use the same units in which the
     threshold was specified in MTTEACH, i.e. an absolute or a relative
     value.
  
  Starting and ending section to analyze, or / to do all sections

HISTORY
  Written by David Mastronarde, May 1989
  4/29/90 - add ability to set range of sections to analyze