Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

SUBIMSTAT(1)							 SUBIMSTAT(1)

NAME
	subimstat - Subtracts one average image from another with a t-test

SYNOPSIS
	subimstat

DESCRIPTION

  SUBIMSTAT subtracts one average image from another and uses standard
  deviation or variance images to find the statistical significance of the
  difference at each pixel, as evaluated by a t-statistic.  It then sets to
  zero all differences that are less significant than the specified level of
  significance.  It can also output pixel values reflecting the level of
  significance rather than the difference.
  
  The average and standard deviation/variance images can be ones produced by
  Imavgstat, Clip, PEET, or other means.  When one starts the program, one
  designates a pair of A files (with average and S.D./variance images) and a
  pair of B files.  One can then subtract any section in B from any section in
  A; A and B may be the same pair of files.  Alternatively, a whole set of
  corresponding sections can be subtracted between the two files.
  
  The user is responsible for keeping track of how many samples were used in
  making each average, and informing this program of those numbers.  The
  program needs these numbers to compute the t-statistic and evaluate its
  significance.
  
  Entries to the program:
  
  Average image file A
  Standard deviation or variance image file A
  Average image file B, or Return if same as file for A
  Standard deviation or variance image file B, or Return if same as file for A
  Output image file to store differences in
  
  0 if the files have standard deviations in them, or 1 if the files
     have variances

  0 to enter each pair of sections separately, with potentially different
  numbers of samples and significance levels, or 1 to enter a list of
  corresponding sections and treat them all the same.

  IF you entered 0, next enter:

    The number of differences to compute

    Then for each difference, enter:

       Section # in file A, section # in file B

       Number of samples making up those averages in A and B

       Significance level for setting differences to zero.  Enter a
          probability value such as 0.05, 0.01, etc.  Differences less
          significant than this value will be set to zero.  Enter a
          negative value to have significant pixels values set to 
          the negative of the log of the probability, or to the positive
          log for negative differences.  For example, positive and
          negative differences with a P of 0.01 would be output as
          2 and -2, respectively.

  IF you entered 1 to treat a set of corresponding sections the same, next
  enter:
    
    The list of sections to subtract between the files, or / to do all
    sections

    The number of samples making up the averages in A and B

    The significance level for settings differences to zero, a positive or
    negative value as just described.
  

HISTORY
  Written by David Mastronarde,  1/27/90
  4/23/90 - have program look up criterion t value.
  4/12/95 - use local subroutines for t-value
  1/19/11 - allow list of corresponding sections