Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

CONTOURMOD(1)							  CONTOURMOD(1)

NAME
	contourmod - to generate contour maps as a model file

SYNOPSIS
	contourmod

DESCRIPTION
  CONTOURMOD will generate contour maps of selected sections in an
  image file and place them into an IMOD model that can then be
  displayed on the images.  You can produce contours at regularly
  spaced intervals or at individually specified levels.  Each contour
  level may have a different color.

  The contours are lines connecting points spaced about 1 pixel apart
  or less; thus a complete set of contour lines for one image can
  have quite a large number of points, especially if the image is
  large or has a lot of fine detail.  The program will give an error
  message and stop adding points to the model if no further points can
  fit in the model storage arrays.  If this happens when contouring
  several sections, you need to make more than one model file.  If it
  happens when contouring a single image, the image is too large or too
  detailed and needs to be reduced in size or filtered.
  
  Entries to the program are:
  
  Name of file with images to contour
  
  Name of model file to place contours into
  
  List of sections to contour, or / for all sections in the image file.
  Ranges may be entered, e.g. 0-2,5,7
  
  X and Y scaling factors to apply to the model relative to the image
  pixels, or / for 1,1.  If you are going to display the contours on
  an image that has been expanded by a certain factor with a
  transformation, it is recommended that you generate the contours on
  the original rather than the expanded image, so as to avoid getting
  a contour model with a vast number of points.  In this case, you
  would enter that expansion factor as the X and Y scaling factors, and
  the contour model would fit the expanded images.
  
  Enter a positive number of contours for regularly spaced contours,
  or the negative of the number of contours if you want to specify
  each contour level individually.
  
  IF you entered a positive number greater than 1, next enter the
  lowest and highest contour levels desired.
  
  IF you entered 0 or 1, instead enter the single contour level
  desired.
  
  IF you entered a negative number, instead enter all of the desired
  contour levels.
  
  Finally, enter an intensity level or color (0 to 255) for each
  contour level.  If you might need to change the colors or turn any
  contours off inside IMOD, it is recommended that you give each level
  a unique color value.  For example, if you want several bright white
  or several black lines, make them 240, 239, 238, etc or 0, 1, 2, etc.
  

HISTORY
  Written by David Mastronarde 12/1/90, using CONTUR package from Tim Baker