Boulder Laboratory for 3-Dimensional Electron Microscopy of Cells

FINDHOTPIXELS(1)				              FINDHOTPIXELS(1)

NAME
  findhotpixels - find pixels to exclude from X-ray analysis in SerialEM

SYNOPSIS
  findhotpixels [options] input_image output_model

DESCRIPTION
  Findhotpixels will analyze a set of CCD camera dark reference images to
  identify relatively hot pixels in the CCD chip and will output a list of the
  pixels in a format suitable for placing in the property file for SerialEM.
  Automatic removal of X-rays from dark references can then be activated in
  SerialEM, and it will then be able to avoid identifying a hot pixel as an
  X-ray.  It is recommended that three long-exposure (e.g., 3 sec) dark
  reference images be used for this analysis.

  The program works by finding pixels that deviation from the image mean by a
  specified threshold.  The lower the threshold, the more pixels it will find.
  You may need to run the program several times to find a threshold that gives
  a reasonable number of hot pixels (under 100).  A threshold on the order of
  0.2% of the dynamic range of the camera should be appropriate.

  Hot columns are excluded from the analysis.  With 4-port readout cameras
  from Gatan, it is important to exclude a fairly large number of bright
  columns near the edges; otherwise you will need to set the threshold higher
  than the optimal level for finding the hot pixels in the rest of the
  camera.  The program could be smarter about this and use a deviation from a
  local mean, but there is no point in doing so under SerialEM uses a local
  criterion as well. 

  The program outputs a list of the hot pixels coordinates and their values
  above the image mean.  At the end is a set of HotPixels and HotColumns
  entries suitable for pasting into the SerialEM properties file.

  The program can be run either interactively or with command line arguments
  processed by the PIP interface (see the man page for pip).  With command
  line arguments, the options are:

 -input OR -InputFile   File name
    Name of input image file with dark reference images.  If this option is
    not entered, the first non-option argument is used

 -output OR -OutputFile   File name
    Name of output model file with a point at every hot pixel.  If this option
    is not entered, the second non-option argument is used.

 -columns OR -HotColumns   List of integer ranges
    List of hot columns to exclude (numbered from 0).  Ranges may be entered.

 -threshold OR -ThresholdDifference   Floating point
    Threshold difference from mean value for seeking hot pixels

 -help OR -usage
    Print help output

  -StandardInput
     Read parameter entries from standard input.


  If no command line arguments are entered, input is requested interactively
  as follows:

  Name of input image file with dark reference images

  Name of output model file with a point at every hot pixel

  List of hot columns to exclude (numbered from 0)

  Threshold difference from mean value for seeking hot pixels

H^HHI^HIS^HST^HTO^HOR^HRY^HY
  Written by David Mastronarde in 2003.  
  Added to IMOD, 10/17/06.