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 cam-
       eras 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 val-
       ues above the image mean.  At the end is a set of HotPixels and Hot-
       Columns entries suitable for pasting into the SerialEM properties file.

OPTIONS
       The program can be run either interactively or with command line argu-
       ments 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.


INTERACTIVE INPUTS
       If no command line arguments are entered, input is requested interac-
       tively 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


HISTORY
       Written by David Mastronarde in 2003.  Added to IMOD, 10/17/06.

BUGS
       Email bug reports to mast at colorado dot edu.



BL3DEMC                              4.7.3                    findhotpixels(1)