Background Masks and Values

To run the background program, strike the <2> key to use default values or use the pull-down "Background" menu for other options (see below). A mask is displayed which should blue-out all particles and TMV in the image. The background in the remaining image, as well as the standard deviation (SD) and number of non-masked points is printed for 16 sub-areas (4 X 4, each containing 16,384 points). The left table is for Ch0 (LA) and the right is for Ch1 (usually SA). Below these tables are averages for the various parameters and an estimate of the dose used in recording the image. The intensity distributions on the Ch0 and Ch1 images are displayed following background computation. Note that the plot is semi-log and some intensity values may be missing due to the action of the look-up table during read-in. Moving the mouse will restore the image.

Insufficient Background

The first thing to note is whether or not enough image was masked (some particles not completely masked) or too much was masked (leaving too few points for valid determination). If the sample is very crowded, this may be a serious problem. If the number of points used (out of 16,384) drops below 1,000, extreme caution is advised. If it is not obvious whether all the proper points are being masked, try the "Show Mask" option in the Background menu. This will redisplay points outside the mask in high contrast (yellow) and points inside in normal contrast so you can see if particle edges are being masked properly.

Changing Background Masking Threshold

The threshold for masking affects the number of points masked. Normally we use 3.0 standard deviations above the mean. Raising the threshold will exclude less background and lowering it will exclude more. Values of 2.0, 2.5, 3.0, 3.5 and 4.0 are options in the "Background" menu. A typical thin carbon film should give a signal value between 20 and 50 with a preamp gain of 10. The program assumes that pixel values of zero are holes and masks them also. In some cases some of the 16 sub-areas may be totally covered, either by a large object or overcrowding of particles. Background values in such areas will be printed in red and will be replaced by the global average. If none of the 16 sub-areas gives valid background, zeros will be entered for all areas and the BKG_VALID flag will not be set.

Updated 4 Oct 2007	Security Notice   Webteam   Site Map   STEM   Biology   BNL