Focus Documentation

The magnification variable defines the nominal magnification of the image. This should be the magnification number that the TEM displayed while recording the image. It is recommended to factor any additional post-magnification factors of the CCD camera or scanner details into the “digitizer step size”.

The stepdigitizer variable defines the pixel size in the image with respect to the micrograph or the screen (in case of CCD images). This number should be given in “micrometers”. an example:

A typical value for a micrography recorded at 50,000x magnification and then digitized with 7 micrometer pixel size would be: magnification=50000, stepdigitizer=7 Or, for a CCD image recorded at 50,000x magnification, with a Tietz CCD camera with 1.5x post-magnification between the TEM screen and the CCD's scintillator, and a CCD pixel size of 14 micrometer: magnification=50000, stepdigitizer=9.333

If you downsample the image with label, then label keeps in the output file the CellA dimensions, i.e. the file still knows what the original image dimensions were. The digitizer step size in that case should be valid for the original image size, not for the down-sampled image. The catch is now that if you then transform the image into TIFF (mrc2tiff.exe) and then back to MRC (tiff2mrc.exe), the information about the original image size is lost and the digitizer step size now needs to be valid for the down-sampled image.

Calculate Magnification from PixelSizes on Recording Medium and Sample Level? [Calc_from_sample_pixel]

When this is 'y', then the parameters for “magnification” and “stepdigitizer” will be calculated from the following parameter “sample_pixel”. If this is 'n', then the pixel size on the sample level is calculated from the values for “magnification” and “stepdigitizer”.

Pixel Size on Sample Level (in Angstroem) [sample_pixel]

This is the size of an image pixel on the sample level, in Angstroems.