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Secondary Ion Mass Spectroscopy Isotope Ratio Tools


(Button parameters are initialized for Allende experiment)

Button window Parameters


Numerator Image                     Select Numerator image.

                                    Can be Raw image, summed image, corrected for dead time or not

                                    as desired.

Denominator Image                   Select Denominator image.

                                    Can be Raw image, summed image, corrected for dead time or not

                                    as desired.

Sum-images                          Shows names (titles) of images selected by above 2 buttons.

                                    Don't use this button to select the images.

Image names                         Names for numerator and denominator images. 

                                    Can be the same as the window titles above.  This is for

                                    convenience in labeling.  The above names come from the          

                                    names of the image files.  Although they can be changed

                                    by using ***Buttons*** / Rename! on the windows BEFORE

                                    selecting with *SIMS Isotope Ratio* / Set Numerator Sum Image!,

                                    the names here might be more convenient to use.

Dead time                           For NIST SIMS instrument, it is 50e-9 secs.  (50 nanoseconds).

Pixels-per-image                    65500.  Not expected to change any time soon.

Image-collection-times              Total time to collect a single image.

                                    Multiplied by the number of images for collection time

                                    for the sum image.

Image Counts                        Number of numerator and denominator images.

Denominator Minimum Clip            Miniminum acceptable number of counts for

                                    the denominator image.  Pixel ratio is zero for

                                    denominator pixel values less than this.

Mass-bias-factor                    "Number to multiply times the ratio to correct for mass bias.

                                    Example:  for Mg26/Mg24, the mass bias correction is

                                          0.55% / AMU.  Two AMU's - 1.10 %.

                                    Mg26 image needs the correction boost,

                                    hence multiply by 1.011."




pixel dwell time = pdt                    calculated by pixel-dwell-times as:

                                    pdt = image-collection-time * image-count / pixels-per-image

dead time correction

DEAD-TIME-CORRECTED-ARA             Corrects for dead time pixel-by-pixel.

                                    pv    = uncorrected (raw) pixel value

                                    cpv   = pixel value corrected for dead time

                                    dt    = dead time  (constant instrument factor)

                                    cr    = count rate

                                    pdt   = pixel dwell time.  Total collection time for pixel.

                                    thus pv = cr * pdt


                                                (pv * ------)        (cr*pdt*dt/pdt)      cr*dt

                                    cpv = pv * e        pdt    = pv e                = pv e


Generating Allende paper figures


1) Read the sum images or recalculate them from raw data:

To read the sum images - just open them.  They are in the sum images folder.

...or... To generate the Mg 26 Sum images  (repeat for Mg24 sum images)


Read the Mg26 images into a data cube

      tools / Data Cube

      **Data Cube**/...

            Read/as Image files                 This reads all of the images into a cube.

            Cube!                               Selects cube image for further operations.

            Image/Sum image from whole cube     The desired sum image.  May be saved as TIFF.

2) Check the percentage dead time in the summed images.  This is a diagnostic step.

To generate the percentage dead time image


Click on one of the summed images.

*SIMS Isotope ratio* / Dead time image.

Dead time image is 0 - 27% for Mg24 image, and 0 - 12% for Mg26 image. 

3) Dead time image and original image look much the same.  This is to compare the

two.  One figure probably would do.

To compare scaled (visual) versions of dead time image with original image


Select both the summed Mg24 and Mg26 images in turn and use

***Buttons***/Adjust/Scale to Integer,  using all the defaults.

This scales the images to the 0 - 255 range used for image display.

Subtract one scaled image from the other.

***Buttons***/Info!  for the difference image shows 0 - 8, which is 3% of the

scaled image value range of 0 - 255.

4) Take the ratio of the two summed images, correcting the counts (values in

each pixel) for the instrumental collection time.

Ratio of raw summed images looks like that in the paper.   


To correct the images for dead time - use the button 'Correct for dead time' on

the front window (Mg24 or Mg26), repeat for the other.

Use ***Buttons***/Arithmetic/Ratio - Clipped, Cdt-Mg26 as numerator.

Clip limits:  nil for numerator, 100 for denominator seem to work.  100 is 0.1% of

the Cdt-Mg24 image.

4) Correct the ratio image for mass bias.  This is just a uniform scaling factor for the ratio image.

It does not change the appearance of the image since the viewed images are scaled for display.

It does change the numerical values for the pixels.

For Mg, on the NIST instrument, the correction is .55% / AMU.  (sugnal drops for higher masses)

The ratio Mg26/Mg24 involves a 2 AMU difference  (1.10% correction), so the ratio image needs to be

multiplied by 1.011.