New Features in CalcImage

[John Donovan]

The CalcImage "Hyper-Cursor" feature now works better than ever- on-line or off-line!  It's available from this menu



You can now correlate all your images and maps based on stage coordinates of, for example, your x-ray maps, phase classification and BSE images as your move the mouse!



What is really fancy about this "Hyper-Cursor" feature is that it is *not* dependent on the image stage extents or magnification, because the cursor position is tied to the actual stage position of every pixel in every image.

So as long as the images were all acquired in the same sample exchange, they can all be correlated by actual stage position.

[John Donovan]

The latest version of CalcImage (v. 10.1.8, 12/15/2013), nicely now handles oxides and excess oxygen output to Surfer.

See attached example of Magnetite analysis using polygon extraction to avoid an inclusion.

And also an example of an oxide element by difference, although the Ce2O3 in this monazite composition is just there for the general matrix correction and assumes no Nd, Sm, etc in the composition. This assumption has been tested and surprisingly, does work well for the U, Th, Pb, Y and La matrix corrections as seen here in some point analyses:

Un    8 Allaz-3
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 50.0  Beam Size =    5
(Magnification (analytical) =  40000),        Beam Mode = Analog  Spot
(Magnification (default) =      400, Magnification (imaging) =    800)
Image Shift (X,Y):                                          .00,   .00
Number of Data Lines:   9             Number of 'Good' Data Lines:   9
First/Last Date-Time: 10/30/2013 12:04:35 PM to 10/30/2013 01:02:35 PM
WARNING- Using Exponential Off-Peak correction for th ma

Average Total Oxygen:       27.194     Average Total Weight%:  100.000
Average Calculated Oxygen:  27.194     Average Atomic Number:   39.773
Average Excess Oxygen:        .000     Average Atomic Weight:   39.299
Average ZAF Iteration:       11.00     Average Quant Iterate:     3.00

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Element Ce is Calculated by Difference from 100%
Element P is Calculated  .25 Atoms Relative To 1.0 Atom of Oxygen

Un    8 Allaz-3, Results in Elemental Weight Percents
 
ELEM:        U      Th      Pb       Y      La      Ce       P       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    DIFF    STOI    CALC
BGDS:      LIN     EXP     LIN     LIN     LIN
TIME:   200.00  200.00  200.00  120.00  120.00
BEAM:    49.82   49.82   49.82   49.82   49.82

ELEM:        U      Th      Pb       Y      La      Ce       P       O   SUM 
   219    .472   3.341    .567   1.826   9.508  43.870  13.179  27.237 100.000
   220    .446   3.334    .524   1.638   9.721  43.952  13.169  27.216 100.000
   221    .237   3.150    .424   1.054   9.937  44.893  13.142  27.162 100.000
   222    .510   3.582    .581   1.695   9.716  43.555  13.161  27.200 100.000
   223    .445   3.923    .599   1.587   9.413  43.725  13.144  27.165 100.000
   224    .512   3.290    .558   1.789   9.884  43.557  13.177  27.234 100.000
   225    .515   3.329    .573   1.865   9.354  43.944  13.180  27.240 100.000
   226    .125   4.790    .400   1.349   8.802  44.278  13.126  27.129 100.000
   227    .446   3.816    .595   1.555   9.514  43.764  13.145  27.167 100.000

AVER:     .412   3.617    .536   1.595   9.539  43.949  13.158  27.194 100.000
SDEV:     .137    .509    .074    .257    .342    .418    .019    .040    .000
SERR:     .046    .170    .025    .086    .114    .139    .006    .013
%RSD:    33.28   14.08   13.75   16.13    3.59     .95     .15     .15
STDS:       15      18     386    1016     836       0       0       0

STKF:    .8725   .8707   .6861   .4480   .6591   .0000   .0000   .0000
STCT:   137.33   44.30  140.31   38.76   33.08     .00     .00     .00

UNKF:    .0035   .0302   .0041   .0116   .0829   .0000   .0000   .0000
UNCT:      .55    1.54     .84    1.00    4.16     .00     .00     .00
UNBG:      .77     .26     .54     .13     .19     .00     .00     .00

ZCOR:   1.1794  1.1961  1.3069  1.3748  1.1510   .0000   .0000   .0000
KRAW:    .0040   .0347   .0060   .0259   .1257   .0000   .0000   .0000
PKBG:     1.71    6.87    2.56    8.82   23.27     .00     .00     .00
INT%:   -14.77    ----   -2.38    ----    ----    ----    ----    ----

Un    8 Allaz-3, Results in Oxide Weight Percents

ELEM:      UO2    ThO2     PbO    Y2O3   La2O3   Ce2O3    P2O5       O   SUM 
   219    .536   3.802    .611   2.319  11.151  51.384  30.198    .000 100.000
   220    .506   3.794    .564   2.080  11.401  51.480  30.175    .000 100.000
   221    .268   3.585    .457   1.339  11.654  52.582  30.115    .000 100.000
   222    .578   4.076    .626   2.153  11.395  51.015  30.157    .000 100.000
   223    .504   4.464    .645   2.015  11.040  51.214  30.118    .000 100.000
   224    .580   3.744    .601   2.272  11.591  51.018  30.194    .000 100.000
   225    .584   3.788    .617   2.368  10.970  51.471  30.201    .000 100.000
   226    .142   5.451    .431   1.713  10.323  51.863  30.078    .000 100.000
   227    .505   4.342    .641   1.974  11.157  51.260  30.120    .000 100.000

AVER:     .467   4.116    .577   2.026  11.187  51.476  30.151    .000 100.000
SDEV:     .156    .580    .079    .327    .401    .490    .045    .000    .000
SERR:     .052    .193    .026    .109    .134    .163    .015    .000
%RSD:    33.28   14.08   13.75   16.13    3.59     .95     .15  375.00
STDS:       15      18     386    1016     836       0       0       0

Un    8 Allaz-3, Results in Millions of Years Ago, EPMA Age (from U, Th, Pb)

         U WT%  Th WT%  Pb WT%   U PPM  Th PPM  Pb PPM Age[My] Calc Pb %Pb(Th)  %Pb(U)
   219 .472289 3.34109 .567045 4722.89 33410.9 5670.45 2323.00 5670.27 64.3415 35.6635
   220 .446398 3.33429 .523589 4463.98 33342.9 5235.90 2208.20 5236.10 65.9074 34.0874
   221 .236642 3.15039 .424494 2366.42 31503.9 4244.94 2226.00 4245.02 77.4650 22.5299
   222 .509558 3.58221 .581436 5095.58 35822.1 5814.36 2231.20 5814.52 64.4655 35.5293
   223 .444676 3.92270 .598909 4446.76 39227.0 5989.09 2258.10 5989.38 69.4054 30.5896
   224 .511685 3.28988 .557768 5116.85 32898.8 5577.68 2252.20 5577.78 62.3314 37.6634
   225 .515049 3.32893 .572963 5150.49 33289.3 5729.63 2285.30 5729.68 62.3537 37.6412
   226 .124814 4.79049 .399875 1248.14 47904.9 3998.75 1650.30 3998.89 91.3724 8.62120
   227 .445556 3.81612 .594983 4455.56 38161.2 5949.83 2281.40 5949.84 68.7099 31.2850

AVER:  .411852 3.61734 .535674 4118.52 36173.4 5356.74 2190.63 5356.83 69.5947 30.4012
SDEV:  .137073 .509306 .073673 1370.73 5093.06 736.728 205.618 736.721 9.41884 9.41990

[John Donovan]

CalcImage now supports output for all quant types (detection limits, analytical sensitivity, log wt.%, mineral end members and U-Th-Pb chem age calculations), for polygon, slice and strip operations.



See attached for examples.

[John Donovan]

Here's another example (attached) using the U-Th-U age with a polygon extraction to get a more accurate average and variance.

Note that the inclusion was not included in the calculation, just the area inside the polygon!

Also the output was generated completely automatically, no manual modifications to the graphical objects!

[John Donovan]

A new feature if your match database (e.g., DHZ.MDB) contains accurate densities for each composition (available in v. 10.1.9 of PFE), is the Mass% for each phase as shown here in this output from CalcImage of a field of view of Mt St. Helens basalt.

See attached.

[John Donovan]

I think I forgot to describe our CalcImage "strip averaging" of intensity or quant maps using horizontal or vertical strips in um units.

This means the user can take an x-ray map and specify the application average the pixel rows or pixel columns to obtain an average of the sample either vertically or horizontally as seen here:

[John Donovan]

One can now calculate and output statistics for all raw and/or quant x-ray maps with a couple of mouse clicks using this new menu:


Note the Project | Output Image Statistics For menu names have now been modified slightly from what you see above...

Here is an example of elemental results for a magnetite standard x-ray map. Note that the average measured and excess oxygen are both properly output:



And here is an example of calculating the average detection limit for an alloy x-ray map using a short (200 msec, 30 nA) dwell time per pixel:



I should also mention that at this point it would be *very easy* to add additional image statistics calculations if there are any that you all think would be useful!

[John Donovan]

See this post on how to edit the sample title output to your presentation images:

http://probesoftware.com/smf/index.php?topic=40.msg1419#msg1419

Another example attached below.

[John Donovan]

We've managed to implement the "aggregate" photon method into CalcImage for all quant operations.

This is response to Aoife McFadden's report here:

http://probesoftware.com/smf/index.php?topic=393.0

and Anette von der Handt's report here:

http://probesoftware.com/smf/index.php?topic=383.0

that this feature seemed to be missing and indeed it was (previously one could only apply the "aggregate" photon method to point analyses in Probe for EPMA, but now one can apply this "aggregate" method for improving sensitivity in CalcImage for x-ray maps!   

Using Aoife's data as an example here is a comparison of the S and Sr background intensity maps with and without the aggregate option applied to the same data (please note that I'm only showing the single spectro 1 for the "normal" quant as that is the channel everything gets "aggregated" to when the aggregate method is applied). This is simply to demonstrate that the aggregated background intensity pixels are higher in intensity because they are summed at the photon level).

For Sr la:



For S Ka:



I think you will also agree that the "aggregated" background intensity maps (on the right side) appear to be less noisy (and of course they should!).

And here are the calculated 3 sigma detection limits (for just the Sr La) to show that the detection limits really are better for the "aggregated" intensities:



Finally here is a page from the presentation output for the normal quant:



and here is the single page output for the "aggregated" photon intensities quantified:



I think everyone will agree that the "aggregated" quant maps for Sr and S are better sensitivity both visually and numerically (as seen by comparing the range of z values in the color scale bar).

[John Donovan]

I've managed to implement the "aggregate" photon method into CalcImage for all quant operations.

I just realized that the above post "starts in the middle", so I should explain a little first.  Here is Aoife's elemental setup in PFE for her probe run:

Last (Current) On and Off Peak Count Times:
ELEM:     S ka    S ka    S ka    S ka    S ka   Ca ka   Sr la   Sr la   Sr la   Sr la
BGD:       MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
BGDS:      MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
SPEC:        1       2       3       4       5       3       1       2       4       5
CRYST:    LPET     PET    LPET    LPET    LPET    LPET    LPET     PET    LPET    LPET
ORDER:       1       1       1       1       1       2       2       2       2       2
ONTIM:   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00   15.00


So there are 5 spectrometers tuned to S Ka, one for Ca Ka and 4 for Sr La. Now here is her data calculated for each spectrometer (normal analysis with totals image not shown):



Now we simply turn on the "aggregate intensity" feature as seen here:



And now, here is her same data, but this time re-calculated with the "aggregate" intensity feature (again without the totals image):



 

[John Donovan]

This is a nice new feature in CalcImage that allows one to output all of the currently open images to Grapher for presentation output. Start by opening only the images you want to export using the Project | Open Images For Current Project or File | Open GRD File menus.

Then click the new Window | Output The Currently Displayed Images menu as seen here:



This nice thing is one can display all sorts of data types all at once, for example this one of Mo atomic%, weight%, analytical sensitivity and detections limits:



Note this works for any number of images displayed, as the Surfer script will auto-generate the additional pages as necessary.

[John Donovan]

When we get Thermo and Bruker on board with this:

http://probesoftware.com/smf/index.php?topic=400.msg2174#msg2174

Then I will enable these controls in CalcImage for true, full featured EDS-Si and WDS quant integration:



Cool!

[John Donovan]

The Copy To Clipboard and Save as BMP (24 bit RGB) buttons are now working:



Download ver. 10.7.8 of PFE when ready.

[John Donovan]

Did you know that you can also perform phase classification in CalcImage using lists of quantitative analysis points from Probe for EPMA using this menu?



Then simply import the export file into CalcImage using this menu:



The resulting phase numbers are listed in the NK column. Furthermore you can "pre-process" quantitative image data from CalcImage in this window to extract ranges based on the sum of each pixel (to remove pixels of epoxy, etc) as seen here:

I'm bumping this forward to remind you all that you can perform kmeans clustering on random points exported from PFE for both WDS *and* EDS elements now.  All data types too- raw, net intensities, elemental wt%, atomic, oxide, detection limits, log wt%, etc. etc.
john

[John Donovan]

Here's a useful new feature in CalcImage...

Open some images in CalcImage and open the Log Window from the Window menu and click the Calculate Currently Displayed Image Statistics menu and you will get the average and standard deviation of all images as see here: