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Software => Probe for EPMA => Topic started by: BenH on November 06, 2017, 10:35:18 AM

Title: Offset (Interpolated) MAN backgrounds
Post by: BenH on November 06, 2017, 10:35:18 AM
For those of us that don't have a perfect set of standards I would like to request something strange.

In many cases my standards have minor and element impurities in them that happen to be elements that I am interested in.  That makes the standard completely useless for a MAN backgrounds.  In yet other cases there are spectral interferences that make the standard useless for MAN curves. 

One way to get around this is to use off peak analyses to avoid the minor element impurities or the spectral interferences.  The MAN value would simply be the interpolated background value.  Would this be possible to implement?
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Probeman on November 06, 2017, 12:35:31 PM
For those of us that don't have a perfect set of standards I would like to request something strange.

In many cases my standards have minor and element impurities in them that happen to be elements that I am interested in.  That makes the standard completely useless for a MAN backgrounds.  In yet other cases there are spectral interferences that make the standard useless for MAN curves. 

One way to get around this is to use off peak analyses to avoid the minor element impurities or the spectral interferences.  The MAN value would simply be the interpolated background value.  Would this be possible to implement?

Hi Ben,
So you saying, measure normal off-peaks on the MAN standards and utilize the interpolated backgrounds for the MAN curve in order to perform MAN corrections on unknowns? That's a really interesting idea as it would avoid issues where the MAN standard does not contain a zero concentration of the element, or has on-peak interferences for that emission line on the MAN curve.  Here are some nice examples of such contamination and interference issues on MAN curves:

http://probesoftware.com/smf/index.php?topic=4.msg1070#msg1070

http://probesoftware.com/smf/index.php?topic=4.msg5136#msg5136

http://probesoftware.com/smf/index.php?topic=4.msg5295#msg5295

That is one nice thing about the MAN method, it lets one know if one's standards are truly clean or not!

Not sure how hard it would be to implement, but here's an even stranger idea that doesn't require any code changes: simply acquire your MAN standards with the on-peak positions slightly to one side of the actual peak positions.  It might not work at low spectrometer angles where the continuum is highly sloped, but at medium to high sin thetas, the backgrounds are relatively flat and would probably give an accurate measurement of the continuum intensities for the MAN fit.

In other words, since Probe for EPMA allows different sample setups for the standards and unknowns you would acquire MAN backgrounds for both your MAN standards and your unknowns, but the on-peak positions would be "offset" for the MAN standards, while the unknowns (and primary standards) would utilize the correct on-peak positions for the MAN corrected samples.

Or you could break down and purchase some decent pure element and oxide standards and do the MAN backgrounds properly!    :)
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 06, 2017, 03:49:09 PM
One problem with the above idea for using "offset" on-peak positions for the MAN standards and normal on-peak positions for the unknowns (and primary stds), is that you won't be able to use any standards in the MAN fit, that are also used as primary standards.

Normally PFE automatically uses a primary standard as an MAN standard if the element in question is not present.  So for example, one can use FeS2 as a primary standard for Fe or S, but one can also use it as a MAN standard for trace elements like Ag, Cu and Ag, if they are not present in detectable amounts. So having a standard acquired with both "offset" and normal on-peak positions is a problem with Probeman's idea.

Basically I think Ben's original idea for using the interpolated off-peak intensities to create the MAN calibration curve is a good idea if I can think of a way to implement it.  One can create an "off-peak" MAN curve easily by simply setting the peak intensity equal to the interpolated background intensity.  But when it comes to calculating the unknown composition we don't want to overwrite the on-peak intensity with the background!

This will take some more thought...
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 07, 2017, 01:26:43 PM
I still need to think about how to apply Ben Hanson's idea to normal samples, but I was able to modify the MAN calibration dialog code so that it loads either normal on-peak (only) intensities for the MAN calibration curve for off-peak sample acquisitions as seen here:

(http://probesoftware.com/smf/gallery/1_07_11_17_12_19_49.png)

or, loads the interpolated off-peak background intensities for the MAN calibration curve as seen here:

(http://probesoftware.com/smf/gallery/1_07_11_17_12_20_06.png)

One interesting thing is that the variance is slightly worse for the interpolated off-peak MAN intensities compared to the on-peak only (off-peak) MAN intensities, as expected, since the interpolated intensity statistics are worse  (1/2 the counting time for each off-peak, compared the on-peak counting time)

I think this is going to work...  what a great idea from Ben Hanson!    It's very cool to see a new approach that should avoid not only problems with standards that are contaminated with trace amounts of the element of interest, but also have on-peak spectral interferences.  The point being that once this off-peak interpolated MAN calibration curve is done, one can simply measure on-peak (MAN) samples (unknowns) and get better statistics in 1/2 the time.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: BenjaminWade on November 07, 2017, 08:19:48 PM
I concur...this is a great idea as I run into this sometimes as well. It would be great if there was a check box somewhere next to the standards list somewhere to let it know which ones to use the off peak interpolation for.

As you say you would have to be careful that you don't have to go miles out to measure interference free background positions where the continuum might be quite different.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 07, 2017, 10:15:25 PM
One application that this new method might work well with is trace O ka. Normally it's difficult to find standards that do not contain oxygen (most metals have some trace amount of oxygen from a native oxide layer), and this method avoids that problem because it uses the interpolated off-peak intensity, instead of the on-peak intensity, for the MAN calibration.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 08, 2017, 10:37:21 AM
Hi Ben,
Some of this may be confusing to others so let's define our terms a bit.  I propose the following:

Ben Hanson originally used the term "offset" MAN backgrounds to mean the interpolated off-peak intensities calculated from the hi and lo off-peak positions as measured in the MAN standards by acquiring them as off-peak standards. These *interpolated* off-peak intensities would then be applied to the MAN background calibration intensities by simply setting the interpolated on-peak intensity to the calculated (interpolated) off-peak intensity.

This is opposed to the existing practice of just using the measured *on-peak* intensities from off-peak measurements on the standards used in the MAN calibration (and ignoring the off-peak measurements altogether). That is using the Analytical | Use Off-Peak Elements for MAN Fit menu option as discussed here:

http://probesoftware.com/smf/index.php?topic=4.msg2255#msg2255

Therefore I think it is less confusing to use the term *interpolated* off-peak intensities to describe this idea of Ben Hanson's which avoids the problem he mentioned where an MAN standard may have a trace amount of the element present (at the peak position).

Instead I would like to propose that the term *offset* MAN backgrounds refer to the "stranger" suggestion I made here:

http://probesoftware.com/smf/index.php?topic=987.msg6444#msg6444

where one might "detune" the on-peak position for standards utilized in the MAN calibration (to a slightly offset peak position) so that one might avoid trace contamination that might be present in one's MAN standards. Of course this idea of mine has it's issues (you can't use the same standard as an MAN standard and also as a primary standard, and one has to modify the peak positions to be different for these MAN standards), but this "stranger" idea has the benefit of not requiring any code changes!   :D

So let's call Ben Hanson most excellent idea the *interpolated* off-peak MAN method. In code, this basically consists of setting the on-peak intensity of the MAN standards (acquired using the normal off-peak acquisition method), to the *interpolated* (that is calculated) off-peak intensity from the measured off-peak intensities.

So to respond to your points here:

I concur...this is a great idea as I run into this sometimes as well. It would be great if there was a check box somewhere next to the standards list somewhere to let it know which ones to use the off peak interpolation for.

If I understand you correctly, there is really is no need for this as the software will automatically figure out which MAN standards to perform this interpolation for.

As you say you would have to be careful that you don't have to go miles out to measure interference free background positions where the continuum might be quite different.

I assume you are referring to  my "stranger" idea of offsetting the on-peak position to avoid trace (on-peak) contamination.  Yes, if we were to utilize this method you'd want to not go too far from the on-peak position so that the continuum intensity is close to the intensity underneath the peak at the on-peak position.

But in the end, I would again suggest that it would probably be preferable to just get pure standards for use with the MAN calibrations!
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 08, 2017, 12:48:01 PM
Ok, I've tested Ben Hanson's new "interpolated" off-peak MAN method and it seems to be working. Please let me know what you all find.

Here are the steps:

1. Acquire intensities on your MAN standards but using normal off-peak measurements instead of the normal MAN acquisition method.

2. Select the Analytical | Use Off-Peak Elements For MAN Fit menu as seen here:

(http://probesoftware.com/smf/gallery/1_08_11_17_12_30_15.png)

This makes sure that these off-peak standards will be found by PFE when you go to make your MAN assignments for each element.

3. Assign MAN standards as usual using the Analytical | Assign MAN Fits menu as usual. In the Assign MAN Fits dialog you will see displayed the *on-peak* intensities (ignoring the off-peak intensities for now!) for those standards that *do not* contain the element of interest).  If your standards are not perfectly pure, you may see that some standards lie above the general trend line from this contamination (of course this could be due to on-peak spectral interferences also).

4. Now we want to analyze our unknown (which was measured using normal MAN acquisition methods), to see the effect where we have subtracted too much background from our on-peak measurements, so we perform a quant on the unknown sample as seen here:

Un   11 pyrite #730
TakeOff = 40.0  KiloVolt = 20.0  Beam Current = 100.  Beam Size =    0

Un   11 pyrite #730, Results in Elemental Weight Percents

ELEM:       Au      Au      Cu      Ag
BGDS:      MAN     MAN     MAN     MAN
TIME:   400.00  400.00  400.00  400.00
BEAM:   100.49  100.49  100.49  100.49

ELEM:       Au      Au      Cu      Ag   SUM 
XRAY:     (la)    (ma)    (ka)    (la)
   627   -.005   -.002   -.010   -.004 100.066
   628   -.002    .003   -.007    .004 100.083
   629    .004   -.001   -.008   -.004 100.078
   630    .000   -.004   -.010    .004 100.077
   631    .002    .004   -.009   -.001 100.082
   632    .001    .000   -.011    .001 100.077

AVER:     .000    .000   -.009    .000 100.077
SDEV:     .003    .003    .001    .004    .006
SERR:     .001    .001    .001    .001
%RSD:     ----    ----  -15.53    ----
STDS:      579     579     529     547

STKF:   1.0001  1.0000   .9975   .9920
STCT:  15401.2  5782.1 13188.3  3764.1

UNKF:    .0000   .0000  -.0001   .0000
UNCT:       .0      .0    -1.0      .0
UNBG:    168.3    12.1    36.4     8.1

ZCOR:   1.4520  1.0366  1.1574  1.3373
KRAW:    .0000   .0000  -.0001   .0000
PKBG:     1.00    1.00     .97    1.00
BLNK#:      11      11    ----      11
BLNKL: .000000 .000000    ---- .000000
BLNKV: -.01444 .010240    ---- .009146

Note that the Cu concentration in our pyrite sample is negative because the MAN trend line was too high. So now we activate Ben Hanson's new interpolated off-peak MAN method by going to the Analytical | Analysis Options menu dialog and check the new option seen here:

(http://probesoftware.com/smf/gallery/1_08_11_17_12_31_38.png)

Now we re-run our unknown sample quant and we obtain these results:

Un   11 pyrite #730
TakeOff = 40.0  KiloVolt = 20.0  Beam Current = 100.  Beam Size =    0

Un   11 pyrite #730, Results in Elemental Weight Percents

ELEM:       Au      Au      Cu      Ag
BGDS:      MAN     MAN     MAN     MAN
TIME:   400.00  400.00  400.00  400.00
BEAM:   100.49  100.49  100.49  100.49

ELEM:       Au      Au      Cu      Ag   SUM 
XRAY:     (la)    (ma)    (ka)    (la)
   627   -.005   -.001    .005   -.004 100.081
   628   -.002    .003    .008    .004 100.099
   629    .004   -.001    .007   -.004 100.093
   630    .000   -.004    .005    .004 100.092
   631    .002    .004    .006   -.001 100.097
   632    .001   -.001    .005    .001 100.092

AVER:     .000    .000    .006    .000 100.093
SDEV:     .003    .003    .001    .004    .006
SERR:     .001    .001    .001    .001
%RSD:  1437.74    ----   22.70 8127.41
STDS:      579     579     529     547

STKF:   1.0001  1.0000   .9975   .9920
STCT:  15401.2  5782.1 13188.3  3764.1

UNKF:    .0000   .0000   .0001   .0000
UNCT:       .0      .0      .7      .0
UNBG:    168.9    11.5    34.7     8.0

ZCOR:   1.4520  1.0367  1.1585  1.3373
KRAW:    .0000   .0000   .0001   .0000
PKBG:     1.00    1.00    1.02    1.00
BLNK#:      11      11    ----      11
BLNKL: .000000 .000000    ---- .000000
BLNKV: -.02000 .019429    ---- .011628

And all we did in the code was to set the on-peak intensity equal to the interpolated off-peak intensity for the standards used in the MAN calibration curve.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: BenH on November 09, 2017, 08:41:33 AM
YES!  Oxide layers on my metal standards make MAN backgrounds impossible for oxygen.  This will be a big help to me.
Thanks again John for doing this!

By the way...I will just count longer on my backgrounds.  Shouldn't sacrifice anything in terms of precision.

 :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o :o
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 09, 2017, 09:09:46 AM
YES!  Oxide layers on my metal standards make MAN backgrounds impossible for oxygen.  This will be a big help to me.
Thanks again John for doing this!

Hi Ben,
Are you quant mapping oxygen?  Using MAN backgrounds for quant mapping is a big time saver of course because one doesn't need to acquire off-peak maps with the MAN method.

By the way, I will modify the code so it automatically sets the "Use Off-Peak Elements For MAN Fits" menu if this new "Use Interpolated Off-Peaks for MAN Intensities" checkbox is checked when closing the Analysis Options dialog.
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: BenjaminWade on November 09, 2017, 06:48:20 PM

I concur...this is a great idea as I run into this sometimes as well. It would be great if there was a check box somewhere next to the standards list somewhere to let it know which ones to use the off peak interpolation for.

If I understand you correctly, there is really is no need for this as the software will automatically figure out which MAN standards to perform this interpolation for.


It's probably me not understanding correctly. For example taking oxygen, I could have standard X that is displaying a poor MAN fit as its oxidised while all others are OK. So I would visually determine that by reviewing the current MAN fit, and would enable the "interpolated" MAN measurement only for that standard X.

Or is it that the "interpolated" MAN is either on or off for all standards at once?

Cheers
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 09, 2017, 08:50:31 PM
Hi Ben,
Yes, please let's keep the interpolated off-peak MAN as all off or all on for the standards!    :)

I think it will work fine like this and one can still add/remove individual standards from the MAN fit manually as before.  Here's an example from a recent trace Au in pyrite run with the new interpolated off-peak MAN flag *off*:

(http://probesoftware.com/smf/gallery/1_09_11_17_8_40_42.png)

Note that because of the interference of Fe Ka III on Au Ma, the standards containing Fe plot above the MAN trend line.  This is because the original default off-peak MAN method utilized the on-peak intensities from the off-peak acquired standards (ignoring the off-peak measurements). 

And here is the same MAN standard data, but with the interpolated off-peak MAN flag turned *on* in the Analytical | Analysis Options dialog:

(http://probesoftware.com/smf/gallery/1_09_11_17_8_41_10.png)

Because we can now optionally utilize (thanks to Ben Hanson), the off-peak measurements by interpolation for the MAN calibration, any on-peak interference (and possible contamination effects) are removed from the MAN calibration. So now we can deal with standards that either have on-peak interferences, and/or are contaminated by the element of interest, and still obtain an accurate MAN curve.

Of course, with the interpolated off-peak MAN method we can still get off-peak interferences, just as we do for normal off-peak measurements, so be forewarned!

Never the less, pretty cool.
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Probeman on November 27, 2017, 03:45:53 PM
So our EPMA class looked at another run we did on some Al, V, Fe, Cr alloys (also analyzing for oxygen), where we'd acquired off-peaks on the standards so we could compare the normal (on-peak) MAN method with the "interpolated" off-peak MAN method as proposed by Ben Hanson and suggested by Ben Wade as possibly interesting for oxygen analysis because the interpolated MAN would avoid the native oxide coating that is normally found on pure metals.

In this case we could only use pure Si and Fe as MAN standards for O Ka as the other metal standards had oxygen declared as a contaminant. Plotting up the MAN curve, it's just a straight line fit as seen here:

(http://probesoftware.com/smf/gallery/395_27_11_17_3_36_00.png)

But as we were only interested in seeing the magnitude of the difference between normal on-peak MAN and interpolated off-peak MAN this will work fine.

So here is an analysis of our Cr metal standard using the normal on-peak MAN:

St  524 Set   1 Chromium metal, Results in Elemental Weight Percents
 
ELEM:       Al      Cr      Fe       V       O
BGDS:      MAN     MAN     MAN     MAN     MAN
TIME:    30.00   30.00   30.00   30.00   30.00
BEAM:    30.14   30.14   30.14   30.14   30.14

ELEM:       Al      Cr      Fe       V       O   SUM
    13   -.002 100.056    .018    .002    .803 100.876
    14   -.009 100.507    .007    .010    .802 101.317
    15   -.011 100.034   -.001    .006    .829 100.857

AVER:    -.007 100.199    .008    .006    .811 101.017
SDEV:     .004    .267    .010    .004    .015    .260
SERR:     .003    .154    .006    .002    .009
%RSD:   -60.66     .27  121.54   68.48    1.90


So about 0.8 wt% oxygen.  And here is the analysis using the interpolated off-peak MAN fit:

St  524 Set   1 Chromium metal, Results in Elemental Weight Percents
 
ELEM:       Al      Cr      Fe       V       O
BGDS:      MAN     MAN     MAN     MAN     MAN
TIME:    30.00   30.00   30.00   30.00   30.00
BEAM:    30.14   30.14   30.14   30.14   30.14

ELEM:       Al      Cr      Fe       V       O   SUM
    13    .015 100.121    .039    .001   1.073 101.248
    14    .009 100.572    .029    .009   1.072 101.690
    15    .007 100.099    .020    .004   1.099 101.229

AVER:     .010 100.264    .029    .004   1.081 101.389
SDEV:     .004    .267    .010    .004    .015    .260
SERR:     .003    .154    .006    .002    .009
%RSD:    43.34     .27   32.72   89.82    1.43


So it's about a 0.2 wt% difference in the measured oxygen, with the larger value using the interpolated off-peak MAN, which makes sense because the on-peak MAN would be affected by the native oxide layer on the Si and Fe standards used for the MAN calibration.  Thus causing a higher background intensity to be subtracted from the sample, but not so for the interpolated off-peak MAN method.

Interesting.
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Probeman on November 28, 2017, 09:58:38 AM
St  524 Set   1 Chromium metal, Results in Elemental Weight Percents
 
ELEM:       Al      Cr      Fe       V       O   SUM
    13   -.002 100.056    .018    .002    .803 100.876
    14   -.009 100.507    .007    .010    .802 101.317
    15   -.011 100.034   -.001    .006    .829 100.857

AVER:    -.007 100.199    .008    .006    .811 101.017
SDEV:     .004    .267    .010    .004    .015    .260
SERR:     .003    .154    .006    .002    .009
%RSD:   -60.66     .27  121.54   68.48    1.90


St  524 Set   1 Chromium metal, Results in Elemental Weight Percents (interpolated off-peak MAN)
 
ELEM:       Al      Cr      Fe       V       O   SUM
    13    .015 100.121    .039    .001   1.073 101.248
    14    .009 100.572    .029    .009   1.072 101.690
    15    .007 100.099    .020    .004   1.099 101.229

AVER:     .010 100.264    .029    .004   1.081 101.389
SDEV:     .004    .267    .010    .004    .015    .260
SERR:     .003    .154    .006    .002    .009
%RSD:    43.34     .27   32.72   89.82    1.43


Upon a second glance I note that the other elements also showed interesting changes going from normal on-peak MAN fitting to the new interpolated off-peak MAN option.   The Al concentration went up from -0.007 to 0.01, the Fe went up from 0.008 to 0.029 and the V went down but by less than a single standard deviation.   

This suggests to me that me that the interpolated off-peak MAN is doing exactly what it is supposed to do, by avoiding small (undeclared) concentrations present in one's standards. Whether one knows they are there or not! 

This means to me that the background intensity decreased for these trace elements because the interpolated off-peak MAN avoided small contaminates or spectral interferences...

This might mean that this interpolated MAN method might be good enough for trace elements to remove the need for a blank correction.  I need to look at some more data!
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Probeman on November 28, 2017, 12:10:25 PM
In thinking about this a bit more, it occurs to me that not only is this interpolated off-peak MAN measurement method likely to be as accurate as normal off-peak measurements, and maybe even a little better, since it's based on a regression of multiple standards (and because off-peak interferences are less likely in the simple metal and oxide standards that are usually utilized for the MAN calibration fit), but the typical time savings and better sensitivity of the MAN method will still apply. That is because we are only utilizing off-peak measurements for our MAN standards, not for the unknown samples using MAN (on-peak only) measurements.

Is anyone interested in writing up a short abstract on this with me?   I'd ask Ben Hanson who came up with the idea in the first place, but he always tells me that Corning Glass won't let him publish anything at all.  We'll certainly acknowledge him of course.
john
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: orlandin on November 22, 2019, 01:11:21 PM
Hello, all! I was really inspired by the forum posts which resulted in the 'use interpolated off peak backgrounds for MAN fit' (https://probesoftware.com/smf/index.php?topic=987.0), because I don't have an optimized MAN standard setup yet. However, it does not seem to work quite how I would expect. After collecting my standards using normal off-peak backgrounds, I check the box under the Analysis dropdown for 'use off-peak standards', and then check the box in Analysis Options for 'use interpolated off peak'. Then I usually also check the box just under 'use off peak standards' so that the MAN correction is applied because it doesn't seem like you should ever not do that, although it doesn't seem likely to influence the problem below.

When I open my 'Assign MAN fits', what I expect to see is every single element for every single standard since I did not use Quick standards and PFE has a calculated/interpolated value for the background intensity under the peak for everything. But instead, I find a rather sparsely populated MAN curve as if I had run all my inappropriate-for-MAN standards as if they were just MAN standards, with several elements reporting having no MAN standard data at all due to everything having a non-zero concentration of that element.

I'm pretty sure I understood the forum post about how to use this feature to have a long standardization but still retain many of the benefits of MAN backgrounds on unknowns, but now I am not sure about what sequence of buttons to press or boxes to tick in order to get PFE to utilize the interpolated/calculated background values from the off-peak standardization. Thank you!
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 22, 2019, 01:39:50 PM
Hi Phil,
You raise an excellent point about using the "interpolated" off-peak MAN feature.

Yes, it makes some sense that one should be able to use all the elements for all the standards for this "interpolated" MAN background curve feature, because as you say, if you're actually using off-peak measurements to calibrate your MAN curves, why not use them all?

Now, as you also say, for normal un-interpolated MAN background calibrations of course we *cannot* utilize standards containing the element of interest, because we wouldn't be measuring the actual background, since we are measuring on-peak.  But if we're using off-peak backgrounds, we could in principle.

But here's the thing, in practice I think it could cause other issues. For example, one might assign their MAN standards using these off-peak interpolated measurements, but then if they uncheck that box, all hell would break loose for those standards that *do* contain the element of interest.

I'll tell you the real reason why we implemented this "interpolated" off-peak MAN method, and that was because Ben Hanson at Corning Glass had a similar problem as you, in that he had standards which weren't quite as well characterized as he thought they were!  Well, at least not as pure as he thought they were.  This happens more often than one might think. Here's an example of undeclared Cl (~200 PPM) in an amphibole standard showing up in the MAN curve for Cl:

https://probesoftware.com/smf/index.php?topic=4.msg5289#msg5289

It turned out that several of Ben's standards had trace amounts of elements that weren't declared in the standard composition database, so of course they showed up as high intensity outliers in the MAN plots.  The same thing can occur when the on-peak position is interfered with as seen here:

https://probesoftware.com/smf/index.php?topic=4.msg5136#msg5136

So basically the idea was to utilize standards that might have undeclared contaminations and/or on-peak interferences that need to be avoided, and by using this "interpolated" off-peak MAN feature we could do just that.  And for these situations it works great.

The other issue that Ben ran into was trying to create an MAN background curve for O Ka.  And as we all know, it's hard to find standards that don't contain oxygen and/or don't have a native oxide layer.  Ge and Au pure metals are the only things I've found that work OK for MAN on O Ka.

So while I understand that you'd like to utilize all your silicate standards for the calibration of the Si Ka background, that's not what it was designed for. I guess I would ask, don't you have a TiO2 standard? Or an MgO standard?  Or an Al2O3 standard? Those would make ideal curves for Si Ka, and other elements as well.

So yes, we will think about this "feature not a bug", and see if we can come up with a way to allow standards with the element of interest to be utilized as an MAN standard, but in the meantime you probably should work on your standards. You won't regret it!  Using the MAN curves for quantitative x-ray mapping is so cool!  No need to acquire off-peak background maps!

By the way, the MAN feature does allow some small concentration of the element of interest to be utilized in the MAN fits. Right now it is defined in the code as seen here:

MANMaximumValue! = 0.01     ' maximum value (wt%) for use as MAN background standard
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: orlandin on November 22, 2019, 02:53:10 PM
Hi John!

Thank you so much for this response! I do think I understand a bit better now why PFE was side-stepping me on this. I am not a coder, but from a user perspective it seems like maybe a stern pop-up warning when un-checking the 'use interpolated off peak' might be enough to get the risk across? If that were ignored or didn't exist, as you say as soon as one looked at their 'Assign MAN Fits' hopefully it would be pretty obvious that something was deeply awry. And even if you ignored that, your results should really make introspection unavoidable?

Yes, I do agree with you that my standard collection will only benefit from more love and attention - right now the only non silicates with reliable documentation that I have is a rutile and some phosphates which find their way into all of my attempts to make MAN backgrounds routine for points and mapping. I have recently inherited this lab, and there is a lot to learn about the decades-old collection here!

That being said, maybe both could be reasonable goals: a better MAN-appropriate collection on my end, and possibly including this as a beneficial PFE feature? The attitude here before I got to this lab seemed to be that MAN was voodoo requiring an expensive special set of otherwise useless standards. Adding a feature like this might make MAN backgrounds more accessible to analysts globally, in addition to all of the other utility that you've pointed out. Looking one post above my question, perhaps this approach could even have a more fundamental benefit when you're willing to take the extra time to use it on a good MAN standard set:

In thinking about this a bit more, it occurs to me that not only is this interpolated off-peak MAN measurement method likely to be as accurate as normal off-peak measurements, and maybe even a little better, since it's based on a regression of multiple standards (and because off-peak interferences are less likely in the simple metal and oxide standards that are usually utilized for the MAN calibration fit), but the typical time savings and better sensitivity of the MAN method will still apply. That is because we are only utilizing off-peak measurements for our MAN standards, not for the unknown samples using MAN (on-peak only) measurements.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 22, 2019, 05:04:10 PM
The attitude here before I got to this lab seemed to be that MAN was voodoo requiring an expensive special set of otherwise useless standards.

I think you meant to say *peer reviewed* voodoo!    ;)

https://pubs.geoscienceworld.org/msa/ammin/article-abstract/101/8/1839/264218

Seriously, yeah, I hear you.  And I must say based on our discussions so far here on the forum (and by email), I'd say you are doing way, way better than anyone without formal training from Probe Software has a right to expect!    :)

The MAN method is a little unintuitive, but worth it for better precision and saving time. And it is neat that it is a physics based (Kramer's Law) approach that works much better than it has any right to (with a continuum absorption correction). And is great for when running lots of points or quant mapping. And I do appreciate your efforts to make it work with your existing standards.

I'm still thinking about how I can balance all the various considerations (but have an idea) so give me some time to consider things. That said, improving the existing standard collection is the very first thing I did when I started at Berkeley on the microprobe back in 1988.  It will pay off for you and your lab, no question.

Here are some links for inexpensive standard materials:

https://probesoftware.com/smf/index.php?topic=308.0

ESPI is awesome, they have lots of pure single crystal oxides and other compounds.  Perfect for use as both primary and MAN standards.

One more point: if you're utilizing MAN background calibrations for point analyses then yes, you'll want to take some care making these calibrations, especially for higher Z materials. Typically one can expect accuracy levels around 200 PPM for common (low to moderate Z) oxides and silicates. But for quantification of x-ray maps, your precisions are usually much worse than for point analyses, and so the background correction accuracies are nowhere near as critical as for point analyses.  It's simply a question of "wise" statistics, e.g., not spending a lot of time measuring your off-peak backgrounds when measuring major element point analyses.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: orlandin on November 23, 2019, 09:51:23 AM
Hi John! Thank you for the kind words - you can give Julien Allaz all of the credit for making sure that this clueless former dog biscuit baker got the best mentoring and education he could provide. And there is really is no understating how valuable this forum is for learning how to do new things, and do old things better!

It may be a while before I can explain how MAN works to users without resorting to 'and then the computer models the background', but I love what I do understand about it. For now, I will take your advice and commit to really sorting out and documenting this collection. Thank you again!
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 23, 2019, 10:09:35 AM
You are welcome. I congratulate you because running a lab is quite a different animal than just running some software!

As for teaching, I know it's a bit dense on statistics, but reading the Amer. Min. MAN paper linked above will really help you understand the gritty details. For the time being just say to the students: Kramer's Law!

Also I don't know if you know this but for teaching EPMA, John Fournelle (at Wisconsin)and Probeman (at Oregon) have useful PowerPoint files from their EPMA courses available for download:

http://www.geology.wisc.edu/~johnf/g777/

https://epmalab.uoregon.edu/lecture.htm

By the way, I think we've almost got this new MAN option working. Give us another 6 or 8 more hours and we should have something for you to update and try.  But unfortunately I think I'm gonna have to prevent this feature being utilized on older versions of the databases. Because since these flags aren't saved in older databases, it can really mess up the MAN assignments when that MDB database is re-opened. Maybe, maybe not. Still working on it.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 23, 2019, 04:15:18 PM
I am not a coder, but from a user perspective it seems like maybe a stern pop-up warning when un-checking the 'use interpolated off peak' might be enough to get the risk across? If that were ignored or didn't exist, as you say as soon as one looked at their 'Assign MAN Fits' hopefully it would be pretty obvious that something was deeply awry. And even if you ignored that, your results should really make introspection unavoidable?

Hi Phil,

OK, I think have something that will work.  What we did was add a new checkbox to the Analysis Options dialog as seen here along with the original Use Interpolated Off-Peaks For MAN Fit checkbox:

(https://probesoftware.com/smf/gallery/1_23_11_19_1_42_36.png)

This new checkbox is called Use Interpolated Off-Peak Intensities Intensities for MAN Even If Element Is Present.  That's a mouthful but I think it does what it says.  What this new flag does is basically just ignore the MAN minimum intensity level for MAN standard assignments that is set at 100 PPM. Now the cool thing is that this new MAN fit option actually reveals several interesting problems with using off-peak intensities for determining backgrounds (off-peak or MAN!).  Three separate issues actually I think.  These issues have been described in detail by many of our colleagues, Mike Jercinovic and others, Julien Allaz, Karsten Goemann among them I'm pretty sure.  You've probably seen them yourself as well.

So backing up a bit, when I first tried checking this new flag on some off-peak measured standards, then checked the Use Off-Peak Elements For MAN Fits menu, selected Clear All MAN Assignments, and opened the Assign MAN Fits dialog, I didn't know what I expected to see, but here is the first MAN fit that displayed which is the Ca Ka MAN fit:

(https://probesoftware.com/smf/gallery/1_23_11_19_1_40_41.png)

Well heck, it's not a great fit but considering that all the circled standards contain at least some Ca, it did a pretty good job. I learn something new every day, thanks to sharp, young guys like you!

Now one could argue that some of those high outliers are a little too much outside of statistics (I should have turned on the error bars option when I captured this image!), but let's not worry about it and go to another emission line, this time K Ka and this time there's definitely a high intensity outlier for the orthoclase standard, which of course contains 15 wt% K:

(https://probesoftware.com/smf/gallery/1_23_11_19_1_40_59.png)

Now what could be causing this?  Well there are at least two things I can think of that would cause a high outlier for off-peak measurements. First, the absorption edge effect. That is, if one of the off-peak backgrounds is on the other side of an absorption edge it might cause an under estimate or an over estimate of the continuum intensity under the peak, depending on which side of the absorption edge, the emission line of interest is on.  The other reason for a high outlier is that the background is curved and we had utilized a linear fit between the off-peaks. Of course then there is the situation that if our off-peak measurement positions are on the tails of the peak (and a major peak from the element is present), we will again also be over estimating the intensity of the continuum intensity under the emission line of interest. Oh yeah, also if there is an off-peak interference, we will over estimate the on-peak continuum using off-peak measurements whether they are applied in the off-peak correction normally, or in the MAN fit as we are doing here.

All good reasons to avoid off-peak backgrounds!    ;D

Now the good news is that if we are using these MAN fits to background correct a major (and even minor) element intensity, an error of a few hundred PPM accuracy error will often be less than our on-peak intensity precision. Also for quant x-ray mapping, where we usually won't have enough precision per pixel for these sorts of background inaccuracies to matter much.

And by the way, these off-peak measurement precision errors? Well they become *accuracy* errors when using the MAN method!  Why? Because we normally repeat our off-peak measurement for each data point, but the MAN background gets calibrated only once or twice in a run!  So given the same average Z, the same background intensity will be estimated! And remember, the average Z precision is controlled by the *major* elements, not the continuum statistics! That's part of the reason the MAN method has higher precision than off-peak measurements. Read the 2016 Amer. Min. paper for details on this subtle issue.

And just to demonstrate that even in the case of a large concentration of the element of interest being present, there's sometimes no significant observable off-peak accuracy effects:

(https://probesoftware.com/smf/gallery/1_23_11_19_1_41_58.png)

This standard 260 is pure synthetic Al2O3 measured at the Al Ka peak position. And while probeman did select the off-peak background positions carefully, it is still pretty good considering the intensity of the Al ka peak.  At least the background in this vicinity is not curved as it is in SiO2!

So please update your PFE and try it out. One helpful hint, you can "use" your MAN intensities from older probe runs by creating a new MDB file, then making a new sample, clicking the Load File Setup button and saying "Yes" to load standard intensities. It won't import your unknowns, but it will allow to to try out this new feature on some existing standard data.

Anyway, I think this new feature should get your MAN fits going, at least until you get some more pure oxide and other synthetic standards.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: orlandin on November 23, 2019, 05:13:42 PM
John, this is amazing, thank you! I can't wait to give this a try tomorrow morning. What a cool way to check if your off-peak placements are appropriate, whether you intend to further use them for unknowns or not. Thank you so much for taking the time to work on this when really, neither one of us should have been worrying about this on a Saturday. Even if I do get a good MAN set going here soon, I think I will derive great satisfaction in getting my more complicated standards to fall along the MAN curve with the rest due to careful placement of off-peaks.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on November 24, 2019, 10:38:52 AM
Ok, so I didn't want to leave everyone thinking that the use of these (interpolated) off-peak measurements for use in the MAN fits is not entirely worthwhile.

It's just that using off-peak intensities for the background correction (whether they are utilized in normal off-peak background corrections or in MAN background corrections), is fraught with a number of issues because, they *are* interpolations. With off-peak background methods, we are *not* measuring the background intensity *at* the actual emission line position, we are interpolating to it.

For one thing these off-peak (interpolated) MAN fits are worthwhile if one doesn't have a nice set of pure simple synthetic oxides. Which is the situation that Phil Orlandini in Austin is in (Phil: please show us some of your interpolated off-peak MAN fits when you get some!). Probeman in Oregon is lucky because he managed to obtain a number of pure synthetic oxides, specifically MgO, Al2O3, SiO2, TiO2, MnO and NiO early in his career and has added these simple oxides to all his standard mounts.

Of course one can also utilize pure metals, but for background correction of common oxides and silicates their average Z values will be roughly between 10 and 18 (SiO2 and Fe2SiO4). So while one can utilize Si metal, and maybe Ti, etc on up for one's MAN calibrations, the Z of Si starts at 14, so not ideal for the lower average Z silicates such as forsterite (Mg2SiO4).

That said, there is one other really nice use for these off-peak (interpolated) MAN fits and that is when one has undeclared concentrations of elements in ones (usually natural) standard materials (as was the case for Ben Hanson at Corning). Let's examine the case here which is a normal (on-peak) MAN fit for Ni Ka showing that the natural chromite standard has an undeclared trace concentration of around 600 to 700 PPM of Ni:

(https://probesoftware.com/smf/gallery/1_24_11_19_10_18_54.png)

Now, of course we can simply remove that standard from the fit as is usually done as seen here:

(https://probesoftware.com/smf/gallery/1_24_11_19_10_18_32.png)

But of course now we can also utilize the (interpolated) off-peak MAN fit as seen here:

(https://probesoftware.com/smf/gallery/1_24_11_19_10_18_12.png)

Note that the above plot also documents the use of the (interpolated) off-peak MAN fit.  The idea with all this stuff being that we can acquire our standards using off-peak measurements, use these off-peak standards to fit our MAN curves as described here:

https://probesoftware.com/smf/index.php?topic=987.msg8889#msg8889

and in other posts in this topic, and then utilize MAN acquisitions on our unknown samples to save time and improve precision for point analyses and quantitative x-ray maps. And depending on the samples, maybe even improve the accuracy of our unknowns by avoiding possible off-peak interferences.   8)
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: orlandin on November 25, 2019, 03:07:34 PM
So, I finally figured out how to get administrator access on my own lab computers and have done some quick experimentation with this new feature. I absolutely love it, and this will really enhance the quality of analyses coming out of this lab. I've attached the results of applying this to an apatite analysis setup that I inherited from another operator in 2014 using File Setup importing. The client said that this worked, they wanted exactly what this guy did that time, and I didn't have time to reinvent the wheel then - but I would love to now!

There aren't any particular notes, but it seems like they really wanted to use MAN from the standard setup but ended up defaulting to off-peak for everything. I used the exact same MAN-spirit setup when I ran these analyses, so this seemed like just the place to start out. These were collected at 10 nA, 10 micron beam, 10-pt TDI. Error bars are 3-sigma. As you can see, maybe I should have started with a simpler project if I wanted to be able to explain everything like John did! I look forward to thinking hard about all of this (maybe using the EPMA Method Development Tool to start off with), but for the time being I will just leave the 'Assign MAN' results here to illustrate maybe an endmember of applying this method:

(https://probesoftware.com/smf/gallery/1892_25_11_19_7_40_02.gif)

(edited to use the cool inline image feature, but be warned that it is 2500x1548 pixels!)
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on August 24, 2020, 10:31:30 AM
As many of you know, the mean atomic number (MAN) background correction method is based on Kramer's Law which states that (all other things being equal), the continuum intensity is a function of the average atomic number of the material.

https://epmalab.uoregon.edu/publ/Improved%20MAN%20(Jour.%20Micros.%20Microa.,%201996).pdf

https://epmalab.uoregon.edu/publ/A%20new%20EPMA%20method%20for%20fast%20trace%20element%20analysis%20in%20simple%20matrices.pdf

Generally this MAN calibration curve is obtained by measuring continuum intensities in standards (of known composition and hence of known average atomic number), at the element emission line position, that *do not* contain the element of interest. For geological work on silicates and oxides this ideally means a selection of pure synthetic oxides, e.g., MgO, SiO2, Al2O3, TiO2, MnO, NiO and/or other pure synthetic oxides or silicates (though it should be mentioned that the MAN method can be applied to any material assuming one has standards with a similar range of average atomic numbers).

Unfortunately some EPMA standard collections consist mainly of natural materials which often contain traces of many elements, thus "interfering" with obtaining a "clean" continuum measurement at the element of interest peak position. To avoid these "contamination" issues when calibrating one's MAN curves, Ben Hanson proposed a modification of the MAN method that would utilize off-peak measurements on standards, which could then use these interpolated continuum intensities for the MAN calibration curve, which would then be applied to unknown samples.  The advantages being faster data acquisitions on unknown samples with improved precision.

Subsequently Phil Orlandini proposed utilizing even standards which contain the element of interest to allow even more standards to be utilized in the MAN calibration curve. See M&M abstract attached below which Phil presented at the virtual M&M earlier this month.

More recently Anette von der Handt inquired as to whether we could also utilize not only traditional off-peak measurements on standards for these MAN calibration curves, but also use the multi-point background (MPB) background method:

https://search.proquest.com/openview/208992e799d48f657d3508a6ef11ca1c

I hadn't considered this option before, but I thought, well why not?  After we examined the code, it appeared to us that this might already be taken into account since an MPB measurement is really just multiple off-peak measurements! So I ran a quick and dirty simulation in Probe for EPMA, acquiring an element using the MPB method on a number of standards, as seen here for Cr Ka in chromium metal:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_21_57.png)

I then checked the menu shown here to enable the program to search for MAN standards even if they were acquired using off-peak (or MPB) methods:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_22_12.png)

Then after opening up the Assign MAN Fits menu dialog we see the following results for Cr Ka:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_22_28.png)

Oh, right, the chromium peak is slightly interfered by the V Kb line in the vanadium metal standard, even in simulation mode! But after deselecting the vanadium standard we update the fit and now obtain a much better MAN calibration curve for Cr Ka:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_22_44.png)

So we now go to the Analyze window and analyze one of our standards (just for fun!) and obtain the following results:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_22_59.png)

Note that Cr is acquired (and still quantified) using the MPB method, while Mo is acquired (and quantified) using the traditional off-peak (linear fit) method. Next we go back to the Analysis Options menu and check the menu for analyzing off-peak elements as though they were acquired using the MAN method as seen here:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_23_15.png)

Now there was one tiny change we did have to make to the code which was a labeling issue when this Use MAN Correction for Off-peak Elements menu is utilized and one opens the Display Multi-Point Backgrounds dialog from the Run menu as seen here:

(https://probesoftware.com/smf/gallery/1_24_08_20_9_23_27.png)

Because previously, it would indicate that the element was acquired as a "shared" MPB. Which is (yet!) another option for using multiple off-peak elements on the same spectrometer and Bragg crystal to create a pseudo MPB sample as described here:

https://probesoftware.com/smf/index.php?topic=9.msg9043#msg9043

Anywho, now we go again to the Analyze window and analyze our standard again, and now the results are based on the MAN calibration curves which utilized interpolated off-peak measurements (MPB for Cr and traditional off-peak for Mo):

(https://probesoftware.com/smf/gallery/1_24_08_20_9_23_41.png)

OK, now data 2 points isn't enough to draw any conclusions with, but it is interesting that the variances for both Cr and Mo are smaller when utilizing the MAN method (as one would expect)!

Does this sound complicated?  Actually it's quite easy once you acquire data on a few standards and take a few moment to go through the menus, but do feel free to ask questions and we'd be happy to help.    :)

The neat thing about these interpolated off-peak options is that one can analyze the same data using both off-peak and MAN background methods and compare the results. Try it out and let us know what you find.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on June 21, 2022, 08:19:39 PM
Greetings, could you precise what model the system use when linked 2 or more off-peak points for develop interpolated on-peak intensity for MAN background curve.
Is this only linear model or we can choose different (exponential, polynomial) models as well?
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on June 21, 2022, 10:15:03 PM
The off-peak background fit utilized for the interpolated MAN option depends on the background acquisition mode, and also the background fitting model that was selected by the user for each MAN standard sample.

This could mean that if the MAN standard samples were acquired using normal two point off-peaks, any of the off-peak models could be selected subsequent to acquisition. For example, linear, exponential, slope, polynomial, etc.

If the background acquisition mode was multi-point background (MPB), then again, the MPB fit model can be selected subsequent to acquisition as either linear, exponential or polynomial.

The MAN calibration curve fit itself can be linear or 2nd order polynomial. Attention should be given to the "Z fraction" Zbar averaging method when analyzing moderate to high Z materials.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on June 21, 2022, 11:09:18 PM
Thank you John,
1. Could you give some recommendations about "Attention should be given to the "Z fraction" Zbar averaging method when analyzing moderate to high Z materials". What is the average range of high Z materials.
2. How I can increase my knowledge about reasons to think about Z when I try to use MAN-method of background correction? 
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on June 22, 2022, 09:07:48 AM
1. Could you give some recommendations about "Attention should be given to the "Z fraction" Zbar averaging method when analyzing moderate to high Z materials". What is the average range of high Z materials.

Well most silicates and oxides are in the range of Zbar of 10 to 20.  Materials with average Z values higher than that would be moderate Zbar and high Zbar materials would even higher than that (higher than 30 or 40?). Check the Standard application which can list your standard materials by average Z from the Standard | List All Standard Names and Average Z menu.

2. How I can increase my knowledge about reasons to think about Z when I try to use MAN-method of background correction?

Here is a general discussion of the various background acquisition/correction methods in PFE:

https://probesoftware.com/smf/index.php?topic=1378.0

I should also note that ideally one should utilize pure synthetic materials for use as MAN standards. This in fact is one of the reasons we should work with Will Nachlas on obtaining, characterizing and distributing (globally) high purity synthetic oxides and silicates as discussed here:

https://probesoftware.com/smf/index.php?topic=1415.0

In fact there are 5 reasons for these high purity synthetic materials:
Here are some other topics to read:

https://probesoftware.com/smf/index.php?topic=1438.0

https://probesoftware.com/smf/index.php?topic=4.msg9953#msg9953
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on June 22, 2022, 04:35:31 PM
1. could you explain, "Attention should be given to the "Z fraction" Zbar averaging method when analyzing moderate to high Z materials" means we have to be very careful when try to use MAN backgrounds for high Zbar materials? We shouldn't use some extra tricks - only think and remember about possible physical mistakes.
2. Thank you.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on June 22, 2022, 06:02:43 PM
I simply mean that at higher Zbars (average atomic number materials), the continuum production is higher (Kramer's Law), and therefore the P/B ratios are lower. That means the background correction is more critical for higher Z materials. 

https://probesoftware.com/smf/index.php?topic=571.0

For common silicate and oxide materials the accuracy of the MAN method is around 200 to 300 PPM. For higher Z materials the accuracy will be lower (larger variance), but can be improved in all cases by utilizing the blank correction with high purity blank standards run as unknowns in Probe for EPMA:

https://probesoftware.com/smf/index.php?topic=307.0

Therefore one should make additional effort to be sure that ones MAN standards properly cover the Zbar range of the standard and unknown materials being investigated.

I also suggest the use of the Z fraction averaging (using Z^0.7 or Z^0.666) method in the MAN curve fits, as the mass bias from using mass fraction Zbar averaging in compounds with elements of different A/Z ratios, will become more visible at higher atomic number.

https://probesoftware.com/smf/index.php?topic=4.msg10036#msg10036

I suggest you read this paper carefully:

https://epmalab.uoregon.edu/publ/A%20new%20EPMA%20method%20for%20fast%20trace%20element%20analysis%20in%20simple%20matrices.pdf
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: JonF on August 02, 2022, 09:01:09 AM
Is it possible to use an interpolated multipoint background to create a MAN curve?

I'm getting an error when trying this. I've collected multipoint off peak backgrounds for carbon on a number of standards.

I enable "Use Off Peak Elements for MAN Fits" and can create a MAN curve that, carbon being carbon, doesn't look great.

I'd like to try using the interpolated background calculated using the multipoint off peaks, so I enable the "Use Interpolated Off Peaks for MAN Fit" in the Analysis Calculations Options window and go back to the "Assign Man Fits" window, but when selecting carbon I get "WARNING - No MAN count data (all marked as missing) was found to calculate the MAN background fit on C ka on spectrometer 3 on crystal LDE2H at 7 keV."   

I can disable the "Use Interpolated Off Peaks for MAN Fit" in the Analysis Calculations Options window and can again see the poor MAN curve.

The "Clear All MAN Assignments (use default)" doesn't make any difference.

Am I doing something daft?

Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on August 02, 2022, 05:35:50 PM
Wow, I don't think we've even thought about using multi-point backgrounds for the interpolated MAN, much less tested it!   :o    Always pushing the envelope, hey Jon?   :)   But it should work I would have thought...

[insert rant on impure natural standards]

https://probesoftware.com/smf/index.php?topic=1415.msg10620#msg10620

I'm at M&M at the moment so we are pretty swamped, but please send me a sample MDB file to my probe software email and we'll look at it later this week.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: JonF on August 03, 2022, 10:11:18 AM
Wow, I don't think we've even thought about using multi-point backgrounds for the interpolated MAN, much less tested it!   :o    Always pushing the envelope, hey Jon?   :)   

I'm finding new and interesting ways to confuse my users.

"What, you don't actually measure the background, and you don't actually measure the background at the energy you don't actually measure it at?"

"err, yeah"

 :o


Impure standards are one thing, but light elements like carbon are a pain because of the deposition and the million different interferences you have to try and avoid. Interpolated MPB-MAN with APF (if necessary) will hopefully be a nice way to dodge the interferences and the carbon deposition and hopefully give good quant maps for light elements using the LDE/PC crystals.   

Hope M&M is going well.


PS I've emailed you an MDB file, hopefully it'll make it through the email filters.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on August 04, 2022, 11:01:38 AM
Wow, I don't think we've even thought about using multi-point backgrounds for the interpolated MAN, much less tested it!   :o    Always pushing the envelope, hey Jon?   :)   

I'm finding new and interesting ways to confuse my users.

"What, you don't actually measure the background, and you don't actually measure the background at the energy you don't actually measure it at?"

"err, yeah"

 :o


It does get rather esoteric, doesn't it...  but hey, it works.

Impure standards are one thing, but light elements like carbon are a pain because of the deposition and the million different interferences you have to try and avoid. Interpolated MPB-MAN with APF (if necessary) will hopefully be a nice way to dodge the interferences and the carbon deposition and hopefully give good quant maps for light elements using the LDE/PC crystals.   

Hope M&M is going well.


PS I've emailed you an MDB file, hopefully it'll make it through the email filters.

That a good point. Because the standard intensities (in Probe for EPMA), are corrected not only for dead time and background, but also for interferences and APF shape/shift effects, this could be quite useful for light elements.  Note that these intensities are also corrected for standard intensity drift (again, in Probe for EPMA).

I got your MDB file and will look at this as soon as I work through the small mountain of notes I have from the meeting.  The meeting went quite well and Tuesday had some great talks on EPMA (if you didn't count mine!).  I ended my presentation talking about the "constant" k-ratio method from John Fournelle and the new dead time correction from Aurelien Moy for WDS as described here:

https://probesoftware.com/smf/index.php?topic=1466.msg11025#msg11025

Actually the conference was great. Really nice to see most of everyone after 3 years.

OK, here's my joke from the conference:  the difference between EDS and WDS is OCD.

 ;D
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on August 05, 2022, 02:27:24 PM
OK, I found that our code was deliberately skipping utilizing multi-point backgrounds (MPBs) for the interpolated MAN method.  Because, you know who would have thought someone would want this?    :o

Anyway that is fixed now and it seems to work. So just update PFE as usual and you should be good to go.  Oh, and thank-you for sending a small test run demonstrating the issue. Usually we get a massive probe run with 400 samples and 27 elements!

By the way, I assume you've looked over this topic on using MAN for trace carbon:

https://probesoftware.com/smf/index.php?topic=48.0

I found it unnecessary to resort to the (interpolated) off-peak MAN method for trace carbon.  So I suspect that your standards are much more contaminated with carbon that you might have thought.  At least that's what I'm seeing with your test run...

In fact, I found that what was really necessary for trace carbon using the normal MAN was the TDI correction and of course the usual spectral interference corrections.

That said, our instrument has a 100K degrees cryo trap that really pumps the hydrocarbons, so this may not be possible on all instruments.

Finally, I'm assuming that both your standards *and* unknowns are uncoated with carbon and carefully cleaned?  Carbon is a non-trivial exercise on most EPMA instruments for sure.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: JonF on August 06, 2022, 03:37:58 AM
Brilliant, cheers John. That fix seems to work beautifully. Below is a before/after for the C Ka energy using the on peak C Ka and the MPB interpolated off peak from a larger range of standards.

Before (on peak C Ka)
(https://probesoftware.com/smf/gallery/796_06_08_22_3_16_45.jpeg)


After (MPB interpolated)
(https://probesoftware.com/smf/gallery/796_06_08_22_3_17_06.jpeg)

This is going to help a lot with light element mapping! It'll certainly help with oxygen, as that's even more a pain to get around. 

The samples are definitely in need of a clean, but I suspect in this case the majority of the contamination is coming from the samples next to the standards. I was provided with a number of 30mm bakelite blocks (!) that took a couple of turns through the JEOL airlock before the software would open the gate valve to the chamber. TDI and interference correction are definitely needed. I guess as long as the contamination rate is linear, the TDI can take care of it with a good degree of certainty.

Preventing contamination is something that I've spent more time than I care to admit looking in to. I've replaced our liquid nitrogen dewar with an in vacuo peltier cold finger, but I'm very interested in the PCC cooler. Do you notice any vibration from the device? It is referred to as "low vibration" in the product documents, but relative to what?
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on August 06, 2022, 09:35:36 AM
After (MPB interpolated)
(https://probesoftware.com/smf/gallery/796_06_08_22_3_17_06.jpeg)

That is cool, but the Be and Al intensities bother me.  Continuum intensity should be proportional to average atomic number.  That is, the intensities should be lowest at the lowest atomic numbers.

If this is real then there could be some interesting physics going on (absorption correction?), but it's probably just some sort of artifact.  Please share some plots with us showing intensities with and without the absorption correction.  Or with different absorption corrections.

Preventing contamination is something that I've spent more time than I care to admit looking in to. I've replaced our liquid nitrogen dewar with an in vacuo peltier cold finger, but I'm very interested in the PCC cooler. Do you notice any vibration from the device? It is referred to as "low vibration" in the product documents, but relative to what?

Here's the Polycold system on our Sx100:

https://probesoftware.com/smf/index.php?topic=646.msg3823#msg3823

It just runs and runs (air cooled) and always stays around 100 Kelvin. It cools a baffle over the diffusion pump. It was originally ordered because we couldn't afford Cameca Turbo system and a diffusion pump plus this cryo baffle was about half the price. 

But now that I see how great it works, I would order another on my next instrument.  In fact I would order a turbo pump with this baffle for sure.  Here's a comparison between the "dry" pumped system at NETL and our cryo pumped system:

https://probesoftware.com/smf/index.php?topic=646.msg10157#msg10157

The black line of carbon contamination is our JEOL "dry" system and the invisible carbon line is our Polycold system. No comparison which is better.

As for vibration, it's true it did add a small amount of vibration originally, but then we added a number of wraps of foam lined lead sheet around the head and the vibrations were completely damped. 

I'm sure there are designs that could eliminate vibrations completely.  And one can always turn the head off temporarily for high mag imaging I guess.
Title: Re: Questions about MAN background use
Post by: Rom on September 04, 2022, 08:12:29 PM
Thank you for answering my previous question.
Now could you explain why "correct for continuum absorption" check box gives worse result for my MAN background. What direction should I look when I want to use this option?
Thank you!
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on September 04, 2022, 09:04:55 PM
Thank you for answering my previous question.
Now could you explain why "correct for continuum absorption" check box gives worse result for my MAN background. What direction should I look when I want to use this option?
Thank you!

I assume this is using the interpolated off-peak MAN method?  You should always use the continuum absorption correction with the MAN background method.  It is especially important for low energy emission lines.  The only reason it can be turned off is to demonstrate the absorption effect magnitude in the Assign MAN Fits dialog. That is, the MAN intensities are always absorption corrected during an actual quantitative analysis.

Hard to say what your specific problem is. Did you show your data to your lab manager?  It can be difficult to utilize the MAN correction for oxygen since many factors can influence the results even when using the interpolated off-peak MAN method, e.g, the background fit (interpolation across absorption edges), off-peak interferences, etc.

You may want to use a normal off-peak method for oxygen, and MAN for the other elements.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on September 04, 2022, 09:57:12 PM
I assume this is using the interpolated off-peak MAN method?  You should always use the continuum absorption correction with the MAN background method.  It is especially important for low energy emission lines.  The only reason it can be turned off is to demonstrate the absorption effect magnitude in the Assign MAN Fits dialog. That is, the MAN intensities are always absorption corrected during an actual quantitative analysis.

Ok, thank you.

Hard to say what your specific problem is. Did you show your data to your lab manager?  It can be difficult to utilize the MAN correction for oxygen since many factors can influence the results even when using the interpolated off-peak MAN method, e.g, the background fit (interpolation across absorption edges), off-peak interferences, etc.

the background fit (interpolation across absorption edges) - how I can check the issue?
off-peak interferences - checked, there are not
what else?

Edited by John to utilize "quote" feature
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on September 05, 2022, 08:05:31 AM
the background fit (interpolation across absorption edges) - how I can check the issue?
off-peak interferences - checked, there are not
what else?

Please utilize the "quote" feature to make your context clear as I have here and as shown in your previous post.

With the normal (on-peak) MAN method both of these issues disappear, but one requires standards that are high purity. So your best bet is to obtain better (high purity) standards, but for oxygen that is difficult because most materials have at least trace levels of oxygen, which is why I suggest you do not attempt the MAN method for oxygen. At the very least, avoid standards for oxygen background by MAN that contain major oxygen!    >:(

If you must use MAN for oxygen I would start with high sensitivity wavescans to check the background regions and try to avoid absorption edges but it is almost impossible to see these spectral details since the peak region is obscured by the major oxygen peak. Again, I would utilize materials that do not contain oxygen! Then the absorption edges will be more visible in your wavescans.

Think about your strategy when using the MAN method: ideally you want to select standards that do not contain the element of interest, and that also cover the range of average atomic number that your standards and unknowns.

Yes, with the interpolated off-peak MAN method, one can utilize standards that contain (major amounts of) the element of interest.  But that doesn't mean that you should!    :)

I suggest using a number of materials that do not contain oxygen (e.g., pure metals or sulfides, etc.), and because they will probably still contain some small amounts of oxygen (from oxidation), use the interpolated (off-peak) MAN method as you are doing.

Just get rid of the standards that contain major oxygen (for the oxygen MAN background calibration) and see if that works better!
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on September 05, 2022, 04:30:03 PM
Thank you, I'll try.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on September 25, 2022, 08:56:27 PM
Hi John,
could you explain a huge difference of Continuum Absorption correction on Cr (close to 2), Sb (close to 2) and InAs (close to 10!).
it means that for InAs the measured data is not so important as correction based only on math.
All measurements (Ka for oxygen) done after WS and based on BG approximation.
Thank you very much. 
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on September 26, 2022, 10:32:50 AM
could you explain a huge difference of Continuum Absorption correction on Cr (close to 2), Sb (close to 2) and InAs (close to 10!).

You do understand x-ray absorption, don't you?   ;D

Is this in reference to measuring O ka as an emitter?  Please take a look at the mass absorption coefficients for oxygen absorbed by other elements.  CalcZAF has a very nice output for this:

(https://probesoftware.com/smf/gallery/1_26_09_22_9_50_35.png)

Notice how the MACs increase until just after In and Sn as absorbers.  Then it drops off. That is called an absorption edge. If you would like to learn more I suggest Goldstein et al., 1992.

it means that for InAs the measured data is not so important as correction based only on math.

Was that a question?  And why do you say "only based on math"?  At least say "only based on physics"!    :)

I assume you meant to say that because there is a large absorption correction (due to a nearby absorption edge for O ka by In), the results are highly dependent on the absorption correction model *and* the MAC values selected for O ka.

One way to evaluate the matrix corrections is to utilize the Use All Matrix Corrections checkbox in the Analyze! window in Probe for EPMA.

One can select the various MAC tables from the Analytical | ZAF, Phi-Rho-Z, Alpha Factor, Calibration Curve Selections menu as seen here:

(https://probesoftware.com/smf/gallery/1_26_09_22_10_27_56.png)

One can also try various MAC tabulations from the literature as described here:

https://probesoftware.com/smf/index.php?topic=1340.msg9631#msg9631
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on September 26, 2022, 05:07:57 PM
I assume you meant to say that because there is a large absorption correction (due to a nearby absorption edge for O ka by In), the results are highly dependent on the absorption correction model *and* the MAC values selected for O ka.

Yes, you are right.
Does it mean it will be better to use (if it is possible) the standards for MAN BG with small MACs?
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on September 26, 2022, 05:54:35 PM
I assume you meant to say that because there is a large absorption correction (due to a nearby absorption edge for O ka by In), the results are highly dependent on the absorption correction model *and* the MAC values selected for O ka.

Yes, you are right.
Does it mean it will be better to use (if it is possible) the standards for MAN BG with small MACs?

Well it depends on what the composition of your unknowns are.

Normally the only thing that matters for the MAN background correction is the average atomic number of the unknown.

But if the unknowns contain elements that yield an very large absorption correction for a particular emission line (e.g., O ka), you are probably better off using MAN standards that contain those elements, just to obtain a self consistent MAN correction for your unknowns.
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: Rom on September 26, 2022, 06:49:01 PM
Ok, thank you very much.
Can I estimate MACs for my standard sample (contains more then 1 element) from "Table of MACs for elements" of PFE soft?
Title: Re: Offset (Interpolated) MAN backgrounds
Post by: John Donovan on September 27, 2022, 09:33:21 AM
Can I estimate MACs for my standard sample (contains more then 1 element) from "Table of MACs for elements" of PFE soft?

You could, by using those mass absorption coefficients with Beer's Law:

https://en.wikipedia.org/wiki/Beer%E2%80%93Lambert_law

Because the mass absorption coefficients are already normalized to mass, you can simply sum the mass fractions of each element's MAC to obtain the average MAC (actually we should be using attenuation coefficients and molar concentrations as is done in PENEPMA!).

But you can do this easily in the CalcZAF application by simply entering the compound (by formula or weight %) with a small amount of the emitting element, and calculating the k-ratios.

Here is an example of InAs with a small amount of oxygen (100 atoms of In, 100 atoms of As and 1 atom of oxygen):

(https://probesoftware.com/smf/gallery/1_27_09_22_9_23_19.png)

After clicking the Calculate button we obtain this output:

(https://probesoftware.com/smf/gallery/1_27_09_22_9_23_36.png)

But again, in cases of extreme absorption, we should not only be using MAN standards that cover the range of average atomic number for our unknowns (and standards), but we may also want to consider elements that are representative of these extremely absorbing matrices (so long as they do not contain major concentrations of the emitting element in order to avoid extrapolating across absorption edges). 

Also remember the rule of thumb: for major elements, the standards and matrix corrections are most important. For trace elements, the background corrections and interference corrections are most important. For minor elements, it's a little of all these concerns.

Performing background corrections for oxygen using the MAN method is especially tricky because it is difficult to obtain materials that do not contain oxygen and that are not oxidized (which is why I assume you are using the interpolated MAN method). However, you might be better off using MAN on your other elements and off-peak methods for oxygen.

Can you share with us what exactly you are trying to characterize?   In other words what major/minor/trace elements are you trying to measure, and in what materials?