Probe Software Users Forum

Software => Probe for EPMA => Topic started by: Mike Spilde on July 01, 2013, 12:55:59 PM

Title: Questions about MAN background use
Post by: Mike Spilde on July 01, 2013, 12:55:59 PM
Hi PFE users,

John asked me to post my questions to the new users forum. I want to use the MAN background correction while measuring REE-bearing pegmatite minerals. I've used the off-peak backgrounds in the past on the JEOL, but for the entire suite of REEs and associated elements (32 total elements in the file), it is extremely difficult to get all the background positions correct. The MAN background method seems like it would be just the ticket. I'm not worried about trace levels, just the general level of REE (HREE vs LREE for example). So, I have some questions that I hope you could help with.

1) Has anything been published on this method? 

2) The reference manual says the method is not good for high atomic number samples. Why not? Has anyone tested it on REE analyses? My samples are in the range of Z=30-60. 

3) Paul showed me how to assign MAN fits using my calibration analyses, but as I am setting up the MAN assignments, what do I look for in terms of the fits? I have a number of standards calibrated and there is a good deal of scatter on some elements, so I take some standards out to get less scatter. What is considered a good intercept? I assume that approaching zero is good but a negative is not? How about the Rel% Deviation? I assume low is better but how low? 3 or less? 10 or less?

4) Does one always want to force a straight-line fit?

5) Are the values reassigned with each new file and calibration? If I copy a previous file but use a new calibration, are the values reassigned or are the previous values used?

Any advice would be appreciated.
Thanks, Mike
Title: Re: Questions about MAN background use
Post by: John Donovan on July 01, 2013, 06:12:07 PM
Hi Mike,
Thanks.  I think others could benefit from my answers to your excellent questions. Therefore...

Hi PFE users,

John asked me to post my questions to the new users forum. I want to use the MAN background correction while measuring REE-bearing pegmatite minerals. I've used the off-peak backgrounds in the past on the JEOL, but for the entire suite of REEs and associated elements (32 total elements in the file), it is extremely difficult to get all the background positions correct. The MAN background method seems like it would be just the ticket. I'm not worried about trace levels, just the general level of REE (HREE vs LREE for example). So, I have some questions that I hope you could help with.

1) Has anything been published on this method? 

The original paper is here:

http://probesoftware.com/Improved%20MAN%20%28Jour.%20Micros.%20Microa.,%201996%29.pdf

But you should contact Karstem Goemann who presented exactly what you want to do (MAN of REE minerals) at M&M in Nashville.

2) The reference manual says the method is not good for high atomic number samples. Why not? Has anyone tested it on REE analyses? My samples are in the range of Z=30-60. 

Yes, I didn't try to "push the envelope" and limited myself to oxides and silicates but Karsten has used this for REE bearing minerals and Dave Wark also with excellent results on high Z super alloys (also presented at the same M&M).  You might want to get their abstracts at least.

3) Paul showed me how to assign MAN fits using my calibration analyses, but as I am setting up the MAN assignments, what do I look for in terms of the fits? I have a number of standards calibrated and there is a good deal of scatter on some elements, so I take some standards out to get less scatter. What is considered a good intercept? I assume that approaching zero is good but a negative is not? How about the Rel% Deviation? I assume low is better but how low? 3 or less? 10 or less?

Rule of thumb : the lowest measured intensity (at a given average atomic number) is by definition the background. Since the intensities are corrected for continuum absorption the only thing that should be problematic are interferences and/or contamination and both of these issues will produce anomalously high intensities.  So deselect the stds that give higher intensities and click the Update Fit button.

4) Does one always want to force a straight-line fit?

I only use that option if I have three points with two very close together so it gives a weird 2nd order fit.  Or for two point fits obviously.

5) Are the values reassigned with each new file and calibration? If I copy a previous file but use a new calibration, are the values reassigned or are the previous values used?

It depends if you also loaded the standard intensities or not when loading a File Setup. If you don't load the standard (and MAN std) intensities, the assignements will be there, but no data.  The standard intensities must be reacquired.

But if you *do* load the std intensities, you can simply reacquire the most important stds, usually for the major elements.  The backgrounds usually do not change significantly for obvious reasons.
Title: Re: Questions about MAN background use
Post by: Gareth D Hatton on July 02, 2013, 12:37:27 AM
Although I have not used MAN for REE analysis I have used it for high Z on low Z with no trouble.  This was not trace but around 1% Pt and 1% Pd on Alumina.
Title: Re: Questions about MAN background use
Post by: John Donovan on July 02, 2013, 08:30:10 AM
Although I have not used MAN for REE analysis I have used it for high Z on low Z with no trouble.  This was not trace but around 1% Pt and 1% Pd on Alumina.

Hi Gareth,
Yes, this is still a low Z analysis for the unknown, but did you use the MAN also for the Pt and Pd standards? 

A feature I don't use often enough is the fact that you can specify different bgds for the std and unk. For example, you could use the MAN bgd for your Al2O3 samples since the Z range is very limited and use off-peaks for the Pt and Pd stds which would be a pain to acquire a wide range of Z MAN stds for.

Of course the bgd on a trace element std (i.e., pure element) isn't very important from a statistical consideration. So in that sense it don't matter especially, but off-peaks on the Pt and Pt metal stds would be quick and easy. I like quick and easy.   :)
john
Title: Re: Questions about MAN background use
Post by: Philipp Poeml on July 02, 2013, 08:42:24 AM
Hi John,

does this mean --- and do you think it would make sense --- if I would use the same approach? Like, using offpeak backgrounds for PuO2, UO2, whatever stadards, but then measure on the sample with plenty of REEs and actinides using the MAN backgrounds? That might be very interesting to try.

Using MAN for standards and unknown did not work out.

Cheers
Ph
Title: Re: Questions about MAN background use
Post by: John Donovan on July 02, 2013, 09:14:19 AM
Hi Philipp,
Yes, you have a special situation with actinides and all.

And I don't think this feature of using off-peak backgrounds on stds and MAN bgds for unkns would help you much because your unknowns are pretty much like your stds. That is both your stds and unks are very, very high Z!   

For Gareth's situation, his samples are almost pure Al2O3 so very low Z compared to his Pt and Pd stds.  These samples are ideal for this bgd feature.

Title: Re: Questions about MAN background use
Post by: Karsten Goemann on July 04, 2013, 06:38:04 PM
All, here is the link to the abstract of my M&M2011 presentation that John was referring to:

http://dx.doi.org/10.1017/S143192761100376X (http://dx.doi.org/10.1017/S143192761100376X)

Let me know if you can't access the abstract and I'll send you a copy.

There's not much about MAN in the abstract and it was also only part of the presentation, the larger part was on using multiple backgrounds to analyse Y, REE and others in uranium minerals like uraninite and coffinite.

The MAN data I presented there was for analysing florencite (a beam sensitive & water bearing REE-Al-phosphate) which only has a MAN of around 22. It worked very well for lower Z elements, still reasonably well for LREE, but not so well for HREE, see attached file. The graph shows an average for around 20 florencite measurements which were acquired using off-peak backgrounds, and comparing those results with the results using MAN backgrounds for the same dataset. The red curve is the "original" and the purple one the final "best" curve after including water by difference and using linear MAN fits.

This plot will show problems with both off-peak and MAN backgrounds. The Al deviation is due to limitations with off-peak positioning, potentially something similar for Ce, and La, but these are all major elements in florencite, so the effect is marginal and I did not investigate further.

The HREE are below detection limit, and the absolute values using MAN were around -0.1wt% for Dy and Er, and -0.05wt% for Yb, which is a bit of a concern. Back then I didn't have the time to sort this out for those particular samples. I tried to use conditions providing stable intensities, but the HREE were measured at the end of the program so there still might have been a issue with damage, sub-surface charging... If that's the case it's strange though didn't affect the later elements on the other spectrometers. One obvious thing to try would be to change the measurement order. The grains were too small to defocus further than 10µm.

Another issue is standards, not only secondary standards, but I also only have the Smithsonian orthophosphates for REE calibration at the moment. It is well known that their LREE standards (La to Gd) contain varying amounts of Pb (see http://dx.doi.org/10.6028/jres.107.056 (http://dx.doi.org/10.6028/jres.107.056)), so Pb needs to be individually determined and corrected in the reference composition, as far as that is possible as concentrations can vary within chips. Some of them contain minor amounts of other REE as well. John already said that both interferences and small amounts of the element in question will push the datapoint up in the MAN plots, so it is better to use the lower values, but if the reference composition of a standard is not correct it can go in any direction. I learned a lot about our standards looking at MAN plots (in terms of reference values, purity, contamination) and many of them are not as well characterised or "clean" as I'd like them to be.

I have since then used MAN to analyse monazite with good results, again majors & minors only, no traces! I'll see if I can put a few more details together and post them. Again, one problem is method validation, as I only have monazite "age" standards, none with a well constrained composition.

Cheers, Karsten

Title: Re: Questions about MAN background use
Post by: John Donovan on September 11, 2013, 12:20:19 PM
There is a simple method to compare the same intensity data using off-peak, MAN and Nth point background corrections.

First acquire a set of data for your elements of interest on some standards using normal off-peak backgrounds. Because you will also be fitting a MAN calibration curve, one also needs to acquire intensity data on standards that *do not* contain the elements of interest. For silicate elements one might select, in addition to the primary stds, standards such as MgO, SiO2, Al2O3, TiO2 and NiO, etc. Again, using full off-peak backgrounds.

Once the intensity data is acquired one can then perform quant analyses on the standards using the acquired off-peak background corrections.

Next, go to the Analytical menu and check the Use Off-Peak Elements For MAN Fit menu as seen here:

(http://probesoftware.com/smf/oldpics/i41.tinypic.com/6dvbc7.jpg)

Now fit your MAN backgrounds as usual using the Analytical | Assign MAN Fits menu, but note that the software will automatically utilize off-peak acquired element intensities for the MAN fit by ignoring the off-peak data for the standards and fit only the on-peak intensities!

Next go to the Analytical menu and check the Use MAN Correction For Off-Peak Elements menu. This tells the software to force off-peak measured elements to utilize the MAN calibration curve for the background correction as seen here:

(http://probesoftware.com/smf/oldpics/i44.tinypic.com/zn8s5l.jpg)

Now you can analyze your standards that were acquired using off-peak backgrounds, but now using the  MAN calibration curve for comparison.

Finally go to the Analytical | Analytical Options dialog and select the Use Nth Point Calculation For Off-Peak Intensities as shown here:

(http://probesoftware.com/smf/oldpics/i39.tinypic.com/voy7ww.jpg)

Now uncheck the Analytical menu | Use MAN Correction For Off-Peak Elements menu and now you can analyze your off-peak acquired standards using *only* the off-peak intensities from the first point of every sample.

This way one can acquire and compare the same data set using off-peak, MAN and Nth Point background corrections. A white paper with more details is attached below.  Remember that one needs to be logged in to see attachments!
Title: Re: Questions about MAN background use
Post by: John Donovan on December 01, 2013, 12:38:25 PM
Maybe this would be a good time to examine the method of Mean Atomic Number (MAN) background correction in more detail.

The example I am utilizing is from Paul Carpenter at Washington University (used with permission) and Paul acquired this MAN calibration data set for use in quantitative x-ray mapping with Probe Image and CalcImage as can be seen in the beautiful quant x-ray maps attached below. Note the stoichiometric *and* total quant maps which can be automatically generated and output with CalcImage.

Of course the MAN background correction is good to a few hundred PPM in silicates and oxides so it really is "overkill" for quant x-ray mapping, but it sure does save a lot of time because one doesn't need to acquire any off-peak x-ray maps!

So, what is the basis for the the MAN correction? The details are available in this publication:

http://probesoftware.com/Improved%20MAN%20%28Jour.%20Micros.%20Microa.,%201996%29.pdf

but it suffices to say that it is based on Kramer's Law, where in the absence of the element under investigation, the on-peak x-ray production of the material can be used to calibrate the continuum background. The MAN correction also contains an adjustment for absorption of the continuum of the emission line being investigated and for the matrix in question (both for the MAN calibration standards and the unknowns).  Since the standard compositions are already known, the calculation of mean atomic number (MAN) is easily performed. In the case of unknowns, the mean atomic number of the sample is calculated during the ZAF or phi-rho-z matrix iteration.

So now let us examine the first element measured in these x-ray maps, Na ka as seen here in the Analytical | Assign MAN Fits menu available in both Probe for EPMA and CalcImage:

(http://probesoftware.com/smf/oldpics/i44.tinypic.com/2eek67n.jpg)

Of course, we can immediately see one problem, and that is that the NBS CuZn alloy is very much an outlier in our Na MAN fit. Why is that? Well it's because of our old friend, the Zn La on Na interference. Now, this interference could be corrected for in PFE- but let's not get carried away! There are plenty of other MAN standards to fit for Na, and besides, we aren't measuring materials with that high an average Z anyway!

So let's unselect that standard from our MAN fit by using a <ctrl> click of the mouse and then we click the Update Fit button to re-plot the fit as seen here.

(http://probesoftware.com/smf/oldpics/i43.tinypic.com/al0upx.jpg)

Note the now much more reasonable fit to the on-peak x-ray intensities from our standards, which is loaded by default based on whether the standard contains the element under investigation. Since the standard composition database indicated no Na in the NBS CuZn alloy, the software loaded that standard intensity. But for other standards that actually contain Na, for example, Kakanui Hornblende, the x-ray intensities for that standard material are not loaded for the default MAN fit.

To demonstrate the necessity of the continuum absorption correction, we can unselect the correction for continuum absorption by unchecking the checkbox and the significantly worse fit is quite evident. Why is this? Because every standard composition absorbs continuum radiation (i.e., at the characteristic energy of our elements of interest) in somewhat different degrees, depending on the physics details- that is why we have absorption edges in our EDS continuum spectra!

(http://probesoftware.com/smf/oldpics/i43.tinypic.com/2cgkmtz.jpg)

So clearly the correction for continuum absorption is necessary, as seen also in this plot of Mg ka in standards  that do *not* contain Mg:

(http://probesoftware.com/smf/oldpics/i39.tinypic.com/91bfiq.jpg)

By including the correction for continuum absorption for Mg ka we are back in business as seen here:

(http://probesoftware.com/smf/oldpics/i42.tinypic.com/2vt41e9.jpg)

Don't worry, the program defaults all these options automatically!   8)

So, let's move on to a different situation as seen here for Mn ka:

(http://probesoftware.com/smf/oldpics/i44.tinypic.com/2w5m3h4.jpg)

Here, again, we see some outliers in our MAN fit, but these are *not* from spectral interferences from other elements, as was the case for Zn La on Na. These are standards which contain small amounts of Mn that have *not* been specified in the standard composition database. Paul puts it himself this way:

"1039 is our wollastonite standard that contains a low concentration of Mn but has not been characterized in the standard analysis yet. 1713 is Elba hematite that is also being adjusted, and the synthetic fayalite 465 also contains very low Mn. On a wavelength scan this level of Mn is not apparent."

By simply unselecting these standards which contain trace amounts of Mn, we can get a more accurate model of the background for our Mn measurements. Remember: background is by definition the lowest intensity one can measure!  Interferences and "contamination" will all cause elevated outliers to the fit.  Of course there are some subtle continuum artifacts as documented here:

http://probesoftware.com/Ti%20in%20Quartz,%20Am.%20Min.%20Donovan,%202011.pdf

but those are in the sub 100 PPM level! So not exactly significant for quant-xray mapping even when measuring off-peak images!

So after removing those standards from our fit which contain "undocumented" Mn, we obtain the following fit:

(http://probesoftware.com/smf/oldpics/i39.tinypic.com/261nntf.jpg)

For an element such as Si or Al we obtain beautiful fits using the default MAN assignments made automatically by the program as seen here:

(http://probesoftware.com/smf/oldpics/i44.tinypic.com/2k545v.jpg)

Now check out the gorgeous quant x-ray maps Paul acquired which are automatically corrected for background, matrix and spectral interferences in the attachments below!

It should also be mentioned that at zero concentration levels, using MAN background acquisition improves measurement precision by roughly the Sqr(2) and at the same time cuts the necessary acquisition time by 50%.

See the attachments posted here for details:

http://probesoftware.com/smf/index.php?topic=29.msg237#msg237

Title: Re: Questions about MAN background use
Post by: Probeman on December 18, 2013, 01:20:33 PM
There is a post on using the MAN correction in conjunction with the blank correction in Probe for EPMA on trace element characterization (for simple matrices such as SiO2, TiO2, ZrSiO4), where a suitable zero or non-zero blank material is available here:

http://probesoftware.com/smf/index.php?topic=29.msg237#msg237

The idea is is that one can obtain excellent precision with the MAN background correction because it is the average of multiple standard points, for example, 5 measurements at 30 seconds each for each standard. If one is utilizing 3 or 4 or more standards per MAN fit (element), then the precision is excellent, much better in fact than counting off-peak for the same amount of time.

To illustrate this see the graph below which compares MAN to off-peak to Nth point off-peaks (where the off-peak is utilized only on the first point and re-used for the subsequent points) using the same data set for all calculations as described above:

(http://probesoftware.com/smf/oldpics/i43.tinypic.com/2eb4e4l.jpg)

The Cr off-peak data shows more variance due to the fact that we are subtracting two measurements from each other, while the MAN correction is essentially a constant at a given average atomic number which should not change much for a say SiO2 matrix.  Of course the beauty of the MAN correction (unlike the Nth point method) is that it *can* account for changes in the matrix (and therefore background intensity) automatically without measuring the off-peaks! Here's another example:

(http://probesoftware.com/smf/oldpics/i43.tinypic.com/sz7g3b.jpg)

The full report can be found attached to this post:

http://probesoftware.com/smf/index.php?topic=4.msg189#msg189
Title: Re: Questions about MAN background use
Post by: Probeman on December 18, 2013, 03:01:58 PM
I'm running some quantitative x-ray maps with a student on some melt inclusions to see if we can detect any variation in the glass chemistry and in setting up the standards I decided to acquire all ten elements using MAN backgrounds. Here is a sample of a standard and the amazing accuracy of the MAN correction (no off-peak measurements) even for trace elements:

St  305 Set   1 Labradorite (Lake Co.)
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 30.0  Beam Size =    5
(Magnification (analytical) =  20000),        Beam Mode = Analog  Spot
(Magnification (default) =     2524, Magnification (imaging) =    736)
Image Shift (X,Y):                                        50.00,   .00

Specimen from HR Wenk, UC Berkeley, Geology
See Wenk and Kroll, Bull. Mineral. (1984), 107, 467-487
Number of Data Lines:   5             Number of 'Good' Data Lines:   5
First/Last Date-Time: 12/17/2013 04:08:12 PM to 12/17/2013 04:17:53 PM
WARNING- Using Time Dependent Intensity (TDI) Element Correction

Average Total Oxygen:         .000     Average Total Weight%:  100.109
Average Calculated Oxygen:    .000     Average Atomic Number:   11.560
Average Excess Oxygen:        .000     Average Atomic Weight:   21.022
Oxygen Equiv. from Halogen:   .010  Halogen Corrected Oxygen:    -.010
Average ZAF Iteration:        4.00     Average Quant Iterate:     4.00

St  305 Set   1 Labradorite (Lake Co.), Results in Elemental Weight Percents
 
ELEM:       Na      Si       K      Al      Mg      Fe      Ca      Mn      Ti       F       O       H
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    SPEC
BGDS:      MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
TIME:    30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00
BEAM:    29.93   29.93   29.93   29.93   29.93   29.93   29.93   29.93   29.93   29.93

ELEM:       Na      Si       K      Al      Mg      Fe      Ca      Mn      Ti       F       O       H      SUM 
    21   2.907  25.278    .101  16.170    .089    .309   9.575    .002    .009   -.014  46.823    .000    101.248
    22   2.852  23.590    .109  16.328    .088    .291   9.500   -.001    .024    .047  46.823    .000     99.650
    23   2.831  23.548    .105  16.421    .087    .359   9.596    .002    .005    .040  46.823    .000     99.817
    24   2.807  23.594    .108  16.406    .087    .359   9.588    .001    .001    .014  46.823    .000     99.789
    25   2.809  23.884    .097  16.474    .085    .284   9.531    .000    .022    .034  46.823    .000    100.043

AVER:    2.841  23.979    .104  16.360    .087    .320   9.558    .001    .012    .024  46.823    .000    100.109
SDEV:     .041    .738    .005    .118    .001    .036    .041    .001    .010    .025    .000    .000       .652
SERR:     .018    .330    .002    .053    .001    .016    .018    .001    .005    .011    .000    .000
%RSD:     1.44    3.08    4.95     .72    1.40   11.39     .43  181.78   83.39  101.80     .00     .00

PUBL:    2.841  23.957    .100  16.359    .084    .319   9.577    .000    n.a.    n.a.  46.823    n.a.    100.060
%VAR:    (.01)     .09    4.03   (.00)    3.72    .42   -.20     .00     ---     ---     .00     ---
DIFF:    (.00)    .022    .004   (.00)    .003    .001   -.019    .000     ---     ---    .000     ---
STDS:      305     358     374     305      12     395     358      25      22     835       0       0     

STKF:    .0155   .2093   .1132   .1275   .4736   .6779   .1693   .7341   .5547   .1715   .0000   .0000 
STCT:    45.98   65.79  225.18  261.40 2197.75  139.51  107.68 1966.75   56.01   27.06     .00     .00 

UNKF:    .0155   .1841   .0009   .1275   .0006   .0027   .0871   .0000   .0001   .0001   .0000   .0000
UNCT:    45.98   57.90    1.86  261.40    2.79     .55   55.42     .01     .01     .01     .00     .00   
UNBG:      .94     .07     .90     .85    1.67     .22     .46    5.03     .06     .06     .00     .00   

ZCOR:   1.8317  1.3023  1.1141  1.2828  1.4496  1.1948  1.0967  1.2151  1.2005  4.1769   .0000   .0000 
KRAW:   1.0000   .8799   .0083  1.0000   .0013   .0040   .5147   .0000   .0002   .0003   .0000   .0000   
PKBG:    50.09  786.71    3.06  307.94    2.67    3.49  121.95    1.00    1.18    1.16     .00     .00   
INT%:     ----    ----    ----    ----    ----     .00    ----    ----    ----     .00    ----    ---- 


I'd call the accuracy (%VAR line) of the K, Mg and Fe results "spurious accuracy" if I didn't see this all the time!  ;)
Title: Re: Questions about MAN background use
Post by: srmulcahy on December 20, 2013, 11:16:35 AM
My question pertains to overall uncertainty estimation on the MAN method.  There is the uncertainty that comes from the variance in the on peak measurement.  But there should also be a component of uncertainty in the estimation of background intensity from the Assigned MAN fits.

I've attached an example from an assigned MAN fit of Ca Ka on PET for some feldspars I'm running this week.  I've applied a 2nd order polynomial fit to the data (I'm using R for this example, but the results are the same as PFE) and the dashed lines are the 1-sigma confidence intervals of that fit.  The estimated slope is 1.044 +/- 0.334 and the intercept is 3.508 +/- 2.802 (standard errors for uncertainty).

(http://probesoftware.com/smf/oldpics/i44.tinypic.com/2l9l4i0.jpg)

When you use this to estimate the Ca Ka background intensity for Lake County Plagioclase with Zbar of 11.5885 you get 17.37 +/- 0.42 cps/30nA, which is a 2.5% 1-sigma uncertainty. Is this propagated through to the final estimate of uncertainty in PFE?  How does that compare to magnitude of the uncertainty in the background intensity from off peak measurements?
Title: Re: Questions about MAN background use
Post by: John Donovan on December 20, 2013, 11:41:44 AM
Hi Sean,
This is a good question, but a little difficult to answer.

Yes, there is an uncertainty about the MAN fit, but that plot is a function of the average atomic number of the MAN fit, not the concentration of the element.

For example, in the following MAN plot, we can see that the one sigma % deviation for K ka is around 2 %, but in our unknown material, the calculation of the average atomic number is essentially a constant- if the material is even roughly homogeneous.

(http://probesoftware.com/smf/oldpics/i44.tinypic.com/2lxjdx1.jpg)

This is why there is such an improvement in precision when using the MAN correction for trace elements as described here:

http://probesoftware.com/smf/index.php?topic=29.msg237#msg237

Now maybe we can just assume that the precision is constant for a given average atomic number (a not unreasonable simplification), so using the previous labradorite example we obtained 0.104 wt% K:

ELEM:       Na      Si       K      Al      Mg      Fe      Ca      Mn      Ti       F       O       H      SUM
    21   2.907  25.278    .101  16.170    .089    .309   9.575    .002    .009   -.014  46.823    .000    101.248
    22   2.852  23.590    .109  16.328    .088    .291   9.500   -.001    .024    .047  46.823    .000     99.650
    23   2.831  23.548    .105  16.421    .087    .359   9.596    .002    .005    .040  46.823    .000     99.817
    24   2.807  23.594    .108  16.406    .087    .359   9.588    .001    .001    .014  46.823    .000     99.789
    25   2.809  23.884    .097  16.474    .085    .284   9.531    .000    .022    .034  46.823    .000    100.043

AVER:    2.841  23.979    .104  16.360    .087    .320   9.558    .001    .012    .024  46.823    .000    100.109
SDEV:     .041    .738    .005    .118    .001    .036    .041    .001    .010    .025    .000    .000       .652
SERR:     .018    .330    .002    .053    .001    .016    .018    .001    .005    .011    .000    .000
%RSD:     1.44    3.08    4.95     .72    1.40   11.39     .43  181.78   83.39  101.80     .00     .00


So maybe we can just assume that the 2% average variance on the MAN fit applies to the "concentration" of the background as well?  So since the background count rate from MAN is roughly 0.9 cps/nA and .1 wt% corresponds to roughly 1.8 cps/nA then the 2% variance of the MAN applies to background of the .1 wt.% or 0.001 wt.% or 10 PPM.

So if we add that to the 0.005 wt.% or 50 PPM (4.95% variance) we already obtained from the measurement, we obtain a total variance of roughly 0.006 wt.% or 60 PPM.

It makes sense because if we improve the precision of the MAN fit, the additional variance approaches zero. How does that sound?

ELEM:       Na      Si       K      Al      Mg      Fe      Ca      Mn      Ti       F       O       H      SUM
STKF:    .0155   .2093   .1132   .1275   .4736   .6779   .1693   .7341   .5547   .1715   .0000   .0000
STCT:    45.98   65.79  225.18  261.40 2197.75  139.51  107.68 1966.75   56.01   27.06     .00     .00 

UNKF:    .0155   .1841   .0009   .1275   .0006   .0027   .0871   .0000   .0001   .0001   .0000   .0000
UNCT:    45.98   57.90    1.86  261.40    2.79     .55   55.42     .01     .01     .01     .00     .00
UNBG:      .94     .07     .90     .85    1.67     .22     .46    5.03     .06     .06     .00     .00


Edit: Actually, in thinking about this some more, the precision of the fit mostly depends on the accuracy of the continuum absorption correction!  Note the change in fit variance with and without the continuum absorption correction checkbox checked in the Assign MAN Fits dialog above.
Title: Re: Questions about MAN background use
Post by: Malcolm Roberts on February 09, 2014, 06:27:38 PM
Hi John
I've just been listening to Karsten and Paul telling us about the wonders of MAN background usage and came back to Perth fired up and reach for the manual (Users guide and reference) which doesn't give any instruction on how to  set it up rather a simple flavour of what might be done. So I'm sitting here scratching my head with the spectre of long mapping sessions with off peak background acquisition as I cannot get  easily to the crux of what needs to be done. Having waded through a morass of questions and answers on the discussion forum, one question remains unasked and unanswered. That is quite simply, how do you do it. This may need a flow chart.
Specifically, do you need to model all backgrounds for all elements of interest on all specs and all crystals or is it sufficient to chose a position to get counts as a function of z per crystal per spec at a specific I and KV?
Please can I have an stepwise idiot's guide.
Cheers,
Malc.
Title: Re: Questions about MAN background use
Post by: John Donovan on February 09, 2014, 06:35:17 PM
No problem, you already have it.  Click the Help | Getting Started Manual menu and scroll down to the Assign MAN Background Calibrations chapter around page 153. It will take you through the process mouse click by mouse click.  Once you see how easily it is done, you will be both surprised and pleased.
john
Title: Re: Questions about MAN background use
Post by: John Donovan on April 03, 2014, 11:41:34 AM
I cannot over emphasize the importance of properly fitting one's standards for the MAN background fits.

The basic "rule of thumb" (and it is merely a "rule of thumb" so there are exceptions!), is that since we are trying to characterize the continuum as a function of average atomic number, and background is, by definition, generally the lowest intensity we can measure, then any standard which plots "above" the fit as seen here, is a good candidate to <ctrl> click to unselect and update the MAN fit:

(http://probesoftware.com/smf/oldpics/i58.tinypic.com/34dsn50.jpg)

In the above case, two standards that both do not contain fluorine, are seen to give an elevated background, why? Because P and Cr both interfere quite well with F ka...

In other situations one might actually find that they have a trace element contamination in their standard that they were not aware of (Probe for EPMA automatically deselects all standards that contain any of the element of interest in the MAN fitting) and therefore that standard will also plot "above" the general trend. Therefore "contaminated" standards should also be deselected and the fit updated similarly as we did with the above apatite and Cr2O3 standards which interfere with F ka.

In practice you do not have to know exactly why a particular standard intensity plots above the general trend of continuum intensities, just unselect and re-fit. Though as is often the case, the physics details might be interesting!

(http://probesoftware.com/smf/oldpics/i59.tinypic.com/2vsgajd.jpg)

For example, why does the copper standard intensity cause the intensity to "curve over" and decrease?  Because in higher average atomic number materials, the self absorption in the material, for low energy x-rays such as fluorine, is increasing faster than the increase in continuum production due to the slowing down of the primary electrons.
Title: Re: Questions about MAN background use
Post by: Owen Neill on April 04, 2014, 02:17:01 PM
John - is it possible to use a combination of MAN and off-peak backgrounds for samples where all elements were originally acquired with off-peak backgrounds?

To elaborate, following your and Karsten's example, I acquired all the samples and standards with off-peak backgrounds, assigned the MAN fits after checking "Use Off Peak Elements for MAN Fit", and then applied them to my unknowns by checking "Use MAN correction for Off-Peak Elements". I was running a routine for REE-phosphates similar to Karsten's, and was looking to do a similar comparison (which turned out to be quite informative).

I noticed that checking the "Use MAN Correction for Off-Peak Elements" option seems to apply the MAN background to all elements. Is it possible to post-process the data using a combination of MAN backgrounds for a few elements, and off-peak backgrounds for the rest? For example, could I use the off-peak backgrounds for the middle-heavy REE's, and use MAN backgrounds for La, Ce and P? Or would I need to have specified MAN or off-peak for each element prior to acquisition? Apologies if I'm missing something obvious here.
Title: Re: Questions about MAN background use
Post by: John Donovan on April 04, 2014, 03:53:47 PM
John - is it possible to use a combination of MAN and off-peak backgrounds for samples where all elements were originally acquired with off-peak backgrounds? To elaborate, following your and Karsten's example, I acquired all the samples and standards with off-peak backgrounds, assigned the MAN fits after checking "Use Off Peak Elements for MAN Fit", and then applied them to my unknowns by checking "Use MAN correction for Off-Peak Elements". I was running a routine for REE-phosphates similar to Karsten's, and was looking to do a similar comparison (which turned out to be quite informative).

Sounds like you did everything correct. This is exactly why I implemented the ability to change all off-peak acquired elements to be treated as MAN background acquired.  This makes sense since the on-peak data is already there, one simply needs to ignore the off-peak data!  That way one can compare the same data using both off-peak and MAN (one can even treat a multi-point background as a normal off-peak sample!).    8)

This was the reason for this post:

http://probesoftware.com/smf/index.php?topic=4.msg189#msg189

Quote from: Owen Neill
I noticed that checking the "Use MAN Correction for Off-Peak Elements" option seems to apply the MAN background to all elements. Is it possible to post-process the data using a combination of MAN backgrounds for a few elements, and off-peak backgrounds for the rest? For example, could I use the off-peak backgrounds for the middle-heavy REE's, and use MAN backgrounds for La, Ce and P? Or would I need to have specified MAN or off-peak for each element prior to acquisition? Apologies if I'm missing something obvious here.

Yes, you can switch all off-peak elements to MAN to compare, but not selected elements. The only thing obvious you are missing is that if this is what you want to do, then do it!    ;)

That is acquire "off-peak backgrounds for the middle-heavy REE's, and use MAN backgrounds for La, Ce and P".  Remember, you can acquire a different background for every element *and* also acquire different backgrounds for the standards compared to the unknowns- if that became necessary...

You might also take a look at this post by Karsten Goemann on looking at REE elements:

http://probesoftware.com/smf/index.php?topic=4.msg17#msg17
Title: Re: Questions about MAN background use
Post by: Owen Neill on April 06, 2014, 05:47:45 PM

Yes, you can switch all off-peak elements to MAN to compare, but not selected elements. The only thing obvious you are missing is that if this is what you want to do, then do it!    ;)

That is acquire "off-peak backgrounds for the middle-heavy REE's, and use MAN backgrounds for La, Ce and P".  Remember, you can acquire a different background for every element *and* also acquire different backgrounds for the standards compared to the unknowns- if that became necessary..

OK, that's what I figured -  thanks!
Title: Re: Questions about MAN background use
Post by: Probeman on August 11, 2014, 02:20:01 PM
There is a simple method to compare the same intensity data using off-peak, MAN and Nth point background corrections...

The above post:

http://probesoftware.com/smf/index.php?topic=4.msg189#msg189

mentions calculating the same data using both off-peak and MAN methods to compare the accuracy and precision.

Please note that one might consider making a copy of the original probe data MDB file to another folder, so that one copy can be treated using off-peak background corrections and the other copy can be treated using MAN background correction methods.

This allows the user to keep the results for each method without having to re-assign and re-calculate.
Title: Re: Questions about MAN background use
Post by: JohnF on August 15, 2014, 10:51:55 AM
I am going to post something about MAN, but first I'll make a suggestion. John, you might consider making a separate MAN discussion page. Cause when you search for MAN or "MAN" you also get hits for many, mania, manuscript, etc.
As I hope MAN use takes off, it might be useful to make it easier for people for find MAN posts.

Just thinking....
Title: Re: Questions about MAN background use
Post by: JohnF on August 15, 2014, 10:59:12 AM
John, can you clarify exactly under what conditions one should click the "Clear all MAN assignments" button?

Case in point. I have set up a 10 element glass MAN setup. I acquire all the MAN backgrounds, and life is good.

A month later, an occasion comes to use the MAN backgrounds but I need to add another element, P. Interesting, I think, as I want to add it on TAP, where it will be at a low angle and thus the background is curved, and since P in a minor element in the basaltic glasses, I have to worry about getting the proper background curvature. But wait.... if I use MAN, I don't have to worry about the modeling of the curvature, since the MAN takes it all into account. Another reason to use MAN, even for minor amounts (I'm expected 0.5-0.9 wt%).

But my question. Since I've added an element, do I need to "start all over" in the MAN assignments (click the clear button), or, preferably, just select "Assign MAN fits" and go thru the procedure. 

Note also that in this procedure, I  am re-acquired (after 2-3 months) the backgrounds on many of the MAN stds I acquired earlier this summer, so I can check how the bkg many have changed, as I assume it probably hasn't but would be nice to be sure.

So the question is, do you recommend clearing the prior MAN background assignment and "starting" fresh?
Title: Re: Questions about MAN background use
Post by: John Donovan on August 15, 2014, 11:18:15 AM
I am going to post something about MAN, but first I'll make a suggestion. John, you might consider making a separate MAN discussion page. Cause when you search for MAN or "MAN" you also get hits for many, mania, manuscript, etc.  As I hope MAN use takes off, it might be useful to make it easier for people for find MAN posts.

I appreciate the thought.  Right now I've tried to contain the MAN discussions into a main area. The main topic is for questions about the current MAN features and how to use them. The correct topic for these types of questions is the current topic:

http://probesoftware.com/smf/index.php?topic=4.0

which was started by Mike Spilde last summer.  Your questions below in the next post are perfectly appropriate for this topic.

In addition there are some "specialty" topics on using MAN bgd corrections, such as...

1. Quantifying carbon using MAN bgd calibration curves:

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

Ironically, the carbon in steel quantification method used by many European EPMA users is a very simple form of our MAN method, but they only utilize a single standard (pure Fe) to obtain a background for carbon and do not perform a continuum absorption correction.

The main downside with using a single standard for the MAN regression is that if the average Z in the sample changes (e.g., unknown alloy steels and/or the carbon standard which is normally Fe3C), the background will be incorrectly calculated because the composition is different and therefore the average Z is different from our pure Fe standard used for the background. Our multi-standard MAN calibration curve allows the user to accurately apply the regression over a range of compositions and hence over a range of average Z.

2. Another MAN topic is using the MAN correction along with the blank correction to improve precision and reduce integration time for trace elements:

http://probesoftware.com/smf/index.php?topic=29.0

See especially reply#5 in the above Ti in Quartz topic.

3. There is also a topic here discussing the relationship between accuracy and precision in the MAN background correction:

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

I look forward to more discussion here as it is not a simple thing to think through.

Title: Re: Questions about MAN background use
Post by: John Donovan on August 15, 2014, 11:21:46 AM
John, can you clarify exactly under what conditions one should click the "Clear all MAN assignments" button? Case in point. I have set up a 10 element glass MAN setup. I acquire all the MAN backgrounds, and life is good.

A month later, an occasion comes to use the MAN backgrounds but I need to add another element, P. Interesting, I think, as I want to add it on TAP, where it will be at a low angle and thus the background is curved, and since P in a minor element in the basaltic glasses, I have to worry about getting the proper background curvature. But wait.... if I use MAN, I don't have to worry about the modeling of the curvature, since the MAN takes it all into account. Another reason to use MAN, even for minor amounts (I'm expected 0.5-0.9 wt%).

But my question. Since I've added an element, do I need to "start all over" in the MAN assignments (click the clear button), or, preferably, just select "Assign MAN fits" and go thru the procedure. 

It's really a six or one half dozen of the other sort of thing. Either way is fine, it's just that if one made many changes to the setup such as adding several elements and changing the background types, etc., etc., it is entirely possible to correct everything in the Assign MAN Fits menu dialog, but it just might be easier to clear them and let the application re-assign everything automatically.

Then simply review all the MAN fits again to make sure they are good.
john
Title: Re: Questions about MAN background use
Post by: UoL EPMA LAB on October 15, 2014, 05:55:03 AM
Hi All

I have a slightly more parochial question on MAN usage - or rather NOT usage.

I have built a pretty large setup for a wide variety of elements, many of which were copied in from old projects or elements.mdb
I decided to set everything up using off-peak backgrounds, so set both my unknowns AND my standards to use off-peak backgrounds in both the acquire>elements/cations AND acquire>acquisition options windows (see attached). I have then run a full set of standards and now when I try and analyse my standard data in the analyse window I get a message telling me I have no MAN data to fit for Ni (also attached). I don't just see this for Ni but all standards in this batch. Why is PfE looking for MAN data when I have set it to use off-peak BGs across the board?

Whats going on, what am I missing here?

Confused
Leeds
Title: Re: Questions about MAN background use
Post by: Probeman on October 15, 2014, 08:38:17 AM
I decided to set everything up using off-peak backgrounds, so set both my unknowns AND my standards to use off-peak backgrounds in both the acquire>elements/cations AND acquire>acquisition options windows (see attached). I have then run a full set of standards and now when I try and analyse my standard data in the analyse window I get a message telling me I have no MAN data to fit for Ni (also attached). I don't just see this for Ni but all standards in this batch. Why is PfE looking for MAN data when I have set it to use off-peak BGs across the board?

Whats going on, what am I missing here?

Hi Leeds,
One possibility is that because of the standard intensity drift correction feature, the program will scan for all undeleted standards and try to load them for the drift interpolation.

So double check that all MAN standards are deleted and try again.  You can also clear the MAN assignments but that shouldn't be necessary.

I also assume the Analytical | Use Off-Peaks For MAN Fits menu is unchecked?
Title: Re: Questions about MAN background use
Post by: Richard Walshaw on October 15, 2014, 10:20:22 AM
Thanks for the reply.

Will try that tomorrow.

Leeds

 :-\
Title: Re: Questions about MAN background use
Post by: UoL EPMA LAB on October 16, 2014, 08:03:14 AM
Hi Again

I've done as you suggested and deleted the old standards, some of which were imported from projects using MAN BG.
My problem has gone away. All is now good.

Thanks Probeman!
 :D 8)
Title: Re: Questions about MAN background use
Post by: Ben Buse on January 21, 2015, 09:04:16 AM
Hi John,

I have a question regarding the collection of backgrounds for quant maps of a single phase  e.g. Mg Calcite or Plagioclase- which we do often. In a single mineral backgrounds are constant & for majors peak to background ratios are high so background represents small percentage - making it tempting to ignore backgrounds. What we should do is MAN backgrounds the only reason we dont is to save time by not collecting standard data for standards which do not contain the elements. But I suppose the machine's pretty stable and we could just calibrate for MAN backgrounds every few months as larger errors for backgrounds would not matter? Have you thought about having an option were you could specify a single background in counts per second for the whole map - for this case were your mapping elements within a single phase e.g. here Mg-calcite for minor and trace elements - and the background could be specified for the map from a single quant point.

Thanks

Ben
Title: Re: Questions about MAN background use
Post by: Probeman on January 21, 2015, 03:59:26 PM
I have a question regarding the collection of backgrounds for quant maps of a single phase  e.g. Mg Calcite or Plagioclase- which we do often. In a single mineral backgrounds are constant & for majors peak to background ratios are high so background represents small percentage - making it tempting to ignore backgrounds. What we should do is MAN backgrounds the only reason we dont is to save time by not collecting standard data for standards which do not contain the elements. But I suppose the machine's pretty stable and we could just calibrate for MAN backgrounds every few months as larger errors for backgrounds would not matter? Have you thought about having an option were you could specify a single background in counts per second for the whole map - for this case were your mapping elements within a single phase e.g. here Mg-calcite for minor and trace elements - and the background could be specified for the map from a single quant point.

Hi Ben,
Good question.

Basically you want to do an MAN background calibration curve using a single point... which assumes of course that you have a constant composition (or at least a constant average Z which is essentially the same). However, as you point out, for major elements the background (if it is smaller than the measurement precision) can be ignored, or at least roughly approximated.

So here's an example of what to do if you wanted to say x-ray map (or point analyze) Ca and Mg on say dolomites that are (roughly) constant in composition. By the way, to include CO3 in the matrix calculation by various methods, see this topic:

http://probesoftware.com/smf/index.php?topic=92.0

Let's start with adding Ca and Mg to a spectrometer and then go to the Acquisition Options dialog as seen here and specify that the standard acquisition use off-peak backgrounds but the unknowns (your dolomite point analyses or maps) use the MAN background. Here is the Acquisition Options dialog:

(http://probesoftware.com/smf/oldpics/i60.tinypic.com/2u63e45.jpg)

This gets more important as one starts to add additional elements to analyze for, but then one will have multiple standards that *do not* contain the element of interest and can therefore be utilized in the MAN calibration for variation in average Z!

Next we select our standard positions and run them:

(http://probesoftware.com/smf/oldpics/i60.tinypic.com/nqz0j8.jpg)

Once the standards are acquired we can analyze them as unknowns because we utilized off-peak backgrounds as seen here:

St  135 Set   1 Calcite (analyzed), Results in Elemental Weight Percents
 
ELEM:       Mg      Ca       C       O
TYPE:     ANAL    ANAL    SPEC    SPEC
BGDS:      LIN     LIN
TIME:    20.00   20.00
BEAM:    30.01   30.01

ELEM:       Mg      Ca       C       O   SUM 
     1   -.017  40.141  12.000  47.952 100.076
     2    .028  39.956  12.000  47.952  99.936
     3   -.010  39.994  12.000  47.952  99.935

AVER:     .000  40.030  12.000  47.952  99.982
SDEV:     .024    .098    .000    .000    .081
SERR:     .014    .057    .000    .000
%RSD:     ----     .24     .00     .00

PUBL:     n.a.  40.031  12.000  47.952  99.983
%VAR:      ---   (.00)     .00     .00
DIFF:      ---   (.00)    .000    .000
STDS:      222     135       0       0


Now we go to assign the MAN background for our unknowns using the Analytical menu as seen here:

(http://probesoftware.com/smf/oldpics/i58.tinypic.com/2lbkwvm.jpg)

But whoa, we now get this error message:

(http://probesoftware.com/smf/oldpics/i59.tinypic.com/29diizd.jpg)

Why? Because our standards were acquired using off-peak backgrounds and so the program ignores the off-peak standards by default for the MAN calibration. So we can change that default by clicking this menu in the same Analytical menu as seen here:

(http://probesoftware.com/smf/oldpics/i59.tinypic.com/2zjgydh.jpg)

Now we click the Analytical | Assign MAN Fits menu again and now we see this for the first element Mg:

(http://probesoftware.com/smf/oldpics/i57.tinypic.com/1z50sqc.jpg)

and this for Ca:

(http://probesoftware.com/smf/oldpics/i62.tinypic.com/6gfy51.jpg)

Yes, we're only using a single point for each MAN calibration curve so it is a constant background intensity for that element, but depending on what standard you pick you'll get a reasonable background estimate for major and maybe even minor elements.  Or you could just acquire one or two more darn standards and get a proper slope for your MAN calibration curves! 

Helpful hint: if you aren't sure which of your standards might have similar average Z values compared to your unknowns, you can use this handy menu the the Standard.exe app as seen here:

(http://probesoftware.com/smf/oldpics/i61.tinypic.com/2prbmhd.jpg)
Title: Re: Questions about MAN background use
Post by: Probeman on January 22, 2015, 10:31:39 AM
In practice you do not have to know exactly why a particular standard intensity plots above the general trend of continuum intensities, just unselect and re-fit. Though as is often the case, the physics details might be interesting!

(http://probesoftware.com/smf/oldpics/i59.tinypic.com/2vsgajd.jpg)

For example, why does the copper standard intensity [cuprite #114] cause the intensity to "curve over" and decrease?  Because in higher average atomic number materials, the self absorption in the material, for low energy x-rays such as fluorine, is increasing faster than the increase in continuum production due to the slowing down of the primary electrons.

After seeing the plot above some might ask, why stop there?  Maybe the std 140 (Rutile) is also either contaminated with fluorine (unlikely I'm guessing) or perhaps the Ti La line slightly interferes with the F Ka line? After consideration of the fact that Ti L emission overlaps *strongly* with N ka, we might guess that perhaps the tail of a Ti L emission line could cause a slight interference for F Ka?

The easiest way to try and answer this question is by examining an x-ray database such as the NIST 2005 database in PFE available from the Xray | Xray Database menu as seen here:

(http://probesoftware.com/smf/oldpics/i57.tinypic.com/2gvpgro.jpg)

Note that the wavelength range was specified by entering F Ka in the Specify Range controls as seen above. Now to see if any Ti emission lines could in principle, interfere with the F Ka line, we can select an element to highlight, in the case Ti, by using the Highlight Element control as seen here:

(http://probesoftware.com/smf/oldpics/i62.tinypic.com/hvujx2.jpg)

Or one can select multiple emitters by clicking the Periodic Table button and using the periodic table dialog as seen here:

(http://probesoftware.com/smf/oldpics/i60.tinypic.com/1z2oz1c.jpg)

In either case no Ti lines are found near the analytical emission line for fluorine.  Another method which can provide a nominal estimate of the possible overlaps is by using the Options | Interferences menu in the Standard.exe app. Begin by selecting a the potentially problematic Ti standard or another similar standard such as synthetic TiO2 as seen here:

(http://probesoftware.com/smf/oldpics/i58.tinypic.com/1zgxqu1.jpg)

This will cause the following window to open with the TiO2 composition loaded automatically as seen here:

(http://probesoftware.com/smf/oldpics/i60.tinypic.com/33axsom.jpg)

Now, using the Unknown button, add a small amount of fluorine to the material because the software only check for elements in the material as seen here:

(http://probesoftware.com/smf/oldpics/i62.tinypic.com/dfhe9g.jpg)

Finally, click the Calculate button to checking for overlaps where as we can see here, nothing is reported for F Ka:

(http://probesoftware.com/smf/oldpics/i60.tinypic.com/fmq2w0.jpg)
Title: Re: Questions about MAN background use
Post by: Ben Buse on January 26, 2015, 08:06:08 AM
Hi John,

Thanks. I get you where the average atomic number is constant (as in a single phase) so we don't have to correct for changing atomic number within the map we can use a single MAN standard. With best MAN data given where atomic number of MAN standard is same as unknown.

By using even a single MAN standard with similar atomic number (as is the case for most silicates/carbonate standards) we improve the quantification compared to no background. The error due to difference in atomic number of MAN standard and unknown is much smaller than the error with no background.

A good compromise for major elements where p/b ratio is large and background is small % (<1%) of total counts?
Title: Re: Questions about MAN background use
Post by: Probeman on January 26, 2015, 01:50:44 PM
Thanks. I get you where the average atomic number is constant (as in a single phase) so we don't have to correct for changing atomic number within the map we can use a single MAN standard. With best MAN data given where atomic number of MAN standard is same as unknown.

By using even a single MAN standard with similar atomic number (as is the case for most silicates/carbonate standards) we improve the quantification compared to no background. The error due to difference in atomic number of MAN standard and unknown is much smaller than the error with no background.

A good compromise for major elements where p/b ratio is large and background is small % (<1%) of total counts?

Hi Ben,
Yes that is correct if you are just measuring trace elements and none of the matrix elements. Of course you can't use a silicate to measure the background for Si ka!

But, if you are measuring just traces in silicates or carbonates, you've already measured a bunch of "on-peak" or MAN backgrounds on the standards you are using for your trace elements, e.g., Fe in TiO2.

So, even if you used off-peak backgrounds for your standard calibration, and you plan on using MAN backgrounds for your unknown quant x-ray mapping runs, you can still use those off-peak measured standards as backgrounds for the MAN calibration.  This involves using the Analytical | Use Off-Peak Elements For MAN Fit menu as described here:

http://probesoftware.com/smf/index.php?topic=4.msg189#msg189
Title: Re: Questions about MAN background use
Post by: John Donovan on May 19, 2016, 03:42:28 AM
In case anyone is interested, I've attached a pdf of the trace MAN presentation I gave at the EPMA 2016 topical conference this week in Madison (remember, you have to be logged in to see attachments).

The full paper will be out in the Aug issue of the Amer. Min. this year.
Title: Re: Questions about MAN background use
Post by: Probeman on October 11, 2016, 04:20:04 PM
Here's a couple of MAN plots from my trace zircon run posted here:

http://probesoftware.com/smf/index.php?topic=73.msg5130#msg5130

In these MAN plots of the P ka line, here is the plot with the defaults assigned by the program:

(http://probesoftware.com/smf/gallery/395_11_10_16_4_07_28.png)

Note that P plots well above the trend.  Quantifying this amount shows an apparent 220 PPM of P in zircon, but is it real?

That is there is either a trace amount of phosphorus in this synthetic zircon or there is a spectral interference from Si or Zr. Since this is a synthetic zircon from Oak Ridge and we know it is very pure, we can check for nominal interferences using the Standard Assignments dialog as seen here:

(http://probesoftware.com/smf/gallery/395_11_10_16_4_14_38.png)

And in fact there is a very small interference from the Zr La line, but it's a big emission line so it doesn't take much of a tail to create an apparent 220 PPM of P.

Once we remove the zircon standard from the MAN fit we obtain this plot:

(http://probesoftware.com/smf/gallery/395_11_10_16_4_07_47.png)

And we are good. Remember, an artifact like this can be corrected for using the normal interference correction in PFE, or we can assign a blank correction (assuming we have a spectroscopically pure zircon standard- or at least one that is well characterized for trace phosphorus using a technique other than EPMA) to deal with it.  Remember, you should not assign both a spectral interference and a blank correction as you will get a "double correction". Fortunately, PFE will remind us that this is a no-no!
john
Title: Re: Questions about MAN background use
Post by: Owen Neill on October 11, 2016, 05:41:00 PM
John - very nice, thanks for sharing. A couple of MAN questions for you:

1) Is it possible to easily extract the raw data behind MAN (i.e. the standard intensities and Z-bar values)? The new graphics are very nice, but being able to extract the raw data to plot up off-line would be very useful for figures/papers/posters/etc. I realize I can export the count rates for the standards from the "Output" menu, and then look up the Z-bar values in the standard database, but... well, I'm lazy.

2) This is most likely operator error on my part, but is there a reason the last element in the MAN list reverts to a curved fit, even when you've told it to force the straight-line fit?

To explain further, I open the "Assign MAN Fits" window, click the last element, and click "Force Straight Line Fit", which does its job nicely. Then I hit OK, and the dialog closes.

After I do this, when I then re-open the "Assign MAN Fits" dialog, and look through the element list, it appears as though the last element is still using the forced straight line fit (i.e. still says "1st" under "Order" in the element list).

However, when I click that last element, the "Order" switches to "2nd", and the display shows a polynomial fit to the MAN intensities with the "Force Straight Line Fit" box unchecked.

This seems to happen regardless of how many elements are measured, or what the last element/X-ray line actually is. Again, only the last element in the MAN list shows this behavior. Using PFE v11.6.6, updated ~15min ago. Have tried with 6 different MDB files (created under previous versions), and all have shown the same behavior.

This is not to advocate for or against forcing MAN fits to be linear, just wondering what I'm screwing up that's making it do this.
Title: Re: Questions about MAN background use
Post by: John Donovan on October 11, 2016, 05:52:37 PM
1) Is it possible to easily extract the raw data behind MAN (i.e. the standard intensities and Z-bar values)? The new graphics are very nice, but being able to extract the raw data to plot up off-line would be very useful for figures/papers/posters/etc. I realize I can export the count rates for the standards from the "Output" menu, and then look up the Z-bar values in the standard database, but... well, I'm lazy.

Hi Owen,
I'm lazy too. That is why the Output | Save Custom Output Format #8 (MAN) already outputs the standard intensities and zbars.

2) This is most likely operator error on my part, but is there a reason the last element in the MAN list reverts to a curved fit, even when you've told it to force the straight-line fit?

To explain further, I open the "Assign MAN Fits" window, click the last element, and click "Force Straight Line Fit", which does its job nicely. Then I hit OK, and the dialog closes.

Well you do realize that one needs to check this "Force Straight Line Fit" checkbox and click the Update Fit button for each element that you want to force a straight line fit for, if you want it to stick...
john
Title: Re: Questions about MAN background use
Post by: Owen Neill on October 11, 2016, 08:03:15 PM
I'm lazy too. That is why the Output | Save Custom Output Format #8 (MAN) already outputs the standard intensities and zbars.

You're a lifesaver! Is this new? I've been looking for this for weeks, thanks HUGE!


Well you do realize that one needs to check this "Force Straight Line Fit" checkbox and click the Update Fit button for each element that you want to force a straight line fit for, if you want it to stick...
john

I do. Try the following:

1) Open an MDB file and click "Assign MAN Fits" dialog from the "Analytical" pull-down.
2) Click on the last element in the list.
3) Click "Force Straight Line Fit."
4) Click "Update Fit." The "Order" will change from "2nd" to "1st", everything seems copacetic.
5) Click OK. The "Assign MAN Fits" dialog goes away.
6) Click "Assign MAN Fits" in the "Analytical" pull-down again.
7) Look at the element list. The last element will still have "1st" listed under "Order".
8.) While watching the "Order" value for the last element, click the last element in the list.
9) The "Order" will change from "1st" to "2nd" with the mouse click.
10) Also, the "Force Straight Line Fit" box will no longer be checked when the MAN plot for the last element is displayed.
11) Finally, the fit will no longer be a straight line.
12) Repeat steps 1-7 for any other element besides the last element in the list, and the behaviors described in 8-11 do not occur.

I realize this may seem like a nitpick, but I caught this while I was reducing some data, and couldn't figure out why the numbers for one element would sometimes change without me (seemingly) doing anything. It's easy to do unwittingly.

Hope this helps.
Title: Re: Questions about MAN background use
Post by: John Donovan on October 11, 2016, 08:27:49 PM
I realize this may seem like a nitpick, but I caught this while I was reducing some data, and couldn't figure out why the numbers for one element would sometimes change without me (seemingly) doing anything. It's easy to do unwittingly.

Yes, very helpful. 

It's clearly a small bug.  I will squash it tomorrow!
john
Title: Re: Questions about MAN background use
Post by: Owen Neill on October 11, 2016, 08:28:47 PM
I realize this may seem like a nitpick, but I caught this while I was reducing some data, and couldn't figure out why the numbers for one element would sometimes change without me (seemingly) doing anything. It's easy to do unwittingly.

Yes, very helpful. 

It's clearly a small bug.  I will squash it tomorrow!
john

Thanks!
Title: Re: Questions about MAN background use
Post by: John Donovan on October 12, 2016, 01:00:53 PM
Hi Owen,
OK.  The fix for that last MAN fit assignment glitch is fixed and ready to download the latest PFE.

It was subtle...  had to do with the order things are loaded!  But it *only* affected the last element for this reason!
john
Title: Re: Questions about MAN background use
Post by: Owen Neill on October 12, 2016, 01:23:18 PM
Hi Owen,
OK.  The fix for that last MAN fit assignment glitch is fixed and ready to download the latest PFE.

It was subtle...  had to do with the order things are loaded!  But it *only* affected the last element for this reason!
john

Awesome! Thanks much!
Title: Re: Questions about MAN background use
Post by: John Donovan on October 12, 2016, 01:49:00 PM
Hi Owen,
OK.  The fix for that last MAN fit assignment glitch is fixed and ready to download the latest PFE.

It was subtle...  had to do with the order things are loaded!  But it *only* affected the last element for this reason!
john

Awesome! Thanks much!

No worries, thanks for the excellent beta testing report!  It's a lot easier to reproduce issues when I get a detailed description!   :-*
Title: Re: Questions about MAN background use
Post by: Julien on November 11, 2016, 01:49:02 PM
I really enjoy using the MAN, really! However, there is a series of error message that really starts to annoy me. The problem occurs when a lot of different standards are loaded in the run and the MAN has not been acquired in all of them. Whereas I do acknowledge and appreciate that the error appears (it can be legit in some case), it get really really really annoying when the same error repeat itself over 50 times for 12 elements (and ~20 standards). Please, please, please... can we find a better way to list this, e.g., buffer in a memory all the problematic standards / element that have missing data, and then maybe simply report it in the log window?

Second, I run into a big problem that actually resulted in a totally screwed up MDB file where I cannot use the MAN anymore (so as all my unknown are acquired with MAN I basically cannot reprocess my data anymore...). The issue started happening when I decided to acquire a new set of MAN acquisition just for the element mapping I was performing for the same user. The difference with my previous MAN acquisition was that I moved the Si Ka from a TAP (used for quant) to a PET (to enable mapping along with Al, Mg [TAP], K [PET] and Fe [LiF]). Ever since I do have this new calibration, calling the assign MAN routine returns me absolutely... nothing (i.e., PfE cannot find any MAN acquisition for any standard, and I know this is not true). To further complicate that story, my latest standardization and MAN acquisition on standard included two column conditions (15 and 10 keV). Clearing the MAN assignment and re-doing everything does not solve the problem. Disabling a set of standard and keeping only the one I need does not help neither. Exporting the results into a new file (and importing the std associate to the mapping setting only) does not solve the problem neither. My ultimate solution: use my backup before the file was screwed up and re-acquire again my standards in, this time, a NEW file. I guess, this is my fault, as I should have prepared a new sample right away for this new setting, but I was hoping to continue using the other MAN assignment for Al, Mg, K and Fe, which had not changed.

Is there a solution to fix this problem? I cannot open the MDB file and manually delete the "faulty" standard acquisitions as I only have access to the newest Microsoft Access software (which cannot read anymore the MDB file format). The file is too big to be attached on this forum, but I can send you (JD) a copy by email.

Best,

Julien
Title: Re: Questions about MAN background use
Post by: John Donovan on November 11, 2016, 03:34:11 PM
I really enjoy using the MAN, really! However, there is a series of error message that really starts to annoy me. The problem occurs when a lot of different standards are loaded in the run and the MAN has not been acquired in all of them. Whereas I do acknowledge and appreciate that the error appears (it can be legit in some case), it get really really really annoying when the same error repeat itself over 50 times for 12 elements (and ~20 standards). Please, please, please... can we find a better way to list this, e.g., buffer in a memory all the problematic standards / element that have missing data, and then maybe simply report it in the log window?

Sorry you are so frustrated. Adding another button to cancel out should be feasible. Note that if you load different standards into a new run you should probably first clear the MAN assignments and then you shouldn't get all these errors.

Is there a solution to fix this problem? I cannot open the MDB file and manually delete the "faulty" standard acquisitions as I only have access to the newest Microsoft Access software (which cannot read anymore the MDB file format). The file is too big to be attached on this forum, but I can send you (JD) a copy by email.

It's difficult to understand what you might have done here. Better send me the MDB file to look at.
john
Title: Re: Questions about MAN background use
Post by: Julien on November 11, 2016, 08:20:21 PM
Hi John,

Thanks for the quick response. This is not so urgent (and this is now the week-end and we probably all need a lot of rest after that week). I learnt from my mistakes. However, I was thinking the MAN code could handle the following situation (sorry for the vagueness of my previous post):

(1) The researcher wanted chlorite analysis. Easy. The day before their venue, I acquired all required elements that we agreed on the week before (Si, Al, Fe, Mn, Mg, Ca, Na, K, F and Cl) in several standards, all with MAN (no element with 2-pts bkg). The automated run I had to get the MAN on all my standards (maybe a little too many, but I’m still testing…) took 2-3 hours.

(2) Once they arrived, they also requested additional elements: Ba, V, Co, Ni and Zn. I didn't want to worry about setting right my background for these element that are expected to be minor (or maybe trace), and I also wanted to ease potential interference correction, two great reasons to opt for the MAN background correction. To avoid re-running all my standards with this now 2 to 3 minute long setup, I opt to just run it in 5 (new!) standards, for Ba (barite), Ni (pentlandite), Zn (sphalerite) and, V and Co (metals - I know, not ideal, but I’m doing with what I have right now...).

(3) So after that, I ended up with many standards that had no data for Ba, V, Co… and 5 other standards that had no data for Si, Al, Fe…

(4) At this point, I managed to get into the MAN assignment tool and set the assignment (after 50+ clicks on these error message). I guess an easy fix for this would be to generate ONE error for ALL elements / standards missing and have that reported at the end in the main log window of PfE (e.g., a red message).

(5) After this, the MAN was properly assigned and the treatment of the unknown analysis worked fine, we got all the data we needed for the day.

(6) Things got complicated during the evening. We opt to perform some quantitative mapping on these chlorite (for Si, Al, Mg, Fe and K). Based on my spectrometer setting, I was in need of putting Si on a PET crystal (the only two TAP reserved for Al and Mg). To enable the MAN correction, I had thus to reacquire MAN data that would include also Si on PET; I did this in a sub-set of my Si, Al, Fe, Mg and K standards. Stupidly enough I did that in the same MDB file...

(7) This is were the files started getting “bogus”. After this acquisition, I started having a bunch of errors than the MAN was not available for Al, or Si, or another element… To solve this error, I opt to clean all MAN assignment, and start from scratch. However, when I returned to the MAN assignment window (after many clicks), the MAN assignment constantly returned me an error that no MAN data were available, and this for every single element in the MAN assignment window. Also, Si is only listed once, whereas it should be listed twice (once for Si on TAP and one for Si on PET - actually there should even be a third entry, as I had also acquired MAN data in my standards for Si on PET at 10 keV (all other data were acquired at 15 keV).

I have sent you the good (early backup) and the bad file (after the latest std acquisition).

Again, no rush on this, I am just wondering why this has screwed up the file (so I won’t reproduce this), and if it is possible to fix this easily.

Best,

Julien
Title: Re: Questions about MAN background use
Post by: John Donovan on November 11, 2016, 10:43:47 PM
Hi Julien,
I will look at your file and see if I can handle this type of situation better.

I will only mention at this time that if I have a run with lot of MAN elements and I want to add some additional trace elements, I generally just add them as off-peak elements- though note that you need to make sure they are specified as off-peak both for both standards and unknowns, as seen in the Acquisition Options dialog.

I think something like the above will avoid the problems you are seeing. That said the software should be able to handle the situation you describe, so I will look into that this weekend. With the current software I think it's just a question of unselecting standards which do not have the MAN data acquired for those elements.
john
Title: Re: Questions about MAN background use
Post by: John Donovan on November 13, 2016, 04:09:54 PM
Hi Julien,
Well I wasn't sure I was going to be able to figure out what the issues were with this probe run file, because I have to hand it to you: you get the EPMA Grand Prize for most complicated probe run ever!

(http://probesoftware.com/smf/gallery/1_13_11_16_4_11_36.jpeg)

I mean, you have duplicate elements, at multiple keVs, using MAN backgrounds, aggregate intensities, with different element setups, etc.... I hardly knew where to start! Anyway, I managed to isolate the culprits and here is the summary of the bug fixes (from the version.txt file):

11/13/16   Fix several bugs in MAN fit code when duplicate elements at different operating voltages are
      present in the same run (Allaz).

Here is a screenshot of the new (and improved!) MAN Fit display dialog (note both 15 and 10 keV elements):

(http://probesoftware.com/smf/gallery/1_13_11_16_12_59_42.png)

Below are two of your standards. First one at 15 keV:

St  340 Set   2 Pyrope, Results in Elemental Weight Percents
 
ELEM:       Al      Mg      Si       K      Fe      Ti      Cr      Mn      Ca       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    SPEC    SPEC    SPEC    CALC
BGDS:      MAN     MAN     MAN     MAN     MAN
MAN1:  1.28970 -.12378 .018498 -.38521 -.03082
MAN2:  .035652 .261638 .012660 .142803 .080721
MAN3:  .003343 -.00301 -.00016 -.00163 -.00074
ABS%:   -28.69  -30.48  -25.48   -5.67    -.14
TIME:    30.00   30.00   30.00   30.00   30.00     ---     ---     ---     ---     ---
BEAM:    19.86   19.86   19.86   19.86   19.86     ---     ---     ---     ---     ---
AGGR:                                              ---     ---     ---     ---     ---

ELEM:       Al      Mg      Si       K      Fe      Ti      Cr      Mn      Ca       O   SUM 
   251 11.5262 12.7897 19.4222  .00188 6.33455  .29975 1.40944  .24008 3.10892 44.7774 99.9101
   252 11.5370 12.7413 19.7032 -.00008 6.37568  .29975 1.40944  .24008 3.10892 45.0867 100.502
   253 11.5198 12.7502 19.4433 -.00427 6.40858  .29975 1.40944  .24008 3.10892 44.7897 99.9655
   254 11.5865 12.7641 19.6021  .00188 6.30480  .29975 1.40944  .24008 3.10892 45.0107 100.328
   255 11.5434 12.7980 19.3988  .00321 6.33253  .29975 1.40944  .24008 3.10892 44.7711 99.9051
   256 11.4746 12.7441 19.4013 -.00203 6.40277  .29975 1.40944  .24008 3.10892 44.6964 99.7753

AVER:  11.5312 12.7646 19.4952  .00010 6.35982    .300   1.409    .240   3.109  44.855 100.064
SDEV:   .03634  .02414  .12715  .00282  .04215    .000    .000    .000    .000    .155  .28413
SERR:   .01484  .00986  .05191  .00115  .01721  .00000  .00000  .00000  .00000  .06335
%RSD:   .31516  .18915  .65223 2853.97  .66281  .00000  .00000  .00000  .00001  .34593

PUBL:  11.4211 12.2716 19.3656    n.a. 6.80919  .29975 1.40944  .24008 3.10892 44.4140 99.3397
%VAR:      .96    4.02     .67     ---   -6.60     .00     .00     .00     .00     .99
DIFF:   .11012  .49296  .12953     --- -.44937  .00000  .00000  .00000  .00000  .44131
STDS:      325     336     301     334     326     ---     ---     ---     ---     ---

STKF:    .4390   .4784   .2543   .1130   .6544     ---     ---     ---     ---     ---
STCT:  1010.49 2735.00  119.94  243.57  431.67     ---     ---     ---     ---     ---

UNKF:    .0800   .0890   .1435   .0000   .0537     ---     ---     ---     ---     ---
UNCT:   184.05  508.70   67.71     .00   35.42     ---     ---     ---     ---     ---
UNBG:     1.57    1.81     .11    1.04     .84     ---     ---     ---     ---     ---

ZCOR:   1.4421  1.4344  1.3582  1.1253  1.1845     ---     ---     ---     ---     ---
KRAW:   .18214  .18600  .56454  .00001  .08204     ---     ---     ---     ---     ---
PKBG:  117.885 282.635 616.119 1.00184 43.3686     ---     ---     ---     ---     ---

And another at 10 keV:

St  336 Set   3 Periclase, Results in Elemental Weight Percents
 
ELEM:       Al      Mg      Si       K      Fe       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    CALC
BGDS:      MAN     MAN     MAN     MAN     MAN
MAN1:  1.10474 .003876 .012899 -.10651 -.11700
MAN2:  .024212 .167921 .009920 .067070 .045766
MAN3:  .001162 -.00215 -.00012 -.00060 -.00051
ABS%:   -30.62  -10.37  -20.36   -2.37     .12
TIME:    30.00   30.00   30.00   30.00   30.00     ---
BEAM:    20.23   20.23   20.23   20.23   20.23     ---
AGGR:                                              ---

ELEM:       Al      Mg      Si       K      Fe       O   SUM 
   329 -.00400 60.2003  .00175  .00322  .04239 39.6411 99.8848
   330 -.01423 60.2350  .00515  .00404  .06666 39.6659 99.9625
   331 -.01595 60.3602 -.00681  .00431  .00401 39.7152 100.061
   332 -.01114 60.3954 -.00088  .00203  .14669 39.7898 100.322
   333 -.00462 60.3592 -.00599  .00016  .10331 39.7532 100.205
   334 -.01185 60.3800 -.01198  .00276  .07546 39.7462 100.181

AVER:  -.01030 60.3217 -.00313  .00275  .07309  39.719 100.103
SDEV:   .00495  .08242  .00628  .00152  .04918    .056  .16341
SERR:   .00202  .03365  .00257  .00062  .02008  .02297
%RSD:  -48.062  .13663 -200.83 55.1365 67.2864  .14164

PUBL:     n.a. 60.3027    n.a.    n.a.    n.a. 39.6973 100.000
%VAR:      ---   (.03)     ---     ---     ---     .05
DIFF:      ---   (.02)     ---     ---     ---  .02127
STDS:      325     336     301     334     326     ---

STKF:    .4702   .5285   .2806   .1146   .6410     ---
STCT:   602.80 1765.08   69.94  100.27   75.88     ---

UNKF:   -.0001   .5285   .0000   .0000   .0006     ---
UNCT:     -.09 1765.08    -.01     .02     .07     ---
UNBG:     1.03    1.36     .08     .51     .30     ---

ZCOR:   1.5250  1.1414  1.2958  1.1365  1.2571     ---
KRAW:  -.00014 1.00000 -.00009  .00021  .00091     ---
PKBG:   .91587 1296.33  .92694 1.04123 1.22577     ---

A couple of notes. First the code now displays and re-checks the fit of each MAN element when you click the OK button. Also, if you are in aggregate intensity mode, the MAN window only displays the first instance of the duplicate element. If you want to see the MAN fit for any subsequent duplicate elements, just unselect the Use Aggregate Intensity mode under the Analytical | Analysis Options menu dialog.

Whew!  In any event, the bottom line is that now Probe for EPMA shouold be able to handle any combination of element setups, with duplicate elements, at multiple keVs, for MAN background processing now.
john

PS For those that are interested, I've attached Julien's MDB file below (with his permission).

PPS This new software will allow one to handle multiple keVs in their MAN background fits for probe runs going back to v. 11.4.0, which is when I added the additional keV arrays for the MAN fit.
Title: Re: Questions about MAN background use
Post by: John Donovan on November 13, 2016, 04:34:53 PM
In going through the MAN fits in Julien's probe run, I noticed that some standards might have certain elements that are not reported in the standard.mdb compositional database.  Remember, the MAN background fit is a fast and easy way to check that your standards are as clean and complete as one would hope.  The outliers will tend to fall above the general trend line of the MAN fit, making them easy to spot.

Now some of these are definitely on-peak interferences, but some may be "contamination" in the sense that they are present- but not accounted for!  For example in the MAN fit for Cl Ka we see this plot:

(http://probesoftware.com/smf/gallery/1_13_11_16_1_00_00.png)

And in fact when we analyze the standard (from the same MDB file as above):

St  328 Set   1 Kaersutite, Results in Elemental Weight Percents
 
ELEM:       Si      Al      Na      Mg       F      Ca      Ti      Cr       K      Cl      Fe      Mn       H       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    CALC
BGDS:      MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
MAN1:  .433228 -.69047 -.22037 -3.8524 -.53121 .458636 -.33698 -.45214 -.33213 -.05578 -.04689 -.11476
MAN2:  .260354 .402656 .195662 .737859 .126105 .092872 .287473 .475453 .137779 .046313 .083034 .060886
MAN3:  .000071 -.00552 -.00238 -.01295 -.00247 .000815 -.00163 -.00079 -.00152 -.00042 -.00079 -.00041
ABS%:   -22.83  -28.84  -49.17  -35.61  -74.17   -3.34   -2.50   -1.34   -4.96  -11.57    -.46    -.83
TIME:    30.00   30.00   20.00   20.00   20.00   30.00   30.00   20.00   20.00   20.00   30.00   30.00     ---     ---
BEAM:    20.01   20.01   20.01   20.01   20.01   20.01   20.01   20.01   20.01   20.01   20.01   20.01     ---     ---
AGGR:                                                                                                      ---     ---

ELEM:       Si      Al      Na      Mg       F      Ca      Ti      Cr       K      Cl      Fe      Mn       H       O   SUM 
    51 18.7167 6.47933 1.83938 7.97634  .33305 7.98541 3.10663 -.00252  .84801  .02933 8.83063  .12070  .23000 42.5990 99.0920
    52 18.7057 6.47333 1.86776 7.85883  .24068 7.91836 3.12160  .01332  .87714  .02290 9.10796  .11198  .23000 42.6275 99.1770
    53 18.4669 6.41391 1.85091 7.78733  .20441 7.86146 3.10923  .00973  .84554  .03115 9.73464  .12887  .23000 42.4083 99.0823
    54 18.7365 6.57265 1.90582 7.86262  .30850 7.89659 3.07578  .01559  .87882  .02731 9.06527  .11481  .23000 42.6877 99.3779
    55 18.8403 6.57865 1.85397 7.99179  .31942 7.90964 3.10957  .01488  .83560  .02806 8.94850  .12863  .23000 42.8628 99.6518

AVER:  18.6932 6.50357 1.86357 7.89538  .28121 7.91429 3.10456  .01020  .85702  .02775 9.13740  .12100    .230  42.637 99.2762
SDEV:   .13735  .07062  .02569  .08651  .05575  .04528  .01710  .00746  .01970  .00308  .35091  .00774    .000    .164  .24125
SERR:   .06143  .03158  .01149  .03869  .02493  .02025  .00765  .00334  .00881  .00138  .15693  .00346  .00000  .07328
%RSD:   .73478 1.08590 1.37868 1.09564 19.8258  .57212  .55081 73.1317 2.29834 11.0899 3.84039 6.40067  .00001  .38431

PUBL:  19.4000 6.30000 1.95000 7.64000  .14000 8.15000 3.01000    n.a.  .84000    n.a. 8.77000  .13000  .23000 43.1680 99.7280
%VAR:    -3.64    3.23   -4.43    3.34  100.86   -2.89    3.14     ---    2.03     ---    4.19   -6.92     .00   -1.23
DIFF:  -.70679  .20357 -.08643  .25538  .14121 -.23571  .09456     ---  .01702     ---  .36740 -.00900  .00000 -.53094
STDS:      301     325     301     336     349     322     344     319     334     350     326     342     ---     ---

STKF:    .2543   .4390   .0509   .4784   .0611   .1623   .5545   .2862   .1130   .0620   .6544   .2861     ---     ---
STCT:   588.46 1014.03  194.06 2765.22   18.32  402.37 1438.72  777.01  242.84   84.89  431.68  164.84     ---     ---

UNKF:    .1433   .0452   .0093   .0511   .0007   .0738   .0265   .0001   .0078   .0002   .0774   .0010     ---     ---
UNCT:   331.56  104.46   35.42  295.25     .22  182.89   68.80     .24   16.84     .32   51.04     .58     ---     ---
UNBG:     2.95    2.57     .98    2.28     .18    1.74    3.04    5.52    1.14     .42     .89     .60     ---     ---

ZCOR:   1.3048  1.4381  2.0061  1.5456  3.9095  1.0729  1.1709  1.1484  1.0941  1.1992  1.1808  1.1990     ---     ---
KRAW:   .56344  .10302  .18252  .10677  .01177  .45452  .04782  .00031  .06934  .00373  .11825  .00353     ---     ---
PKBG:  113.266 41.6888 37.2975 130.257 2.21103 105.973 23.5975 1.04375 15.7533 1.75341 58.0413 1.96671     ---     ---

we obtain about 270 PPM of Cl.
john
Title: Re: Questions about MAN background use
Post by: Julien on November 15, 2016, 10:29:10 AM
Many thanks, John! For the price - of course - that I gladly accept. However, this is not yet my most complicated run, you got to wait my new idea for fast, precise and accurate monazite analysis (and other REE minerals ;) 30+ elements, expecting to use MAN, TDI, n-th point, multipoint bkg... Potentially also multiple analytical conditions (trace vs major) and use of EDS... This got to be causing other troubles, so get ready :D :D :D

And thanks A LOT for these fixes! Effectively it works great now!

About the Kaersutite standard, the MAN is here used on this secondary standards (and many many more) to indeed check for the presence of an unlisted element. My periclase for instance contains some Fe (not so much a surprise), but also Al (and maybe Si), around 130-180 ppm Al, and is clearly visible on the MAN plot (data from a "regular" TAP crystal)!

(https://probesoftware.com/smf/gallery/1_25_11_19_8_17_48.png)

I might also remind other readers that peak interference will obviously also be a problem. I am here thinking of the analysis of REE minerals, for which multiple interferences exists and the MAN will pick it! And here is again another Wonderful MAN power: once you identified the peak interference, you can just use the data acquired on your standards for the MAN. No data are lost!

Let's recap:
- Identification of impurities or unrecognized element in standard at the ~100 ppm level maybe lower (??? to check ???)
- Cut your analysis time in half
- Allow identification of peak interference, and unusable MAN bkg data due to this interference can then be use for the interference correction itself!
- No worry about potential interferences on background.

I still wonder what (a) the long term stability is, (b) what is the variability, and (c) what is the error on the calibration curve (it should be possible to calculate an error envelope on the MAN fitting line / curve, using the repeated background measurement on the standards). I am getting some nice data on the long term reproducibility as I type, I might one day share this... Just need time to compile a huge set of data covering 3 month of testing and many standards. There are still some behavior on the MAN fits I cannot explain with impurity in std or peak interference, notably on the REE business... Got some idea, though (problem of absorption edges in the standard?)... More to come soon - hopefully!

Cheers to the PfE Master!

Julien
Title: Re: Questions about MAN background use
Post by: Probeman on November 15, 2016, 11:32:18 AM
And thanks A LOT for these fixes! Effectively it works great now!

You are most welcome.  It is a pleasure to work with so many experts such as yourself.  As someone once said: it takes a village!   :)

I still wonder what (a) the long term stability is, (b) what is the variability, and (c) what is the error on the calibration curve (it should be possible to calculate an error envelope on the MAN fitting line / curve, using the repeated background measurement on the standards). I am getting some nice data on the long term reproducibility as I type, I might one day share this... Just need time to compile a huge set of data covering 3 month of testing and many standards. There are still some behavior on the MAN fits I cannot explain with impurity in std or peak interference, notably on the REE business... Got some idea, though (problem of absorption edges in the standard?)... More to come soon - hopefully!

The error on the MAN calibration curve regression is discussed in detail in my recent Amer. Min. paper here:

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

However, I can summarize:

1. Because we generally only measure the standards for the MAN calibration curve once per analytical session or mapping run, the regression error on the MAN fit *must* be treated as an accuracy error, as opposed to a precision error.   Yes, if we remeasured the MAN regression curve for each point analysis or each mapping pixel, then we would need to include the MAN regression error as a precision issue.  But no one would ever re-run the MAN calibration for every analysis or pixel!  We need to think carefully about this as it is not an intuitive conclusion, but it is (surprisingly) correct.  If you don't agree, please read the above paper (see tables 3a, 3b and 3c in particular), and maybe also read this post here:

http://probesoftware.com/smf/index.php?topic=307.msg3190#msg3190

2. The stability of the measured continuum intensities over time are exceptionally good so far as I have seen, mostly because we are measuring the intensities at the on-peak positions when the element is *not* present. Therefore there is no peak, only a smooth x-ray continuum.

3. In fact, if one re-measures the MAN curve within a single probe run, any changes in the continuum intensities over time are automatically applied to the unknown samples using the built-in drift correction in PfE, just as the primary and interference standards are drift corrected with multiple standard sets! But since the MAN intensities are not actually on a peak (though they are *at* the peak position!), the stability is much better than the primary standards or the interference standards. Especially better than the interference standard intensities, where the interfering intensities are often measured on the *side* of a peak (causing the the spectral overlap!)  :o

4. That said, a difference in detector bias voltage or PHA window, could change the absolute intensity of the continuum for the MAN curves, so I generally re-measure both the primary standards and the MAN standards for each new run or re-run.  It only takes a few minutes as the primary standards and the MAN standards are often the same standard (though not for the same element!).

5. However, if you are only utilizing MAN standards for major and even minor elements, you can probably skip re-measuring the MAN standards, but as I said above, it won't hurt to re-measure them and it only takes a few minutes for typical run of 5 or 10 elements.

6. Finally, absorption edges in the MAN standards are automatically taken care of by performing an absorption correction on the continuum intensities. This is because each MAN standard absorbs a particular continuum energy depending on the composition of that MAN standard. This was John Armstrong's contrbution to the paper. If you want to see the effect of absorption edges in the MAN curve, just turn off the continuum absorption correction in the Assign MAN Fits dialog.  There are also examples in the above Amer. Min. paper for Na Ka and K Ka with and without the continuum absorption correction.  The absorption correction is generally only noticable at low energies.

john
Title: Re: Questions about MAN background use
Post by: glennpoirier on November 16, 2016, 06:11:16 AM
Hi John,
I'm using the newest version of PfE (11.6.9) and I'm getting some odd behaviour when I'm trying to assign man fits, I'm getting some errors about missing standards at the start, but then when I get to the window and verify the fits and hit OK the display cycles through  all the elements  generates a warning  ("Warning no man standards have been assigned yet to calculate the man background fit  on spectrometer 2 on crystal TAP at 20 keV"  which is odd because Na on spectro 2 is not part of this particular sample) and stops. The only way to get out of the MAN assignment and fit window is to hit cancel, which I assume cancels the man fit. Is this a bug or is my run not set up properly?

Cheers

Glenn
Title: Re: Questions about MAN background use
Post by: John Donovan on November 16, 2016, 08:09:21 AM
I'm using the newest version of PfE (11.6.9) and I'm getting some odd behaviour when I'm trying to assign man fits, I'm getting some errors about missing standards at the start, but then when I get to the window and verify the fits and hit OK the display cycles through  all the elements  generates a warning  ("Warning no man standards have been assigned yet to calculate the man background fit  on spectrometer 2 on crystal TAP at 20 keV"  which is odd because Na on spectro 2 is not part of this particular sample) and stops. The only way to get out of the MAN assignment and fit window is to hit cancel, which I assume cancels the man fit. Is this a bug or is my run not set up properly?

Hi Glenn,
This is because of Julien's issue above where he had multiple samples with different elements, but he still wants all of the MAN fits to be assigned to *all* MAN elements in *all* samples in the run.

So, yes. The new behavior of the software is to go through all samples in the entire run (if they are not disabled), and check for missing MAN assignments.  So if you are getting warnings for a sample you don't care about, just disable it and re-load the MAN fits. Or acquire at least one MAN standard for that element with missing MAN standards.

Sorry for the change in behavior, but because of the potential of multiple sample setups with different or duplicate MAN elements, I had to check all samples in the probe run (unless they have been disabled).
john
Title: Re: Questions about MAN background use
Post by: Probeman on November 16, 2016, 09:55:45 AM
Hi Glenn,
I was thinking that instead of disabling the offending samples so they don't get included in the MAN fit assignments, one could also just use the disable quant flag for the specific element causing the problem in the Elements/Cations dialog.  But when I look closer, although I am checking for the disable acquisition flag, I am not checking for the disable quant flag.

But I wonder if you can utilize the disable acquisition flag for the offending element, in the offending samples, to avoid the missing MAN standard warnings?   I note that one can disable acquisition on a specific element on a specific sample, so long as it doesn't have any data...
john
Title: Re: Questions about MAN background use
Post by: Ery Hughes on February 20, 2017, 03:00:59 PM
Hi there,

I'm using MAN backgrounds for analysis of hydrous basaltic glasses as it reduces the analysis time by half reducing the chance of beam damage (also running TDI in case there still is beam damage). Just wanted to check that a specified by difference element (H in this case) is included in the iterative calculation of the mean atomic number?

Thanks!

Ery
Title: Re: Questions about MAN background use
Post by: John Donovan on February 20, 2017, 03:11:06 PM
Hi there,

I'm using MAN backgrounds for analysis of hydrous basaltic glasses as it reduces the analysis time by half reducing the chance of beam damage (also running TDI in case there still is beam damage). Just wanted to check that a specified by difference element (H in this case) is included in the iterative calculation of the mean atomic number?

Thanks!

Ery

Hi Ery,
Good question.  Here is how it works:

The average Z for the standards used in the MAN fit is calculated (as expected) based on the composition of the standards as defined in the standard.mdb database.  So as long as the standard composition never changes, the average Z will always be the same.

However for unknowns, we have to utilize the average Z from the calculated composition. So, the average Z calculation for MAN includes the measured elements and also the specified elements whether they be by stoichiometry or by difference. So yes.

More details are in my recent trace MAN paper:

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

Of equal importance is the fact that when calculating water (or any element) by difference (or by stoichiometry), one must include these elements by difference in the matrix correction, as is the case with Probe for EPMA. See the paper attached to this post, comparing water by difference included and not included in the matrix correction:

http://probesoftware.com/smf/index.php?topic=61.msg4303#msg4303

john
Title: Re: Questions about MAN background use
Post by: John Donovan on February 20, 2017, 10:29:03 PM
Hi Ery,
I just realized that you can see the calculated Z-bar or average Z in two places in Probe for EPMA. First here in the log window output:

Un   27 MAM IW2 C4-ext-1
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 20.0  Beam Size =   10
(Magnification (analytical) =   8000),        Beam Mode = Analog  Spot
(Magnification (default) =     1267, Magnification (imaging) =   1267)
Image Shift (X,Y):                                         .00,    .00
Number of Data Lines:   6             Number of 'Good' Data Lines:   6
First/Last Date-Time: 03/13/2007 06:29:57 PM to 03/13/2007 06:49:54 PM
WARNING- Using Exponential Off-Peak correction for p ka
WARNING- Using Time Dependent Intensity (TDI) Element Correction

Average Total Oxygen:       43.852     Average Total Weight%:  100.331
Average Calculated Oxygen:  43.852     Average Atomic Number:   13.324
Average Excess Oxygen:        .000     Average Atomic Weight:   22.489
Average ZAF Iteration:        3.00     Average Quant Iterate:     3.00

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction

And also here in the Analyze! window:

(http://probesoftware.com/smf/gallery/1_20_02_17_10_24_23.png)

The average Z value will change visibly as the specified concentrations or elements by difference are modified.
Title: Re: Questions about MAN background use
Post by: Ben Buse on April 10, 2017, 02:09:50 AM
Hi,

I've just noticed something. When you have elements on multiple spectrometers - and your viewing the MAN curves individually (not something you would normally do - only for testing, comparing spectrometers.. etc). The MAN is wrong for those standards which contain a high abundance of the element on multiple spectrometers.

e.g. If I view Al individually  for Al2O3 and have it on 3 spectrometers.
Total is 189.46 (3*47.5 plus oxygen 47.075) and z-bar is 11.761

Whereas if I aggregate the spectrometers - Total is 100% and Z-BAR is correct 10.666

This is not a problem for analysis - for you'd never use something with 190% total, BUT something to be aware of when doing such tests

Ben
Title: Re: Questions about MAN background use
Post by: Ben Buse on April 10, 2017, 02:40:20 AM
Hi John,

I think I missing something obvious - but using the custom output #8 (MAN) - what's the difference in units for intensity - I can't get them to match.

(http://probesoftware.com/smf/gallery/453_10_04_17_2_37_19.png)

(http://probesoftware.com/smf/gallery/453_10_04_17_2_37_32.png)

The intensity scale is difference. But if I divide rawcnt by seconds and nA it does not help (e.g. 8/10sec/20nA).

Also 520 Al-metal looks different

Thanks

Ben
Title: Re: Questions about MAN background use
Post by: John Donovan on April 10, 2017, 08:49:59 AM
Hi Ben,
The difference is that the raw MAN intensities output to a file are *not* corrected for continuum absorption, but the intensities in the MAN plot are corrected for continuum absorption.

Try comparing the raw intensities to the raw plot, by unchecking the Correct for Continuum Absorption checkbox.

That doesn't mean that I have gotten something mixed up somewhere!    :D
john
Title: Re: Questions about MAN background use
Post by: John Donovan on April 10, 2017, 09:07:09 AM
I've just noticed something. When you have elements on multiple spectrometers - and your viewing the MAN curves individually (not something you would normally do - only for testing, comparing spectrometers.. etc). The MAN is wrong for those standards which contain a high abundance of the element on multiple spectrometers.

e.g. If I view Al individually  for Al2O3 and have it on 3 spectrometers.
Total is 189.46 (3*47.5 plus oxygen 47.075) and z-bar is 11.761

Whereas if I aggregate the spectrometers - Total is 100% and Z-BAR is correct 10.666

This is not a problem for analysis - for you'd never use something with 190% total, BUT something to be aware of when doing such tests

Hi Ben,
Yes, when one has a 190% total, how should one calculate the matrix correction (or average Z) for such a non-physical situation?  Answer: any way you feel like!  ;D

The reason the average Z calculation is off when the spectrometers are not aggregated in your example is (I think) because you have several times the Al (from three spectrometers) relative to the specified oxygen (from the standard database), so the average Z is biased towards Al (Z = 13), rather than oxygen (Z = 8 ). 

Try analyzing it in Analyze! using the stoichiometric oxygen option (in Calculation Options dialog).
john
Title: Re: Questions about MAN background use
Post by: Ben Buse on April 10, 2017, 09:19:58 AM
Hi John,

The difference is that the raw MAN intensities output to a file are *not* corrected for continuum absorption, but the intensities in the MAN plot are corrected for continuum absorption.

Thanks  - that makes sense - and was it!


Try analyzing it in Analyze! using the stoichiometric oxygen option (in Calculation Options dialog).
john

Thanks - that worked - keeping Al and O in proportion - great suggestion

Ben
Title: Re: Questions about MAN background use
Post by: Ben Buse on April 20, 2017, 09:33:53 AM
Hi,

I just found what I was looking for - on the MAN output to excel you have both

rawcnt: data uncorrected for absorption.
corcnt: data corrected for absorption

Thanks

Ben
Title: Re: Questions about MAN background use
Post by: John Donovan on April 20, 2017, 04:10:22 PM
I just found what I was looking for - on the MAN output to excel you have both

rawcnt: data uncorrected for absorption.
corcnt: data corrected for absorption

Yes, that's right.  In fact it also outputs all the matrix corrections for those MAN standards so you could also work backwards from the corrected counts...

Note that years ago I originally tried a continuum specific correction from NIST (because the continuum correction should be different from the bulk correction due to the anisotropy of the continuum emission), but it gave worse results than the bulk correction, so the bulk matrix correction term is what we currently use for the MAN continuum absorption correction.
john
Title: Re: Questions about MAN background use
Post by: Heather Lowers on August 01, 2017, 08:17:57 AM
Is there an option to output the intercept, slope, curvature, Rel % Deviation for the MAN fits for all the elements in a run, and maybe even which standards are being used?  Playing around with different standards, off peak positions, forcing straight line versus not, etc.  Be nice to have these values easily tabulated.
Title: Re: Questions about MAN background use
Post by: Probeman on August 01, 2017, 10:31:21 AM
Is there an option to output the intercept, slope, curvature, Rel % Deviation for the MAN fits for all the elements in a run, and maybe even which standards are being used?  Playing around with different standards, off peak positions, forcing straight line versus not, etc.  Be nice to have these values easily tabulated.

Currently these parameters are output from the Output | Save Custom Analysis Output | Save Custom Analysis Format #8 (MAN):

LINE        Data file line number
SNUM        Sample number (standard number)
SNAM        Sample name (standard name)
ZBAR        Sample average atomic number
RAWCNT      Raw count intensity
CORCNT      Corrected count intensity (absorption corrected)
ZEDCOR      Atomic number correction factor
ABSCOR      Absorption correction factor
FLUCOR      Fluorescence correction factor
ZAFCOR      Total ZAF correction factor
ONTIM       On-peak (MAN) counting time
BEAM        Beam current in nA
BEAMCUR     Beam current (combined condition samples)


And if you put the software in DebugMode from the Output menu, you will see this output in the log window:

Elements:
      si      fe      mg      ca       p      al      na      ba       k      ti

MAN Assignments:
     835     835     336     374     336      12     835     336     358     336
      12      12     374     835     374      14      12     358     835     358
      22      14     835      14     835      27      14      12      12     374
      27      22      14      22      12      28      22      14      14     835
      28      28      22      28      14     285      27      27      22      12
     285     285      27       0      22       0      28      28      27      14
       0       0      28       0      27       0     285     160      28      27
       0       0       0       0      28       0       0     285     160      28
       0       0       0       0       0       0       0       0     285     160
       0       0       0       0       0       0       0       0       0     285
BackgroundTypes:
     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN     MAN
MAN Fit Orders:
       2       2       2       2       2       2       2       2       2       2
MAN Absorption Correction Flags:
      -1      -1      -1      -1      -1      -1      -1      -1      -1      -1
MAN Counts:
    74.1    21.7    13.9    29.4     3.5    16.7    22.1    44.1    30.3     1.3
    26.1     6.2    16.2    92.0     3.6    27.2     9.4    47.4    81.6     1.6
    51.7     6.1    22.4    26.3     9.3    32.1     6.8    42.3    25.5     1.9
    55.3     9.5    13.9    43.0     3.3    30.3     8.1    44.1    24.0     8.8
    58.4    15.3    15.7    59.7     3.0    29.4     8.3    93.4    39.2     1.2
    50.0     8.4    17.6      .0     5.5      .0     7.8    94.5    53.7     1.2
      .0      .0    14.5      .0     6.9      .0     9.2    49.2    54.8     3.4
      .0      .0      .0      .0     6.3      .0      .0    55.5    32.0     3.5
      .0      .0      .0      .0      .0      .0      .0      .0    34.4     1.4
      .0      .0      .0      .0      .0      .0      .0      .0      .0     2.0

MAN Fit Coefficients:
 -14.766 -3.2199 -6.5750 -8.5227 -.40542 30.2930 .112198 -.54570 -5.1947 .052925
 5.84314 .946438 2.68385 3.62923 .482494 -.80475 1.00449 3.86722 3.24887 .100007
 -.05119 -.00766 -.02100 -.02692 -.00311 .097303 .019536 -.00100 -.02401 .002169
Title: Re: Questions about MAN background use
Post by: Probeman on August 01, 2017, 10:38:11 AM
And this output as well:

MAN fit data and coefficients for si
Order 2, npts 6
StdAss:      835      12      22      27      28     285
Z-bars:  45.8151 10.4267 16.3920 22.9433 23.7170 14.4794
Counts:  74.1008 26.1434 51.6858 55.3129 58.4085 50.0244
AbsCor:  1.96292 1.57869 1.28689 1.61488 1.68766 1.17433
Counts:  145.454 41.2723 66.5140 89.3238 98.5737 58.7449
Coeffs:  -14.745 5.84054 -.05111

MAN fit data and coefficients for fe
Order 2, npts 6
StdAss:      835      12      14      22      28     285
Z-bars:  45.8151 10.4267 10.8047 16.3920 23.7170 14.4794
Counts:  21.6734 6.21936 6.07033 9.48054 15.2525 8.44972
AbsCor:  1.10816 .996548 .998913 1.03724 1.00089 1.02129
Counts:  24.0175 6.19789 6.06373 9.83355 15.2662 8.62964
Coeffs:  -3.2217 .946670 -.00767

MAN fit data and coefficients for mg
Order 2, npts 7
StdAss:      336     374     835      14      22      27      28
Z-bars:  11.0372 11.9907 45.8151 10.8047 16.3920 22.9433 23.7170
Counts:  13.8886 16.2342 22.3551 13.8539 15.7346 17.5643 14.4872
AbsCor:  1.54794 1.44002 3.23244 1.38991 1.87119 2.72537 2.94422
Counts:  21.4987 23.3775 72.2615 19.2557 29.4423 47.8691 42.6536
Coeffs:  -6.5667 2.68299 -.02098

MAN fit data and coefficients for ca
Order 2, npts 5
StdAss:      374     835      14      22      28
Z-bars:  11.9907 45.8151 10.8047 16.3920 23.7170
Counts:  29.4093 91.9869 26.2621 42.9830 59.6713
AbsCor:  1.07150 1.10091 1.04570 1.00488 1.05021
Counts:  31.5120 101.269 27.4624 43.1929 62.6674
Coeffs:  -8.5125 3.62767 -.02687

MAN fit data and coefficients for p
Order 2, npts 8
StdAss:      336     374     835      12      14      22      27      28
Z-bars:  11.0372 11.9907 45.8151 10.4267 10.8047 16.3920 22.9433 23.7170
Counts:  3.49284 3.59269 9.28106 3.25934 3.04344 5.48866 6.90243 6.28710
AbsCor:  1.36107 1.34961 1.63430 1.35544 1.40684 1.16702 1.38028 1.42656
Counts:  4.75401 4.84874 15.1680 4.41783 4.28163 6.40539 9.52732 8.96890
Coeffs:  -.40611 .482553 -.00311

MAN fit data and coefficients for al
Order 2, npts 5
StdAss:       12      14      27      28     285
Z-bars:  10.4267 10.8047 22.9433 23.7170 14.4794
Counts:  16.7464 27.2437 32.0534 30.2572 29.4431
AbsCor:  1.95626 1.20535 2.01195 2.13817 1.31384
Counts:  32.7604 32.8382 64.4899 64.6951 38.6836
Coeffs:  30.2930 -.80475 .097303

MAN fit data and coefficients for na
Order 2, npts 7
StdAss:      835      12      14      22      27      28     285
Z-bars:  45.8151 10.4267 10.8047 16.3920 22.9433 23.7170 14.4794
Counts:  22.0557 9.42896 6.80209 8.13324 8.26629 7.81730 9.16492
AbsCor:  3.95005 1.49808 1.75421 2.60603 4.07311 4.48371 2.06884
Counts:  87.1213 14.1254 11.9323 21.1955 33.6695 35.0505 18.9608
Coeffs:  .115846 1.00402 .019550

MAN fit data and coefficients for ba
Order 2, npts 8
StdAss:      336     358      12      14      27      28     160     285
Z-bars:  11.0372 12.2316 10.4267 10.8047 22.9433 23.7170 12.6937 14.4794
Counts:  44.0832 47.4109 42.3110 44.0621 93.3551 94.4881 49.2239 55.5154
AbsCor:  .951038 .972255 .942275 .948707 .946385 .952120 .960851 1.00869
Counts:  41.9249 46.0955 39.8686 41.8020 88.3499 89.9640 47.2968 55.9981
Coeffs:  -.54606 3.86727 -.00100

MAN fit data and coefficients for k
Order 2, npts 9
StdAss:      358     835      12      14      22      27      28     160     285
Z-bars:  12.2316 45.8151 10.4267 10.8047 16.3920 22.9433 23.7170 12.6937 14.4794
Counts:  30.2908 81.6375 25.5278 23.9502 39.1737 53.7147 54.8469 31.9706 34.4008
AbsCor:  1.04931 1.14161 1.05343 1.06993 1.01340 1.06181 1.07488 1.05296 1.05273
Counts:  31.7845 93.1984 26.8917 25.6251 39.6985 57.0348 58.9537 33.6638 36.2146
Coeffs:  -5.1908 3.24845 -.02400

MAN fit data and coefficients for ti
Order 2, npts 10
StdAss:      336     358     374     835      12      14      27      28     160     285
Z-bars:  11.0372 12.2316 11.9907 45.8151 10.4267 10.8047 22.9433 23.7170 12.6937 14.4794
Counts:  1.28070 1.59672 1.94603 8.76543 1.19729 1.19741 3.37633 3.52606 1.44701 1.97932
AbsCor:  1.01933 1.04191 1.03182 1.04960 1.01001 1.01684 1.01439 1.02050 1.02978 1.08067
Counts:  1.30545 1.66364 2.00795 9.20017 1.20928 1.21758 3.42492 3.59834 1.49010 2.13899
Coeffs:  .053961 .099936 .002170
Title: Re: Questions about MAN background use
Post by: Heather Lowers on August 01, 2017, 02:16:59 PM
The forum...it does work  ;)
Title: Re: Questions about MAN background use
Post by: Ben Buse on September 05, 2017, 06:34:34 AM
Hi,

I was just doing MAN for fluorine, clearly a tricky element, it seems to work better without correction for continuum absorption

With absorption correction TiO2, SrTiO3, Cr2O3 plot much higher compared to Barite and HfO2

(http://probesoftware.com/smf/gallery/453_05_09_17_6_33_12.png)

(http://probesoftware.com/smf/gallery/453_05_09_17_6_33_25.png)

In the second image, only those standards containing Fe lie significantly above the curve - due to Fe La interference (see wavescan below). giving following.

(http://probesoftware.com/smf/gallery/453_05_09_17_6_41_38.png)

Removed Fe standards - TiO2 disappointingly low

(http://probesoftware.com/smf/gallery/453_05_09_17_6_37_03.png)
Title: Re: Questions about MAN background use
Post by: Probeman on September 05, 2017, 09:06:22 AM
Hi Ben,
Yes, I've seen this too.

Because there are so many elements (e.g., L lines) that interfere with fluorine, it is difficult to find a decent set of MAN standards that will work. I generally use the off-peak method for minor/trace fluorine.

An unrelated issue for oxygen is that almost any standard one could utilize for the oxygen MAN curve is oxidized. I have tried MAN calibrations for oxygen using Ge and Au, but haven't found an MAN standard useful at low Z.
john
Title: Re: Questions about MAN background use
Post by: Probeman on September 05, 2017, 10:39:04 AM
Hi Ben,
Also, on the issue of the low intensity for F Ka in TiO2, note that the MAC for F ka in Ti is quite large, around 14500 (actually that is for F Ka in pure Ti. In TiO2 the MAC is more like 13700).

So by not utilizing the continuum correction in the MAN curve you are significantly undercorrecting the F Ka intensity in TiO2.

Here is your F Ka MAN calibration curve at 20 keV (F Ka at 20 keV?), with the continuum absorption correction and with  the Fe bearing standards removed. As you point out there are some on-peak interferences from Fe L lines on the F Ka peak position.  So removing those gives us this:

(http://probesoftware.com/smf/gallery/395_05_09_17_10_29_25.png)

The high outlier is Cr2O3 and I would suspect a small interference from Cr L also (as I tell my students, if you have a high outlier in the MAN curve it is usually an interference or contamination- so just remove it from the fit- after all background is by definition the lowest thing we can measure).  So now we get this curve:

(http://probesoftware.com/smf/gallery/395_05_09_17_10_29_41.png)

It's not a terrible fit, but it is worth noting (as you did) that without the absorption correction the fit is better, but the TiO2 is way low as one would expect from the MAC.  It might be worth looking at a wavescan of F ka on your barite standard and see if there is anything unusual in the background shape.

This is worth further study I think.  It reminds me of something that Paul Carpenter once said: using the MAN background method is a good way to check for undeclared elements in one's standards.  See here for that discussion:

http://probesoftware.com/smf/index.php?topic=4.msg499#msg499

john
Title: Re: Questions about MAN background use
Post by: BenjaminWade on September 05, 2017, 07:00:10 PM
Hi all
I saw this post with interest. F is something that our Geo's always want to measure, and I have resigned myself to never using the MAN fit for it due to the many L line interferences on it when constructing MAN fits. More recently however we have started to quant map fluorine in micas (which needs correction for Fe and a small Mg II order correction for high Mg micas), so I went on a quest to find a set of standards that would work OK for creating a MAN fit for F. I have attached a couple of the latest with/without some higher Z stds. Its seems to work OK, but bear in mind this is not quanting super low level F. It seems to have reasonable accuracy when compared to spot analysis of the same mineral down to ~0.5 wt%.

Haven't had a chance to refine it any further yet though, although I am sure there are some better standards I can use on my other standard blocks to fit it a bit better now that I know what to expect.

If you are interested this is the list of standards populating that MAN fit:
Astimex albite
Astimex Barite
Astimex Sanidine
In-house kyanite standard
Astimex BN
P&H Orthoclase
P&H Corundum
P&H Periclase
Astimex Gold
Astimex Hafnium metal
Astimex Zinc metal
Astimex Germanium metal
Astimex Cuprite

Cheers

P.S. forgot to mention, is anyone else getting that weird display bug as seen in the first image in the MAN fits when they display errors..?
Title: Re: Questions about MAN background use
Post by: John Donovan on September 05, 2017, 08:55:55 PM
Hi Ben,
This is all good stuff.

I haven't looked into F by MAN myself, so the fact that you and Ben are investigating this is quite interesting to me.

I see the display bug, and it looks like it's related to the display of error bars.  I've seen this kind of thing before in other plots, so I will try to reproduce it myself so I can fix it, but if you don't mind could you send me your MDB file to my email?  It's not very reproducible because I just looked at 15 or so MAN plots and none of them show that issue so far...

Thanks!
john
Title: Re: Questions about MAN background use
Post by: BenjaminWade on September 05, 2017, 09:13:08 PM
Hi John
Yes its definitely related to displaying the error bars. You are right its a little random when it will happen or not. Sometimes after excluding a standard and updating the fit it will appear, sometimes not. Sometimes after zooming in and out on the MAN fit it will appear, sometimes not...
I will email you the dropbox link for the displayed MDB file

Cheers
Title: Re: Questions about MAN background use
Post by: Ben Buse on September 06, 2017, 02:30:09 AM
Thank you John and Ben, that's very helpful; Ben I think I'll try some of the metal standards you suggest; and John good point about TiO2 MAC.
Title: Re: Questions about MAN background use
Post by: Ben Buse on September 06, 2017, 05:17:13 AM
I wonder if its the very high MACs for F in Ti and Cr that are the problem when using absorption correction. I've tried it for TAP crystal where interferences no longer problem - such as Fe. And Ti and Cr still elevated. - Picture to be uploaded

I guess the point is for F when generating MAN curve, avoid interferences and high MACs where possible

Ben
Title: Re: Questions about MAN background use
Post by: Malcolm Roberts on September 06, 2017, 11:32:44 PM
About time I said something. Too quiet for too long. I've taken to always doing F by MAN along with everything else. Ben W... your ideas on stds for this are good and in line with those I tend to apply too. Interferences stick out like a dog's balls and can be removed easily, but make sure you've plenty of standards to give choice. I've been doing this routinely for plenty of apatites - along with the STDI corrections to sort out issues for F analysis on apatite (and restricting the counting time to 40 s) - and phyllosilicates. I make abundant use of references to provide confidence in what I am up to.
Title: Re: Questions about MAN background use
Post by: Probeman on September 08, 2017, 10:09:49 AM
Hi John
Yes its definitely related to displaying the error bars. You are right its a little random when it will happen or not. Sometimes after excluding a standard and updating the fit it will appear, sometimes not. Sometimes after zooming in and out on the MAN fit it will appear, sometimes not...
I will email you the dropbox link for the displayed MDB file

Cheers

Hi Ben,
I found and fixed the MAN display issue you noticed with regard to errors bars and the "Defaults" button.  You should be able to update later tonight and all should be good.
john
Title: Re: Questions about MAN background use
Post by: Probeman on September 08, 2017, 12:30:56 PM
About time I said something. Too quiet for too long. I've taken to always doing F by MAN along with everything else. Ben W... your ideas on stds for this are good and in line with those I tend to apply too. Interferences stick out like a dog's balls and can be removed easily, but make sure you've plenty of standards to give choice. I've been doing this routinely for plenty of apatites - along with the STDI corrections to sort out issues for F analysis on apatite (and restricting the counting time to 40 s) - and phyllosilicates. I make abundant use of references to provide confidence in what I am up to.

Hi Malc,
If you get a chance it would be interesting to see a few of your MAN plots for fluorine.
john
Title: Re: Questions about MAN background use
Post by: BenjaminWade on September 11, 2017, 10:43:54 PM
Hi all
Following on from Ben's data, I have collected a bit more data for F on PC0 and TAP xtals, and attached images of the MAN fits on PC0 and TAP with/without continuum correction. I think at least on my setup, I arguably get a better fit with absorption correction (esp. in the specific higher Z stds I am using).

Interestingly for both PC0 and LTAP, std 559 (TiO2) sits above the plot with continuum absorption correction ON, much like your data. As per the database there is a 6th/7th order overlap of Ti on F for PC0...buts its so miniscule and high order that it has to be inconsequential? There is no reported overlap for Ti on F for TAP?

On PC0, when the absorption correction is removed, the point sits far below the fitted line. Conversely on LTAP when absorption correction is removed the point sits in line with other data.

Any thoughts..?

Cheers
Title: Re: Questions about MAN background use
Post by: Probeman on September 11, 2017, 10:50:23 PM
It has to be an interference from Ti L or oxygen K. Anyone have a high precision scan of F Ka in TiO2 handy?
john
Title: Re: Questions about MAN background use
Post by: BenjaminWade on September 12, 2017, 05:16:32 PM
I have one and it's not super high resolution or super high count times (steps of 4 units, 4 sec/point), but I still can't see anything obvious in this scan on one of my TiO2?

Cheers
Title: Re: Questions about MAN background use
Post by: Malcolm Roberts on September 13, 2017, 12:56:01 AM
Here you go John... as requested. One of the more recent ones.......
Title: Re: Questions about MAN background use
Post by: Probeman on September 13, 2017, 07:30:55 AM
Hi Malc,
It would be really interesting to see how your TiO2 standard plots on this curve. Do you have a F ka MAN plot with TiO2?
John
Title: Re: Questions about MAN background use
Post by: Probeman on September 13, 2017, 07:46:55 AM
It would also be interesting to see how Ti metal plots up on these F Ka MAN curves, but it would be important that the Ti metal is freshly polished at least. The F Ka emission volume is very shallow, so the oxidation layer should be as thin as possible so the continuum absorption calculation is accurate.
Title: Re: Questions about MAN background use
Post by: Probeman on September 13, 2017, 11:50:01 AM
With regard to Ben Wade's MAN plots for F Ka on TAP and the TiO2 outlier, here are some more of my wandering thoughts.

1. The MACs for F Ka in TiO2 are quite large.  For F Ka in Ti the tables MACs (from CalcZAF) are:

MAC value for F Ka in Ti =   14588.35  (LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV)
MAC value for F Ka in Ti =   14540.00  (CITZMU   Heinrich (1966) and Henke and Ebisu (1974))
MAC value for F Ka in Ti =        .00  (MCMASTER McMaster (LLL, 1969) (modified by Rivers))
MAC value for F Ka in Ti =   14986.59  (MAC30    Heinrich (Fit to Goldstein tables, 1987))
MAC value for F Ka in Ti =        .00  (MACJTA   Armstrong (FRAME equations, 1992))
MAC value for F Ka in Ti =   14277.71  (FFAST    Chantler (NIST v 2.1, 2005))
MAC value for F Ka in Ti =   14500.00  (USERMAC  User Defined MAC Table)

and for F ka in O they are:

MAC value for F Ka in O =   12439.63  (LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV)
MAC value for F Ka in O =   12390.00  (CITZMU   Heinrich (1966) and Henke and Ebisu (1974))
MAC value for F Ka in O =        .00  (MCMASTER McMaster (LLL, 1969) (modified by Rivers))
MAC value for F Ka in O =   11927.75  (MAC30    Heinrich (Fit to Goldstein tables, 1987))
MAC value for F Ka in O =        .00  (MACJTA   Armstrong (FRAME equations, 1992))
MAC value for F Ka in O =   11863.62  (FFAST    Chantler (NIST v 2.1, 2005))
MAC value for F Ka in O =   12400.00  (USERMAC  User Defined MAC Table)

I don't have Ben's MDB file handy at the university, but yesterday from home I tried selecting the lowest MAC table values (FFAST), and the MAN fit for TiO2 (#559) was still about the same amount over the trend line.  So it doesn't seem possible that the MAC could be off that much.

Interestingly if we look at the calculated MAN absorption corrections as seen here (from running PFE in DebugMode):

MAN fit data for Mg ka, SP4 TAP, 15 keV
     Std       J  MANSet    Npts   Z-bar     Cps  AbsCor
     504       1       1       1 14.3913 .715813 1.58141
     501       2       1       2 10.7106 .523931 1.49128
     541       3       1       3 12.0184 .548867 1.43226
     559       4       1       4 16.3937 .584618 1.83249   <- TiO2
     578       5       1       5 20.5879 .668368 2.41281
     701       6       1       6 10.7190 .618357 1.33443
     503       7       1       7 13.4430 .615176 1.54753
     549       8       1       8 6.12880 .349537 1.25008
     571       9       1       9 11.7470 .557961 1.40367
     575      10       1      10 10.6460 .638117 1.31164
     589      11       1      11 14.0000 .831370 1.09576
     594      12       1      12 4.00000 .280255 .964030
     602      13       1      13 27.0000 .713668 3.01841
     619      14       1      14 21.0000 .834364 1.82118
     514      15       1      15 26.6522 .592982 3.27371

we can see that the largest corrections are for F Ka in some of the other standards. So it could be the MAN continuum absorption correction, but why is TiO2 more of an outlier than the other standards with larger corrections?

Note: many years ago I attempted to apply a true continuum absorption correction using Myklebust's continuum expression, but I got worse regression results than just using the normal phi-rho-z bulk absorption correction...
Title: Re: Questions about MAN background use
Post by: John Donovan on November 29, 2017, 10:37:45 PM
I split off the rest of the discussion regarding this F Ka ROI mystery peak artifact on TAP crystals (and possibly related standards containing Ti) to a new topic:

http://probesoftware.com/smf/index.php?topic=992.0

This is because we suspect this mystery peak to be a diffraction artifact of some kind.  Another topic of interest could also be this one:

http://probesoftware.com/smf/index.php?topic=611.0

on JEOL H-type crystal artifacts, or this one on peak shape changes over time:

http://probesoftware.com/smf/index.php?topic=854.0

john
Title: Re: Questions about MAN background use
Post by: JohnF on July 17, 2018, 07:00:57 AM
There are times (like right now) where I have been using a MAN fit I created days ago, and there is no need to go thru revising it. Someone is asking me to show/prove that it as good as I say it is. However, I see no way where I can simply show the display. Nor is there any where where I can find a listing of which standards I ended up using for each element MAN fit, nor of the fit parameter.

Is there a feasible way that these plots could be stored somewhere? (There are many many Display options under the "Run" tab.) Likewise there are many List options under the same Run tab; might the MAN standard options be listed?   Or is all of that data volatile?
Title: Re: Questions about MAN background use
Post by: John Donovan on July 17, 2018, 07:40:00 AM
Hi John,
I don't see a problem with using the existing MAN plot dialog.  You don't have to "revise" anything, just click on each element to see the MAN plot for it, and optionally click the Copy to Clipboard button to capture the plot graphics to paste into a document or whatever.

If you accidentally change some assignments in the MAN dialog and don't want to have them saved, just click Cancel button instead of the OK button to exit.

Am I missing something?
john
Title: Re: Questions about MAN background use
Post by: JohnF on July 17, 2018, 07:52:08 AM
Roger.
Title: Re: Questions about MAN background use
Post by: JohnF on July 17, 2018, 08:05:22 AM
I am doing some quality control checking of MAN results at minor and trace el levels: Mg, Sr, Mn and Fe in carbonates (using defocused 20 micron beam). I have wavescan data to compare the MAN-predicted bkg counts with. Sr, Mn and Fe MAN numbers match nicely with the wavescan numbers. The particular sample which I am testing has a mean Z of 12.6.

From both wavescans and discrete background measurements on the sample (which has a very small distinct peak; backgrounds are clear), the background should be 12.5.

However, the MAN fitted background, using the continuum absorption correction, gives a background of 17, which doesn't seem correct. If I turn off the cont. abs. correction, there is a wonky curve but the value at a mean Z of 12.6 is closer to the actual measured background level.

(Note: conincidence that the carbonate Z is 12.6, and the actual back ground is 12.5 c/s/20nA)

Again all other 3 elements, Sr, Mn and Fe work great with the con. abs. corrected MAN values being what the wavescans show.

Could there be something weird going on for Mg?

MAN stds were acquired in normal acquisition mode (not TDI). Carbonates later were run in TDI.

Attached are 2 plots
Title: Re: Questions about MAN background use
Post by: Probeman on July 17, 2018, 08:29:47 AM
Hi John,
Both plots are correct.  But it is a little unintuitive, so good question!

The plotted (absorption corrected) MAN intensities in the Assign MAN Fits dialog are the "ideal" background intensities. They cannot be compared to actual measurements.  But by turning off the absorption correction in the MAN dialog, you are seeing the raw measured values, however which cannot be fitted together, because each MAN standard has different matrix physics.   But if the unknown matrix is the same as an individual MAN standard, then you can compare this "raw" intensity to off-peak measurements, as you observed. Please re-read the Donovan, et al. 2016 paper in Amer. Min for a complete explanation:

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

In short, this is because each MAN standard is a different matrix and therefore needs to be corrected for the specific emission line individually before fitting.  Then once we have the equation of fit for these "ideal" intensities for the MAN standards, we can apply that fit to an actual sample after it is "de-corrected" for the actual absorption in the sample.

If you want to compare the calculated MAN background intensity with off-peak measurements, see the procedure here:

http://probesoftware.com/smf/index.php?topic=4.msg189#msg189

Then compare the line in the output labeled "UNBG:". Which are the MAN *or* off-peak intensities for the sample.
john
Title: Re: Questions about MAN background use
Post by: Julien on January 28, 2019, 09:07:07 AM
Hi John,

It is my understanding that if we do have a MAN correction curve for an element, and if we do have analyzed an element with 2-point background, it should be possible to switch between the 2-point background correction and the MAN. And even if it is not the case, we could use the 2-point background for determining a MAN background correction curve.

My problem is that - for testing purpose - I want to switch between the 2-points background and the MAN background, yet I can NOT change the background type in elements/cations window. The background field are all grayed out, and I cannot change a thing...

(https://i.ibb.co/stYrhL0/Screenshot-2019-01-28-at-13-21-55.png) (https://ibb.co/jHXFd7c)

I do have checked the option "Use MAN correction for Off-peak measurement..." in menu Analysis, and I do have a correct set of MAN correction (the program indeed asked me to reset the MAN correction, which I did).

(https://i.ibb.co/fXG0f8N/Screenshot-2019-01-28-at-13-20-55.png) (https://ibb.co/zmHfp82)

(https://i.ibb.co/0y7PH1x/Screenshot-2019-01-28-at-13-24-27.png) (https://ibb.co/1GgHFBk)

Maybe I'm doing something wrong? Note that at first, I was using the “shared background” in this run. To enable the MAN background, I did the following:
Nonetheless, in each case (with shared bkg or with linear 2-pts bkg after resetting the MAN fit), the MAN option in elements/cations remain unavailable… Am I doing something wrong? Any help would be greatly appreciated!

Julien
Title: Re: Questions about MAN background use
Post by: John Donovan on January 28, 2019, 09:57:25 AM
Hi Julien,
I think you are basically doing it correctly.   You don't need to change anything in the Elements/Cations dialog. Those options are for the background *acquisition* type (we'll modify the description to make it more obvious!).

I don't quite understand how you are seeing the MAN curve fits if you acquired off-peak standards and the Use Off-Peak Elements for MAN Fits menu is unchecked.  Maybe you had it checked earlier at some point?

Anyway, see here for an explanation of using standards acquired using off-peak bgds, but for the MAN fit:

https://probesoftware.com/smf/index.php?topic=4.msg189#msg189

The steps to use MAN backgrounds based on your off-peak acquired standards, is to first check the Use Off-Peak Elements for MAN Fits menu and then assign the MAN fits.  This allows the program to use standards acquired with off-peak backgrounds, for the MAN assignments, by "throwing away" the off-peak measurements on those standards.

Next if your samples are acquired using MAN backgrounds you are done. But if your samples are off-peak, then you need to check the next menu down which is the Use MAN Correction for Off-Peak Elements menu. This will force the program to utilize MAN background corrections even if the sample (std or unk) data was acquired using off-peak backgrounds.

To get real fancy you can also check the Use Interpolated Off-Peaks for MAN Fit checkbox in the Analytical | Analysis Options dialog as described here:

https://probesoftware.com/smf/index.php?topic=987.0

With this method, first suggested by Ben Hanson at Corning, the program obtains the MAN background intensities by interpolating the off-peak measurements.  This option can be very useful when you want to use MAN backgrounds for faster acquisition (especially quant x-ray maps), but your standards are contaminated with traces of the element of interest, for example using MAN fits for O ka!

I hope this makes sense, but let me know if you are still having trouble.  Feel free to also send me your MDB file.
john
Title: Re: Questions about MAN background use
Post by: BenjaminWade on January 28, 2019, 03:43:02 PM
Hi John and all
My wish would be to be able to (post acquisition) mix and match elements with MAN and off-peak post acquisition rather than all one or the other... I am sure it probably wouldn't be simple to implement though...

Cheers
Title: Re: Questions about MAN background use
Post by: John Donovan on January 28, 2019, 05:07:36 PM
Hi John and all
My wish would be to be able to (post acquisition) mix and match elements with MAN and off-peak post acquisition rather than all one or the other... I am sure it probably wouldn't be simple to implement though...

Cheers

Hi Ben,
Yeah it would be more than a little bit of work, I'll have to think how it might be possible.   But you can always do what I do, which is decide which elements should be MAN and which elements should be off-peak *before* you acquire data!   ;)
john
Title: Re: Questions about MAN background use
Post by: Julien on January 31, 2019, 06:42:00 AM
Thanks John,

I agree with Ben and it might be possible if you would enable the background fields two-point, MAN, MPB... in the Elements/Cations window. Then you could ask your software to check which option is being selected in the Elements/Cations window, and if MAN is selected (and if a MAN correction is available), then it uses the MAN for the background and if the two-point option is selected, then it would use the two-points. This solution could be further extended (with certainly more work...) for the MPB and more specifically shared background. Right now, you have an option to enable or remove the shared background, but if you do have a shared background, and if the MPB option in Elements/Cations is set to MPB, then it uses the shared background. Otherwise it would use the classical two-point background or the MAN background. Of course, if you do so, the software should be able also to determine if (a) MAN background is available, and (b) if a set of MPB or shared background is available.

This solution might also add some more clarity: the user can simply check in the Elements/Cations to see what background correction is being used for that specific element, whereas the current solution (your answer to my question) is done by clicking an option in a menu.

Julien
Title: Re: Questions about MAN background use
Post by: JakubHaifler on June 07, 2019, 01:40:40 AM
Hi,
I have been trying to use some advanced measurement (or rather processing) techniques, i.e. multi-point background fitting, interference corrections and (now) mean atomic number background calculation WITHOUT Probe for EPMA (Punk’s not dead!). Although it is quite demanding, I have been quite successful in some example tasks (in all these approaches) having only measured intensities, CalcZAF and MATLAB.

Measurement of Pb in my complex material (REE-, actinide-, Zr-, Ti-, Nb-rich minerals) seems to be very complicated. Recently, I have been trying MAN method. So, here I share my experience with fitting the Z vs background curve without PfE, but I also have a question.

I carefully selected some standards for background measurement at PbMb position (c. 58010 on LPET of our Cameca SX100). The intensities were measured at 15kV, 180 nA for 240-300 s.   

The approach of how to calculate the continuum absorption is mentioned in Ware and Reed (1973), which is referred in Donovan et al. (2016). However, for better understanding, I recommend a book “Scanning Electron Microscopy and X-ray Microanalysis” by Goldstein and co-workers and its electronic supplement, where the method of Philibert, Duncumb and Heinrich is explained in detail. At first, I tried to calculate their example on NiKa absorption in Ni-Fe alloy in Excel, then I got the same results in CalcZAF. Continuum absorption is calculated similar to the absorption of a characteristic line with the exception of zero concentration of the emitter in the former case. The values of f(chi), which is the fraction of the generated x-rays, which were not absorbed, can be simply and quickly calculated in CalcZAF. First of all I selected Philibert/Duncumb-Reed matrix correction and MAC table (Ware and Reed refer to Heinrich, 1966; however MAC’s for PbMb are not published in this set – see below). Then, I loaded a standard from our dataset, e.g. GdPO4. Subsequently, I added PbMb line to the calculation with Pb concentration set to zero. After the calculation, the value of f(chi) for PbMb can be found in results. This approach seems to work well.

(https://probesoftware.com/smf/gallery/1783_07_06_19_1_29_52.jpeg)

Here is my average Z vs corrected background intensity diagram:

(https://probesoftware.com/smf/gallery/1783_07_06_19_1_32_31.jpeg)

Somewhat enigmatic for me are the deviations of the two Zr-bearing standards, ZrO2 and pure Zr. I have studied a WDS scan of a wide region around PbMb performed on a pure Zr, but there should be absolutely no noticeable zirconium (or some contaminant) peak at that position – according to the scan as well as according to the x-ray spectral database. Any idea for this behaviour?

(https://probesoftware.com/smf/gallery/1783_07_06_19_1_34_05.jpeg)

According to calculated absorption corrections, Zr is a somewhat stronger absorber (f(chi)=0.55) than most other standards, at least those with similar Z. Surprisingly, the raw background intensities before the correction seem to be much closer to the general trend of the most other standards (except for TiO, which shows much higher f(chi)=0.85 = much weaker absorber that the others, which usually have c. 0.6-0.7 or lower).

(https://probesoftware.com/smf/gallery/1783_07_06_19_1_35_40.jpeg)

One observation I find interesting or surprising: I tried to explain the deviation of the Zr-bearing standards in my diagram. So, I decided to compare the values of all the MAC’s of PbMb in Zr (originally, I selected Heinrich, 1966) among various datasets. Then, I found out, that there are no values for absorption of PbMb in the dataset of Heinrich, 1966 and CalcZAF automatically took MAC’s from a different dataset (McMaster, I think). The MAC's for PbMb in Zr from different datasets, however, are relatively similar, so the backgrounds of Zr-bearing still deviate. 

One more question, on PfE – is the continuum absorption correction done using the approach by Philibert (1963) as referred in Ware and Reed (1973) in all cases or can it be switched to a different approach?

Best regards, Jakub Haifler   
Title: Re: Questions about MAN background use
Post by: Probeman on June 07, 2019, 03:11:18 PM
Hi Jakub,
Wow.  Very impressive work.  I must say, I think you would really have a blast with PFE on your instrument, maybe someday?

As to why the Zr containing materials are behaving like this, there are a lot of parameters involved here so it will be interesting to figure this out.  As you point out, the mass absorption coefficient values being the most dominant for this correction. I will have to try some MAN measurements myself, using the Pb Mb emission line, and see what I can see, but in the meantime I will try to answer a few of your questions as much as possible.

But first I ran a *simulation* of these MAN curves in Probe for EPMA (in demo mode) and got this MAN curve for your standard calibration materials:

(https://probesoftware.com/smf/gallery/395_07_06_19_2_38_24.png)

Turning off the continuum absorption correction I got this:

(https://probesoftware.com/smf/gallery/395_07_06_19_2_38_39.png)

Note that stds 40 (Zr oxide) and 540 (Zr metal) both drop below the curve without the absorption correction, so that is consistent with your measurements.  The default MAC table in Probe for EPMA (and CalcZAF) is Henke (for emission lines less than 10 keV). Looking in CalcZAF we can see the MACs for this emission line in Zr:

MAC value for Pb Mb in Zr =    2580.40  (LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV)
MAC value for Pb Mb in Zr =        .00  (CITZMU   Heinrich (1966) and Henke and Ebisu (1974))
MAC value for Pb Mb in Zr =    2750.53  (MCMASTER McMaster (LLL, 1969) (modified by Rivers))
MAC value for Pb Mb in Zr =    2620.36  (MAC30    Heinrich (Fit to Goldstein tables, 1987))
MAC value for Pb Mb in Zr =        .00  (MACJTA   Armstrong (FRAME equations, 1992))
MAC value for Pb Mb in Zr =    2528.02  (FFAST    Chantler (NIST v 2.1, 2005))
MAC value for Pb Mb in Zr =    2620.00  (USERMAC  User Defined MAC Table)

The Henke MAC is quite a bit smaller than the MAC30 table value which you used. So this might cause the over correction you are seeing for the Zr containing materials.

As to what continuum absorption correction is being utilized in Probe for EPMA for the MAN curve fit, it is whatever absorption correction is currently selected in the ZAF/Phi-Rho-Z method.  Originally we tried several absorption corrections specifically intended for continuum emissions, but we got worse results than just using the absorption corrections from the currently selected matrix correction.  So now the MAN method in PFE just uses the absorption correction from whatever matrix correction has been selected.

By the way, you might want to contact Julien Allaz, Mike Jercinovic and Karsten Goemann as both have worked on using the MAN method with complex high Z materials. All three will be at the QMA 2019 conference in Minnesota later this month and all will be giving presentations on various background correction methods including MAN, off-peak and MPB (multi-point backgrounds) and Karsten will present the MPB method with "shared" backgrounds (that is utilizing normal off-peak measurements from other emitters measured on the same spectrometer).

Also see these topics:

https://probesoftware.com/smf/index.php?topic=4.msg17#msg17

https://probesoftware.com/smf/index.php?topic=9.msg7764#msg7764

Or maybe your materials are slightly contaminated in Pb? I can assure you that some of the Smithsonian REE standard are contaminated with Pb!  Note how my MAN curves excluded these materials automatically because it knows from the standard composition database that these materials contain Pb!
john
Title: Re: Questions about MAN background use
Post by: JakubHaifler on June 12, 2019, 03:40:24 AM
Hi John,

thank you very much for your answer. As you wrote, PfE would be a great help, particularly for such complicated measurements I am doing at the moment. On the other hand, these are extraordinary and are only for my research, I do not perform such calculations for routine measurements. So, the increased effort is acceptable in this case. Unfortunately, I am not powerful enough to affect what software and hardware equipment we have in our laboratory. But as you wrote – maybe sometime. I hope, my little DIY is not going to break your business with PfE  :), but may allow some people, particularly students, to try how the method works.

As for my data: I did some additional measurements. Something is clearer now, something not. I did two 5-point background measurements on Zr (btw, we have two pure Zr standards – intensities in both somewhat differ, but neither is compatible with my MAN curve). I observe that intensities at PbMb position are c. 7% higher than what I would expect from the exponential fit through the other four points. So, some contamination seems to be highly probable (may be Pb, Mo, Bi, Nb... at this position). On the contrary, the theoretical background at PbMb calculated from the fit remains incompatible with the MAN curve.

(https://probesoftware.com/smf/gallery/1783_12_06_19_3_29_13.jpeg)

So, after additional measurements, following 12 standards are compatible within a single fit: YAG, Fe2O3, YPO4, LaPO4, GdPO4, GdAlO3, MnTaO4, CrTa2O6, CaWO4, Hf, Ta, W. I excluded TiO and Ti, as TiKb(II) shows overlap with PbMb. Similar to Zr, Sn also have PbMb-intensity higher than a fit through 4 other points nearby, so the contamination may also occur. Pure elemental standards Cr, Fe are not compatible with the MAN curve (they give higher PbMb-intensities), but I do not have additional data for resolving the reason.

(https://probesoftware.com/smf/gallery/1783_12_06_19_3_30_41.jpeg)

Very mysterious for me is the behaviour of cheralite, CaTh(PO4)2, intensity of which shows very deep “negative” anomaly. It has avg. Z of 51.158, but PbMb-intensity of only 1.24 cps/nA (based on 3 measurements). CaWO4 and MnTaO4 with very similar avg. Z give c. 1.53-1.54, which is the theoretical, MAN-curve-compatible, background value at that Z.

I read some older comments on the MAN method (from about 2013). According to them, the method works well for low-avg Z matrices, while not so well for high-avg Z, which is not a very good message for me. However, I have not found much information on that. I think, my MAN curve looks relatively nice (of course, I have not explained incompatibility of Fe, Cr and particularly cheralite yet). Moreover, the used standards are relatively simple compounds (pure elements, binary or ternary compounds). So, I guess, the complex natural material is going to be much more tricky.
I am somewhat confused of a more general question of whether there are some serious limits and irregularities in this method. Or what should be the main pitfall for the high-Z matrices?
One example: from the many posts in this thread we can see that the MAN curve is usually fitted by a linear/exponential/2nd order polynomial, fluently increasing, function. This seems to be a rule: the higher Z, the higher the (corrected) background intensities. But for example in this post, John's data show a concave curve (which John explains there). 
https://probesoftware.com/smf/index.php?topic=4.msg1070#msg1070   

Best regards, Jakub     
Title: Re: Questions about MAN background use
Post by: Probeman on June 12, 2019, 11:16:58 AM
Hi Jakub,
Please understand that there is nothing extraordinary about using the MAN background correction.  My guess is that, at least for geologists who utilize the software, the MAN correction is used almost all the time, at least for the major and minor elements (note that one can utilize a mix of MAN and off-peak elements for any given sample setup). The reason for it being utilized so often, is that the MAN correction saves so much time time (and improves precision) on major, and even minor elements, where very small accuracy errors in the MAN calibration curve, are generally smaller than the precision of the peak intensity measurement. 

For typical geological samples with K emission lines and low to moderate average Z materials, this is usually the case.  In my experience with typical silicates and oxides, the MAN background correction is accurate down to 200-300 PPM, even without a blank correction.  The use of the MAN correction with higher Z matrices and high Z emission lines is still an area of active investigation.   But maybe a little "MAN" history would be appropriate here...

The very first rationale for the MAN considerably preceded my own initiation to EPMA, and was invented to deal with EPMA instruments which utilized fixed monochromaters for commonly measured elements. For example, on my first EPMA instrument, which I inherited at UC Berkeley in the 1980s, it had 4 fixed monochromaters (for Si, Fe, Ca and Al), and 4 tunable spectrometers for another 4 elements. The reason of course being that fixed monochromaters *cannot* be de-tuned for the off-peak measurement!  So people came up with the idea of utilizing a calibration curve of standards which did not contain the elements of interest, for the background correction for these "fixed" spectrometers. Which meant of course that using the MAN correction, we could measure 8 elements in 10 seconds!  This was very useful as you might imagine for beam sensitive materials.

Since then the MAN background correction has been significantly improved and as my Amer. Min. 2016 paper showed, the MAN background correction can even be utilized for improving sensitivity for trace elements.  Basically this results in a 40% or more improvement in detection limits, in 1/2 the acquisition time, because only the on-peak intensity is measured.  And of course, of interest to you, one automatically avoids off-peak interferences, because there are no off-peak measurements when using the MAN correction!  In addition, interpolation issues with non-linear backgrounds and/or absorption edges simply disappear with the MAN method because, again, only the on-peak position is utilized.

But even though the MAN method can result in better accuracy than off-peak methods when such off-peak issues are present, the main caveat for the MAN method remains accuracy (at least at trace levels), because we are not performing a direct measurement of the continuum on the sample.  Therefore for ultimate accuracy, the MAN method is commonly combined with the so-called "blank" correction. The blank correction works well for relatively simple matrices where suitable (usually synthetic) blank samples can be obtained, e.g., quartz, zircon, pyrite, TiO2, Fe2O3, Fe3O4, etc.  Of course for complex materials, zero blanks may be difficult to obtain. But it is also of interest to note that the blank correction as implemented in Probe for EPMA, can be applied to non-zero blank samples, so there is that option.

Now having said all that, the remaining practical difficulties of the MAN method is obtaining pure standards that do not contain the element of interest.  As you pointed out in the linked post, many standards have not been properly characterized for trace elements. For example, I have two synthetic zircons, one appears to have a couple hundred PPM more phosphorus than the other. I have heard from many colleagues that utill they started utilizing the MAN method, they had not realized how contaminated some of their standard materials were.  On the other hand, the MAN method can teach us quite a lot that we didn't already know about our standards!

Just as a small aside, Ben Hanson at Dow Corning came up with a really crazy idea for the MAN method, which is to utilize the *off-peak* interpolated intensities for the MAN calibration curve, or "offset MAN" as he called it, as described here:

https://probesoftware.com/smf/index.php?topic=987.msg6447#msg6447

"Crazy as a fox" as they say!  The reason he requested this because he found that many of his standards weren't as pure as he thought they were. I thought it was a good idea for another reason: sometimes I've wanted to utilize the MAN method for oxygen analysis, and it's difficult to find standards that don't contain even trace oxygen (since we live in an ocean of oxygen)!  Whatever.

It boils down to this: almost without exception, the lowest intensity one can measure (by definition!) is the background.  Yes, there are possible sample and/or detector absorption edges and "holes" in the background continuum due to secondary Bragg diffraction (e.g, the hole in the continuum seen in FeS2 near the Au Ma position and in some PET crystals at the Ti Ka position, though there is still some debate about this), but these are fairly rare. So in general, any standards that fall above the general trend of the MAN calibration curve are either from contamination (from the element being present), or an interference from another analytical peak.

The general strategy at the user level is to simply remove those (higher intensity) offending standards from fit of the MAN curve. Now because you are conducting a bit of a research project here with your high Z materials, you are interested in exactly what is causing these outliers in the MAN calibration curve.  And that is great and you should pursue this line of inquiry because it is interesting and helpful for greater understanding of the details.

As to particular difficulties with high Z matrices, the main difficulty is due to the fact that the P/B ratios are worse for high Z matrices since from Kramers Law we know that we produce more continuum in higher Z materials. Second, when analyzing high Z emission lines, we are generally restricted to L or even M emissions and these are also typically lower P/B than K emissions. So combined this means that the calibration of the MAN curve is even more critical for high accuracy work in high Z materials, especially at low concentrations.

That said, there are advantages to using the MAN method even in complex high Z materials, as has been pointed out (no off-peak interferences and no interpolation). But I think other approaches such as the MPB (multi-point background) and even "shared" bgds can be useful for such matrices. I believe Karsten Goeman and Julien Allaz have published these methods and also have examples of these alternative off-peak methods posted elsewhere on the forum.
Title: Re: Questions about MAN background use
Post by: Probeman on February 10, 2021, 12:26:08 PM
Just wanted to point out that the MAN fit calculations in the Assign MAN Fits dialog in Probe for EPMA can be modified to utilize the more physically accurate electron fraction or Z fraction averaging method. Of course, this only pertains to average Z calculations for compounds.

That is to say, when compared to the traditional mass fraction based methods for calculating average Z. The mass fraction averaging method includes the mass of the neutrons, which has little to no effect on continuum (or backscatter) production, and therefore adds arbitrary errors to average Z calculations. See attached abstract from 2019 below (login to see attachments).

Here is an example for the Ca Ka emitter which is a fairly moderate energy x-ray using the traditional mass fraction average Z method:

(https://probesoftware.com/smf/gallery/395_10_02_21_12_09_19.png)

And here is the same data, utilizing the electron or Z fraction method, specifically Z^0.7 electron fraction averaging:

(https://probesoftware.com/smf/gallery/395_10_02_21_12_09_50.png)

Why the 0.7 exponent? It's because that is necessary to account for the screening of nuclear charge by the inner orbital electrons in higher Z atoms.

In fact this is why we see the backscatter vs. Z trend start to "curve over" around atomic number 30:

(https://probesoftware.com/smf/gallery/395_10_02_21_12_24_38.png)