Recent Posts

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1
Probe for EPMA / Re: Si in glasses
« Last post by bgarcia on July 01, 2020, 11:05:30 am »
I've definitely been using the coating correction. For the originally Au-coated glasses, it made a difference, but not enough seemingly. That probably stems from the fact that they were coated in another lab with a questionable amount of Au (~5nm estimate apparently not correct).

Getting all standards and unknowns coated in C, by me, has made a huuuge difference. On my unknowns, the stoichiometric vs calculated oxygen is off by less than 2 wt%, so I think I'm doing something right.

And thanks for that link; it clears up a lot of questions I had about the coating correction. Cheers!
2
General EDS Issues / Re: Quantitative EDS References From NIST
« Last post by NicholasRitchie on July 01, 2020, 10:00:16 am »
Another reference that people might find useful:  While it is called "Proposed practices for validating the performance of instruments used for automated inorganic gunshot residue analysis", it really is about validating the performance of an SEM/EDS system.  It is available (for free) from here: https://www.sciencedirect.com/science/article/pii/S2468170920300400?via%3Dihub
3
General EDS Issues / Re: Improving EDS Analysis
« Last post by NicholasRitchie on July 01, 2020, 09:57:51 am »
The Forensics Chemistry journal isn't necessarily on your radar but there is a paper in there https://www.sciencedirect.com/science/article/pii/S2468170920300400?via%3Dihub that I published recently with some GSR colleagues that is relevant to this topic.  It basically discusses validation procedures to ensure that an SEM/EDS system is performing and QC procedures to check and document the performance.

NIST paid the tariff so it is available for free under the Creative Commons license.
4
Probe for EPMA / Re: Si in glasses
« Last post by John Donovan on July 01, 2020, 08:57:30 am »
I've been working all week on this, and I think that the largest source of error for the USGS glasses was that they were Au-coated.  :-\  That's it.

Obviously I've done a lot of other things to tighten up my probe work, but taking off the Au and coating with C puts Si-Al-Mg compositions within 3% or less variance. I wish it would have been higher on my "Things To Check" list!

I'm also finding that for Na K, mineral standards seem to work better when analyzing glass SRMs as unknowns.

Now I just have the original challenge of how to analyze a glass. Thanks for all the help and time, John!

Hi Ben,
Well that would indeed explain your quant issues if some standards were carbon coated and some were gold coated.

By the way, Probe for EPMA does include a coating correction for differences in coating between the standards and the unknowns, even different coatings for different standards as described here:

https://probesoftware.com/smf/index.php?topic=23.msg1256#msg1256

The main caveat is that one needs to know the actual coating thickness (and density) of each standard (and unknown). If these are known (and it's not so easy to be sure), the coating correction works quite well.  But if you read through the topic you can see that even determining the density of carbon in a carbon coat is not straight forward.

That is why we usually just make sure that we either coat both the standards and unknowns at the same time (in which case we can ignore the coating correction), or we make sure to use the same coater on both standards and unknowns and use a thickness monitor or other method to ensure reproducibility for the coating.
5
Probe for EPMA / Re: Si in glasses
« Last post by bgarcia on June 30, 2020, 03:32:21 pm »
I've been working all week on this, and I think that the largest source of error for the USGS glasses was that they were Au-coated.  :-\  That's it.

Obviously I've done a lot of other things to tighten up my probe work, but taking off the Au and coating with C puts Si-Al-Mg compositions within 3% or less variance. I wish it would have been higher on my "Things To Check" list!

I'm also finding that for Na K, mineral standards seem to work better when analyzing glass SRMs as unknowns.

Now I just have the original challenge of how to analyze a glass. Thanks for all the help and time, John!
6
We've recently been working with Julien Allaz to fix the way in which the oxygen-halogen correction is applied to standards in Probe for EPMA as first reported by Ben Wade:

https://probesoftware.com/smf/index.php?topic=1247.msg9305#msg9305

During that time we realized that these recent halogen correction issues for standards (when oxygen is calculated by stoichiometry rather than a fixed concentration), are somewhat similar to the excess oxygen calculation using the Droop method of charge balance (hey- it's all about charge balance!). Again only for standard samples, when oxygen is calculated by stoichiometry (as opposed to added by fixed concentration from the standard database).

Previously, for the excess oxygen from ferric iron calculation, we simply did not allow one to perform this excess oxygen calculation for standards (only for unknown samples). But we realized yesterday that it's the same issue in that a double correction is applied for standards if the excess (or deficit) oxygen is already included in the standard database, and the excess (or deficit) oxygen correction for ferric oxygen (or halogen equivalence) is applied in Probe for EPMA, *and* the oxygen in the standard is calculated by stocihiometry.  Whew!

So what we did was enable the calculation of excess oxygen for standards (just as we have had for the halogen correction), so if the standard analysis is using the default fixed oxygen concentration from the standard database, all is well.  This can be seen is this output:

Excess Oxygen From Ferric Iron was not Included in the Matrix Correction (because oxygen was not calculated by cation stoichiometry)

St  395 Set   1 Magnetite U.C. #3380, Results in Elemental Weight Percents
 
ELEM:        F      Fe      Al      Mg      Mn       O
TYPE:     ANAL    ANAL    SPEC    SPEC    SPEC    SPEC
BGDS:      LIN     LIN
TIME:    20.00   20.00     ---     ---     ---     ---
BEAM:    29.98   29.98     ---     ---     ---     ---

ELEM:        F      Fe      Al      Mg      Mn       O   SUM 
    10    .051  71.844    .201    .072    .054  27.803 100.025
    11    .073  72.195    .201    .072    .054  27.803 100.398
    12    .026  72.209    .201    .072    .054  27.803 100.365

AVER:     .050  72.083    .201    .072    .054  27.803 100.263
SDEV:     .023    .207    .000    .000    .000    .000    .207
SERR:     .014    .119    .000    .000    .000    .000
%RSD:    46.70     .29     .00     .00     .00     .00

PUBL:     n.a.  72.080    .201    .072    .054  27.803 100.210
%VAR:      ---   (.00)     .00     .00     .00     .00
DIFF:      ---   (.00)    .000    .000    .000    .000
STDS:      835     395     ---     ---     ---     ---

STKF:    .1715   .6779     ---     ---     ---     ---
STCT:    57.18  228.22     ---     ---     ---     ---

UNKF:    .0002   .6779     ---     ---     ---     ---
UNCT:      .07  228.22     ---     ---     ---     ---
UNBG:      .32     .49     ---     ---     ---     ---

ZCOR:   2.2854  1.0633     ---     ---     ---     ---
KRAW:    .0013  1.0000     ---     ---     ---     ---
PKBG:     1.23  466.16     ---     ---     ---     ---

Ferrous/Ferric Calculation Results:
        Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3 
    10        .000        .000        .000        .000
    11        .000        .000        .000        .000
    12        .000        .000        .000        .000

AVER:         .000        .000        .000        .000

But in the case where the user changes the standard analysis calculation to calculate oxygen by stoichiometry, the program will now zero out the excess oxygen (just as it now does for the deficit oxygen from halogens), and not perform a double correction as seen here:

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Oxygen Equivalent from Halogens (F/Cl/Br/I) was Subtracted in the Matrix Correction
Excess Oxygen From Ferric Iron Calculated and Included in the Matrix Correction
Charge Balance Method of Droop (1987), Total Cations= 3.00, Total Oxygens= 4.00

St  395 Set   1 Magnetite U.C. #3380, Results in Elemental Weight Percents
 
ELEM:        F      Fe      Al      Mg      Mn       O
TYPE:     ANAL    ANAL    SPEC    SPEC    SPEC    CALC
BGDS:      LIN     LIN
TIME:    20.00   20.00     ---     ---     ---     ---
BEAM:    29.98   29.98     ---     ---     ---     ---

ELEM:        F      Fe      Al      Mg      Mn       O   SUM 
    10    .051  71.838    .201    .072    .054  27.742  99.957
    11    .073  72.206    .201    .072    .054  27.908 100.514
    12    .026  72.215    .201    .072    .054  27.859 100.427

AVER:     .050  72.086    .201    .072    .054  27.836 100.299
SDEV:     .023    .215    .000    .000    .000    .085    .300
SERR:     .014    .124    .000    .000    .000    .049
%RSD:    46.75     .30     .00     .00     .00     .31

PUBL:     n.a.  72.080    .201    .072    .054  27.803 100.210
%VAR:      ---   (.01)     .00     .00     .00     .12
DIFF:      ---   (.01)    .000    .000    .000    .033
STDS:      835     395     ---     ---     ---     ---

STKF:    .1715   .6779     ---     ---     ---     ---
STCT:    57.18  228.22     ---     ---     ---     ---

UNKF:    .0002   .6779     ---     ---     ---     ---
UNCT:      .07  228.22     ---     ---     ---     ---
UNBG:      .32     .49     ---     ---     ---     ---

ZCOR:   2.2865  1.0633     ---     ---     ---     ---
KRAW:    .0013  1.0000     ---     ---     ---     ---
PKBG:     1.23  466.16     ---     ---     ---     ---

Ferrous/Ferric Calculation Results:
        Ferric/TotalFe   FeO        Fe2O3    Oxygen from Fe2O3 
    10        .674      30.092      69.266       6.940
    11        .678      29.937      69.966       7.010
    12        .671      30.591      69.252       6.938

AVER:         .674      30.207      69.495       6.963


So now, the code for dealing with this is seen here:

Code: [Select]
If sample(1).Type% = 1 Then
analysis.WtPercents!(chan%) = ConvertTotalToExcessOxygen!(Int(1), sample(), stdsample())
If UseOxygenFromHalogensCorrectionFlag And sample(1).OxideOrElemental% = 1 Then
If analysis.WtPercents!(chan%) < 0# Then analysis.WtPercents!(chan%) = 0#  ' zero out oxygen deficit from standard database
End If
If sample(1).FerrousFerricCalculationFlag And sample(1).OxideOrElemental% = 1 Then
If analysis.WtPercents!(chan%) > 0# Then analysis.WtPercents!(chan%) = 0#  ' zero out oxygen excess from standard database
End If

' For unknowns, use specified oxygen weight percent
Else
analysis.WtPercents!(chan%) = stdsample(1).ElmPercents!(ip%)
End If

One possible remaining issue is when one has both halogens and ferric iron present in a standard, and one tries to calculate oxygen by stoichiometry, the excess/deficit oxygen might not be handled perfectly. In this case, we would just say, simply use the default to calculate oxygen elementally (fixed concentration from the standard database) and all will be well.  But I think it will work, because if both the oxygen-halogen correction *and* the ferric iron calculation correction are turned on, you'll get a zero value for excess/deficit oxygen, so it should all work.

Remember, in all cases, the calculations for unknown samples are handled just fine. This is all pretty complicated we know, but please ask us any questions you may have.

In the meantime, update Probe for EPMA from the Help menu and these options are all available now.
7
Probe for EPMA / Re: Halogen correction
« Last post by John Donovan on June 28, 2020, 11:47:39 am »
Julien Allaz and I have been discussing the oxygen-halogen correction in PFE and wanted to share our recent efforts to improve the way PFE handles oxygen-halogen containing samples.  It's a little complicated.

First of all it should be noted that the program properly handles the oxygen-halogen correction on unknown samples for all situations, particularly when oxygen is calculated by stoichiometry. It also handles the situation where an unknown is calculated by simply specifying the amount of oxygen. But of course in that case, the oxygen-halogen correction has already been applied.

PFE also handles the situation where a standard is analyzed and the oxygen in the standard database was *not* already corrected for the oxygen-halogen equivalence (#282). As seen here:

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Oxygen Equivalent from Halogens (F/Cl/Br/I), Subtracted in the Matrix Correction

St  282 Set   2 Fluor-phlogopite (synthetic), Results in Elemental Weight Percents
 
ELEM:        F      Si      Mg      Al       K       O
TYPE:     ANAL    SPEC    SPEC    SPEC    SPEC    CALC
BGDS:      LIN
TIME:    20.00     ---     ---     ---     ---     ---
BEAM:    29.99     ---     ---     ---     ---     ---

ELEM:        F      Si      Mg      Al       K       O   SUM 
     6   8.453  20.002  17.307   6.404   9.281  38.218  99.665
     7   8.766  20.002  17.307   6.404   9.281  38.086  99.846
     8   8.536  20.002  17.307   6.404   9.281  38.183  99.713

AVER:    8.585  20.002  17.307   6.404   9.281  38.163  99.741
SDEV:     .162    .000    .000    .000    .000    .068    .094
SERR:     .094    .000    .000    .000    .000    .039
%RSD:     1.89     .00     .00     .00     .00     .18

PUBL:    9.020  20.002  17.307   6.404   9.281  41.775 103.789
%VAR:    -4.83     .00     .00     .00     .00   -8.65
DIFF:    -.435    .000    .000    .000    .000  -3.612
STDS:      835     ---     ---     ---     ---     ---

Note that the "published" (PUBL) amount of oxygen from the standard database is based on the assumed cation stoichiometry, and is not correct, but the halogen correction does make the proper correction.

Previously if the standard composition was already corrected for the oxygen-halogen correction as in the following standard (#284), the program performed a double correction of the oxygen-halogen equivalence (see above posts). However, Julien and I added some code that checks for a negative excess oxygen from the standard database, and if it is negative, it zeros out the deficit oxygen before entering the matrix correction routine. The new code is seen here:

Code: [Select]
If sample(1).Type% = 1 Then
analysis.WtPercents!(chan%) = ConvertTotalToExcessOxygen!(Int(1), sample(), stdsample())
If UseOxygenFromHalogensCorrectionFlag And sample(1).OxideOrElemental% = 1 Then
If analysis.WtPercents!(chan%) < 0# Then analysis.WtPercents!(chan%) = 0#  ' zero out oxygen equivalence of halogen from standard database
End If

' For unknowns, use specified oxygen weight percent
Else
analysis.WtPercents!(chan%) = stdsample(1).ElmPercents!(ip%)
End If

Here is an example of a standard, already corrected for the oxygen equivalence of halogens, analyzed with the oxygen-halogen correction:

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Oxygen Equivalent from Halogens (F/Cl/Br/I), Subtracted in the Matrix Correction

St  284 Set   2 Fluor-phlogopite (halogen corrected), Results in Elemental Weight Percents
 
ELEM:        F      Si      Mg      Al       K       O
TYPE:     ANAL    SPEC    SPEC    SPEC    SPEC    CALC
BGDS:      LIN
TIME:    20.00     ---     ---     ---     ---     ---
BEAM:    30.01     ---     ---     ---     ---     ---

ELEM:        F      Si      Mg      Al       K       O   SUM 
     9   8.806  20.002  17.307   6.404   9.281  38.069  99.870
    10   8.832  20.002  17.307   6.404   9.281  38.059  99.885
    11   8.824  20.002  17.307   6.404   9.281  38.062  99.880

AVER:    8.821  20.002  17.307   6.404   9.281  38.063  99.878
SDEV:     .013    .000    .000    .000    .000    .006    .008
SERR:     .008    .000    .000    .000    .000    .003
%RSD:      .15     .00     .00     .00     .00     .01

PUBL:    9.020  20.002  17.307   6.404   9.281  37.980  99.994
%VAR:    -2.21     .00     .00     .00     .00     .22
DIFF:    -.199    .000    .000    .000    .000    .083
STDS:      835     ---     ---     ---     ---     ---

STKF:    .1715     ---     ---     ---     ---     ---
STCT:    59.95     ---     ---     ---     ---     ---

Note that both the published concentration of oxygen is corrected for in the standard database, and the stoichiometric oxygen in the standard is properly corrected as expected.

Part of the reason for this issue is that many, many years ago we decided to allow the user to handle the deficit (or excess) oxygen in the standard compositional database, but then include that deficit (or excess) oxygen in the matrix calculation. For example, when analyzing magnetite, the default is to include the excess oxygen by simply loading the speciifed oxygen concentration from the standard database.

But (and here it gets complicated), if the user decides to simply calculate oxygen by stoichiometry for this standard (instead of loading the specified oxygen from the standard database as is the default), the program automatically includes the deficit (or excess) oxygen from the standard database.

But if the standard composition in the standard database is already corrected for the deficit (or excess) oxygen, this results in an double correction during the matrix correction. The new code above should prevent this double correction.
8
Probe Image / Re: No more rainbows!
« Last post by Probeman on June 25, 2020, 07:16:41 pm »
Good to know.

Yeah, this fire color palette:

https://probesoftware.com/smf/index.php?topic=707.msg9302#msg9302

is essentially a thermal (incandescent) color palette with a little blue just before the black.
9
Probe Image / Re: No more rainbows!
« Last post by SteveSeddio on June 25, 2020, 12:28:51 pm »
This is slightly on the wrong board... but at customer request, we added (in Pathfinder x.x) an "incandescent" option to replace the rainbow scheme for COMPASS component maps.
It can be set in the NSSMachineSettings.ini file.
In the [Image] group.
Set UseIncandescent=1.


10
Probe for EPMA Utilities / Re: Grapher/Surfer Tips and Tricks
« Last post by Probeman on June 25, 2020, 10:35:08 am »
A few colleagues and I are writing up a paper on quant mapping and we decided to utilize a color palette that is intuitive even when printed in B&W and also helpful for color blind users. This "fire color" palette was developed by Greg Dumond at U Mass Amherst working with Julien Allaz and Mike Jercinovic:



Attached below are the .CLR files for use with Golden Software's Surfer app and also a PhotoShop palette (.ACT file).

Edit by John: Probably should also reference the "No More Rainbows!" topic started by Anette von der Handt:

https://probesoftware.com/smf/index.php?topic=1003.0
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