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1
EPMA Standard Materials / Re: Consensus K-Ratio Measurements
« Last post by John Donovan on May 15, 2022, 05:57:48 PM »
We added a new feature to Probe for EPMA to assist in the accurate acquisition of consensus k-ratios.

If you're like some people and utilized element setups from the SETUP.MDB element database or loaded a sample setup from a previous Probe for EPMA run, you probably loaded the element setups, then peaked the spectrometers, checked the PHA settings and maybe even re-ran a wavescan sample to check on your off-peaks, but that might not be enough.

Recently Probeman contacted us to let us know that although he did all of the above, when loading the element setups from previous runs, he neglected to note that the dead time constants for his WDS spectrometers had since been re-calibrated. Therefore that the stored elemental setups still referenced the old dead time constants, from prior to the dead time re-calibration.  And they should of course since they are a record of that calibration!  ::)

But to prevent this from happening again, in the latest version of Probe for EPMA, if one has updated the dead time constants in the SCALERS.DAT file since those element setups were saved, Probe for EPMA will now check for this and provide the following user dialog, if it finds that the dead time constants have been updated since then:



Therefore this new PFE update will allow one to utilize older element setups but with the new dead time calibrations from the SCALERS.DAT file.

Of course one can always manually update these dead time constants "after the fact" using the Analytical | Update Dead Time Constants menu dialog as described here:

https://probesoftware.com/smf/index.php?topic=1442.msg10641#msg10641
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Probe for EPMA Utilities / Re: Grapher/Surfer Tips and Tricks
« Last post by John Donovan on May 15, 2022, 05:43:05 PM »
I recently demonstrated the Surfer mapping output from Probe for EPMA for a customer that did not purchase our Probe Image quantitative mapping software yet.

As some of you know, Probe for EPMA provides quantitative mapping output for grids of single points or even random single points for display of quantitative mapping information as shown here:

https://probesoftware.com/smf/index.php?topic=943.0

https://probesoftware.com/smf/index.php?topic=60.0

However, we had not utilized this output feature for some time, and when I attempted to run the script for the customer in the latest Surfer version, it gave an error regarding the default color palette file. This error is now fixed in the latest Probe for EPMA version.

For those of you unfamiliar with this PFE output, it is performed using the Output | Output Standard and Unknown XY Plots menu and the dialog selections are as shown:



When this auto-generated script is run in the Surfer Scripter application, one of the many output types are as shown here:



Also this modified code now automatically handles the JEOL "anti-Cartesian" stage axes orientations for recent Surfer version supporting "reverse" X/Y axses orientations.

Yes, the acquisition of many points for this output type is slower than quantitative mapping in Probe Image and CalcImage, but one can obtain amazing sensitivity and with the MAN background acquisition, it goes faster than one would think.

Think of it as high sensitivity, low spatial resolution mapping...
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by John Donovan on May 13, 2022, 06:29:12 PM »
Quote from: Brian Joy on May 13, 2022, 05:53:06 PM
Quote from: John Donovan on May 13, 2022, 08:30:05 AM
Of course for most amphiboles, it's a relatively small effect, but for Fe-Ti oxides and magnetites the effect is surprisingly large. For hematites/magnetites it's a >1% change in the Fe concentrations:

https://probesoftware.com/smf/index.php?topic=92.msg8593#msg8593

Remember that I was the one who tried to point this out to you several years ago after I'd built this capability into my own program (i.e., automated recalculation of Fe2O3/FeO for simple oxides and silicates), but you hadn't yet in PFE.

Yes, I remember that very well.  In fact, it was one of the reasons we implemented this feature in CalcZAF for off-line calculations and in Probe for EPMA for on-line data acquisition.  I only mentioned the small matrix effect of ferric oxygen in amphiboles because you said you hadn't implemented it yet in your code. But I agree, it's a surprisingly large effect in Fe-Ti oxides. 

In fact, it's similar in magnitude to the effect on Si of including water by difference into the matrix correction for hydrous glasses (versus just applying the water by difference calculation in Excel without a subsequent matrix re-correction):

https://probesoftware.com/smf/index.php?topic=11.msg235#msg235
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by Brian Joy on May 13, 2022, 05:53:06 PM »
Quote from: John Donovan on May 13, 2022, 08:30:05 AM
Of course for most amphiboles, it's a relatively small effect, but for Fe-Ti oxides and magnetites the effect is surprisingly large. For hematites/magnetites it's a >1% change in the Fe concentrations:

https://probesoftware.com/smf/index.php?topic=92.msg8593#msg8593

Remember that I was the one who tried to point this out to you several years ago after I'd built this capability into my own program (i.e., automated recalculation of Fe2O3/FeO for simple oxides and silicates), but you hadn't yet in PFE.
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by Brian Joy on May 13, 2022, 05:38:32 PM »
Quote from: AndrewLocock on May 13, 2022, 01:25:31 PM
Quote from: AndrewLocock on May 13, 2022, 08:30:47 AM
...it is possible to force the ratio of Fe3+/ΣFe to 0 (all ferrous iron), or to 1 (all ferric iron), or to any particular value-of-interest
...the user can force the use of any, some, or all of the normalization schemes....

One does not have to rely on the algorithm.

As quoted above, it is possible to make one's own selections.
There are thus at least 7 options: all ferrous iron, all ferric iron, some arbitrary fixed value, or any 1 of the 4 normalization schemes. And of course, one could invoke the use of 2 or more normalization schemes....

Yes, there is no way to extract a highly-accurate estimate of Fe3+/ΣFe from an amphibole analysis performed solely by routine EPMA.
That is the essence of the discussion of Schumacher (1997), and the reason behind the normalization schemes discussed therein.

Propagation of error in mineral formulas is dealt with Giaramita & Day (1990) American Mineralogist 75, 170-182.
It is not germane to the calculation of Fe3+/ΣFe itself, but rather the utility (accuracy and precision) of the calculation's outcome.

The constituent that most greatly affects the calculation of Fe3+/ΣFe is, in fact, OH-content.
Many classical analyses of amphibole will report insufficient amounts (as discussed by Leake 1968 in GSA Special Paper 98) or excess amounts (probably due to inclusions of other minerals), and of course EPMA does not directly determine H at all.

I've attached a paper by DeAngelis and (Owen) Neill (2012, Computers and Geosciences 48:134-142), who wrote a program that implements the error treatment of Giaramita and Day (1990).  Anyone who recalculates analyses for Fe2O3 should explore the propagated counting error.

Determination of H2O was difficult even in classical analytical work.  My only point in emphasizing systematic error in SiO2 is that I'm not sure that people necessarily consider this issue when recalculating for Fe2O3.
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by AndrewLocock on May 13, 2022, 01:25:31 PM »
Quote from: AndrewLocock on May 13, 2022, 08:30:47 AM
...it is possible to force the ratio of Fe3+/ΣFe to 0 (all ferrous iron), or to 1 (all ferric iron), or to any particular value-of-interest
...the user can force the use of any, some, or all of the normalization schemes....

One does not have to rely on the algorithm.

As quoted above, it is possible to make one's own selections.
There are thus at least 7 options: all ferrous iron, all ferric iron, some arbitrary fixed value, or any 1 of the 4 normalization schemes. And of course, one could invoke the use of 2 or more normalization schemes....

Yes, there is no way to extract a highly-accurate estimate of Fe3+/ΣFe from an amphibole analysis performed solely by routine EPMA.
That is the essence of the discussion of Schumacher (1997), and the reason behind the normalization schemes discussed therein.

Propagation of error in mineral formulas is dealt with Giaramita & Day (1990) American Mineralogist 75, 170-182.
It is not germane to the calculation of Fe3+/ΣFe itself, but rather the utility (accuracy and precision) of the calculation's outcome.

The constituent that most greatly affects the calculation of Fe3+/ΣFe is, in fact, OH-content.
Many classical analyses of amphibole will report insufficient amounts (as discussed by Leake 1968 in GSA Special Paper 98) or excess amounts (probably due to inclusions of other minerals), and of course EPMA does not directly determine H at all.
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by John Donovan on May 13, 2022, 01:13:51 PM »
Quote from: Brian Joy on May 13, 2022, 12:38:42 PM
Quote from: AndrewLocock on May 13, 2022, 08:30:47 AM
As stated in Computers & Geosciences 62, 1–11:
“How should an algorithm determine which schemes are most appropriate for a given analysis? Hawthorne et al. (2012) showed that the constraints on the amphibole formula arising from the various cation normalization schemes could be treated as criteria. As the criteria are not each satisfied by every amphibole endmember, and as real analyses are imperfect, there will usually be deviations from the criteria. In the spreadsheet, for each of the four normalization schemes, the maximum magnitude of the deviations of the formula proportions from the following criteria is determined: Si < 8 apfu; non-H cations < 16 apfu; sum Si to Ca (+Li) < 15 apfu; sum Si to Mg (+Li) > 13 apfu; sum Si to Na > 15 apfu. The normalization schemes with the smallest maximum deviations are used. To allow for the imperfection of real data, a threshold of 0.005 apfu is used for the deviations, and for the separation of the normalization schemes.”

The spreadsheet therefore automatically determines which normalization scheme or schemes are appropriate, based on the smallest maximum deviations from the criteria listed above.

I'd rather see the results of all normalizations and then choose for myself while applying some petrological guidance.  There is no simple means of extracting an accurate value of Fe2O3 from an electron microprobe analysis of an amphibole.  This has been my point from the beginning.

And what about propagated counting error?  In addition, systematic error in SiO2 (due to choice of standard or matrix corrections) will contribute additional significant uncertainty.

You know what the good news is?  You don't have to use this ferrous/ferric amphibole method, and can instead export the data and use Andrew's spreadsheet externally, or even your own spreadsheet.  It's nice to have choices.   ;D

But since this feature has been requested by a number of our colleagues, and because we're so nice, we developed this method with Andrew's and Aurelien's help, and then implemented it in Probe for EPMA and CalcZAF for everyone, and made all the source code available.   8)

On counting errors the other good news is that because Probe for EPMA always calculates an average and standard deviation for each sample, along with the analytical sensitivity and t-test errors, these things can readily be estimated. As for accuracy propagation, one can simply select the "Use All Matrix Corrections" option in the Analyze! window in Probe for EPMA and/or the Calculate ZAF or Phi-Rho-Z Corrections window in CalcZAF, and observe the variation in the ferrous/ferric ratios due to matrix correction and/or MACs.

Pretty cool, hey?
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by Brian Joy on May 13, 2022, 12:38:42 PM »
Quote from: AndrewLocock on May 13, 2022, 08:30:47 AM
As stated in Computers & Geosciences 62, 1–11:
“How should an algorithm determine which schemes are most appropriate for a given analysis? Hawthorne et al. (2012) showed that the constraints on the amphibole formula arising from the various cation normalization schemes could be treated as criteria. As the criteria are not each satisfied by every amphibole endmember, and as real analyses are imperfect, there will usually be deviations from the criteria. In the spreadsheet, for each of the four normalization schemes, the maximum magnitude of the deviations of the formula proportions from the following criteria is determined: Si < 8 apfu; non-H cations < 16 apfu; sum Si to Ca (+Li) < 15 apfu; sum Si to Mg (+Li) > 13 apfu; sum Si to Na > 15 apfu. The normalization schemes with the smallest maximum deviations are used. To allow for the imperfection of real data, a threshold of 0.005 apfu is used for the deviations, and for the separation of the normalization schemes.”

The spreadsheet therefore automatically determines which normalization scheme or schemes are appropriate, based on the smallest maximum deviations from the criteria listed above.

I'd rather see the results of all normalizations and then choose for myself while applying some petrological guidance.  There is no simple means of extracting an accurate value of Fe2O3 from an electron microprobe analysis of an amphibole.  This has been my point from the beginning.

And what about propagated counting error?  In addition, systematic error in SiO2 (due to choice of standard or matrix corrections) will contribute additional significant uncertainty.
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Probe for EPMA / Re: Latest version changes for Probe for EPMA (and CalcImage) v. 13.1.2
« Last post by John Donovan on May 13, 2022, 08:49:00 AM »
Quote from: John Donovan on May 11, 2022, 09:24:41 AM
The latest version of Probe for EPMA implements Andrew Locock's amphibole recalculation code for the purposes of determining ferrous and ferric iron. Thanks to Andrew and Aurelien Moy who worked with us on this quite complicated code.

This expanded feature is found in the Analyze! window Calculation Options button dialog as seen here:



Remember, for in depth evaluation of your amphibole mineralogy, one should instead utilize the Locock spreadsheet output format (seen in the previous post) and utilize Andrew's recalculation spreadsheets externally to PFE.

But for the purposes of ferrous/ferric ratios these generic options seem to work well.  In case any one is interested in how we set Andrew's spreadsheet flags, we decided upon the following code:

Code: [Select]
' Sodic amphibole
If Droop_option_for_amphibole% = 1 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1

REQUIRE_SUM_SI_TO_CA_LE_15% = 0
REQUIRE_SUM_SI_TO_MG_GE_13% = 1
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 1

' Calcic amphibole
ElseIf Droop_option_for_amphibole% = 2 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1

REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 1
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0

' Na-Ca amphibole
ElseIf Droop_option_for_amphibole% = 3 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1

REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 1

' Fe-Mg-Mn amphibole
ElseIf Droop_option_for_amphibole% = 4 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1

REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0

' Oxo amphibole
ElseIf Droop_option_for_amphibole% = 5 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1

REQUIRE_SUM_SI_TO_CA_LE_15% = 1
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 0
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0

' Li amphibole
ElseIf Droop_option_for_amphibole% = 6 Then
ORTHORHOMBIC% = 0
USE_INITIAL_M3_OVER_SUM_M% = 0
If tipresent Then ESTIMATEOH2_2TI% = 1
If waterspecified Then REQUIRE_INITIAL_H2O% = 1

REQUIRE_SUM_SI_TO_CA_LE_15% = 0
REQUIRE_SUM_SI_TO_MG_GE_13% = 0
REQUIRE_SUM_SI_TO_NA_GE_15% = 1
REQUIRE_SUM_SI_TO_K_GE_15_5% = 0
End If

Please let us know if you have any questions.

In case any one is wondering how we decided on the amphibole recalculation flags for Andrew's code, see the attached documents from Andrew below showing the results of Andrew's investigations into which flags would be most appropriate for each amphibole type.

Again, if one prefers to set these amphibole flags manually, please utlize the Locock amphibole spreadsheet output menu by right clicking the sample(s) in the Analyze! window sample list.
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Discussion of General EPMA Issues / Re: Amphiboles normalization
« Last post by AndrewLocock on May 13, 2022, 08:30:47 AM »
The calculation of the proportion of ferric iron in an amphibole composition is most thoroughly examined by Schumacher (1997) in the Appendix 2 of the Leake et al. (1997) report on amphibole nomenclature. Table A-2 of Schumacher (1997) uses a particular analysis from Appendix 1 of Deer et al. (1966, p. 515); the subtitle of this latter appendix is “Calculation of a chemical formula from a mineral analysis, hornblende analysis”.

This topic is reprised in Appendix III: Calculation of Fe3+ and (OH) in Amphiboles of the Hawthorne et al. (2012) report on amphibole nomenclature. Appendix Table 1 of Hawthorne et al. (2012) uses the same analysis from Deer et al. (1966, p. 515)

For the Excel spreadsheet to classify chemical analyses of amphiboles following the IMA 2012 recommendations that I authored, the topics of formula normalization and Fe3+ estimation are discussed in the paper published in Computers & Geosciences 62, 1–11.

To clarify: in that spreadsheet it is possible to force the ratio of Fe3+/ΣFe to 0 (all ferrous iron), or to 1 (all ferric iron), or to any particular value-of-interest, by entering the appropriate wt% FeO and/or Fe2O3 values and setting the option “use initial M3+/ΣM? (TRUE or 1/FALSE or 0)” to True or to 1. (Recall the conversion wt% FeO = 0.8998085 Fe2O3).

However, in general, the ratio of Fe3+/ΣFe is not known a priori, and thus some sort of formula normalization must be used, following Schumacher (1997). In the spreadsheet, 4 schemes of cation normalization are possible (modified from Schumacher 1997 to include known Li-content):
1. Sum of all cations from Si to K = 16 apfu.
2. Sum of cations from Si to Na = 15 apfu.
3. Sum of cations (includes Li) from Si to Ca = 15 apfu.
4. Sum of cations (includes Li) from Si to Mg = 13 apfu.
Methods of estimation of Fe3+ contents of amphibole are generally inaccurate in comparison to measured values, but are usually better than no estimate at all.

As stated in Computers & Geosciences 62, 1–11:
“How should an algorithm determine which schemes are most appropriate for a given analysis? Hawthorne et al. (2012) showed that the constraints on the amphibole formula arising from the various cation normalization schemes could be treated as criteria. As the criteria are not each satisfied by every amphibole endmember, and as real analyses are imperfect, there will usually be deviations from the criteria. In the spreadsheet, for each of the four normalization schemes, the maximum magnitude of the deviations of the formula proportions from the following criteria is determined: Si < 8 apfu; non-H cations < 16 apfu; sum Si to Ca (+Li) < 15 apfu; sum Si to Mg (+Li) > 13 apfu; sum Si to Na > 15 apfu. The normalization schemes with the smallest maximum deviations are used. To allow for the imperfection of real data, a threshold of 0.005 apfu is used for the deviations, and for the separation of the normalization schemes.”

The spreadsheet therefore automatically determines which normalization scheme or schemes are appropriate, based on the smallest maximum deviations from the criteria listed above.
However, the user can force the use of any, some, or all of the normalization schemes, by setting the following options to True or 1:
Require Si–Ca&Li<=15? (TRUE or 1/FALSE or 0)
Require Si–Mg&Li>=13? (TRUE or 1/FALSE or 0)
Require Si–Na>=15? (TRUE or 1/FALSE or 0)
Require Si–K<=16? (TRUE or 1/FALSE or 0)
If one is deeply interested in the details of this calculation, I recommend to look in the spreadsheet ( version 9.8 ) at the 3.Calculation worksheet, specifically rows 5495 to 5554.

Schumacher (1997) did list additional stoichiometric constraints for certain metamorphic amphiboles.
This is partially captured in Warnings section of the Output of the spreadsheet, specifically if the sum of high-valence C cations (M3+ and M4+) is greater than 2 apfu.

The calculation of the formula proportions of an amphibole does not depend on the subsequently determined name of that amphibole.

References:

Deer, W.A., Howie, R.A., Zussman, J., 1966. An Introduction to the Rock-Forming Minerals. Longman Group Limited, London, U.K.

Hawthorne, F.C., Oberti, R., Harlow, G.E., Maresch, W.V., Martin, R.F., Schumacher, J.C., Welch, M.D., 2012. IMA report, nomenclature of the amphibole supergroup. American Mineralogist 97, 2031–2048.

Leake, B.E., Woolley, A.R., Arps, C.E.S., Birch, W.D., Gilbert, M.C., Grice, J.D., Hawthorne, F.C., Kato, A., Kisch, H.J., Krivovichev, V.G., Linthout, K., Laird, J., Mandarino, J.A., Maresch, W.V., Nickel, E.H., Rock, N.M.S., Schumacher, J.C., Smith, D.C., Stephenson, N.C.N., Ungaretti, L., Whittaker, E.J.W., Guo, Y., 1997.
Nomenclature of amphiboles: report of the subcommittee on amphiboles of the International Mineralogical Association, Commission on New Minerals and Mineral Names. Canadian Mineralogist 35, 219–246.

Schumacher, J.C., 1997. Appendix 2. The estimation of the proportion of ferric iron in the electron-microprobe analysis of amphiboles. In: Leake, B.E., et al. (Eds.), Nomenclature of Amphiboles, vol. 35. Canadian Mineralogist, pp. 238–246.
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