Starting a new topic to focus on the correct method to tune one's PHA settings because proper tuning of PHA is a "black box" to most analysts! Including myself until quite recently! >:(
This link is to the "Limits of EPMA Accuracy" which explores this topic in broader detail ("peak shift" matching, dead time calibration, and better standards):
https://smf.probesoftware.com/index.php?topic=1831.0
Let's start by analyzing Ti Ka in synthetic SrTiO3 using TiO2 as a primary standard (without "count rate" matching our primary standard to our secondary standard or unknown!).
Running a PHA scan using the default PHA settings we obtain this scan on the TiO2 standard (remember, we always want to adjust our PHA settings on a material with the highest concentration (generally the primary standard) at the highest beam current we expect to utilize (that is, at the highest count rate we expect to see, that is, tuning our PHA to avoid pulse height depression effects which can cause non-linear responses)
(https://smf.probesoftware.com/gallery/395_14_06_26_11_03_22.png)
Note first that we are in "integral" PHA mode. In integral PHA all photons to the right are still counted, even those that plot (invisibly!) to the right of the maximum x axis displayed!
Next we clearly see that the baseline level is too high and is intersecting the PHA peak. Why is that a problem? Because if the peak shifts to the right or left, the baseline level cuts off more or less of the PHA peak and we obtain a non-linear response in our counting electronics!
However, we can make two adjustments to avoid this: first by lowering our baseline level below the PHA peak, and second, increasing our gain (for Cameca instruments) or our bias (for JEOL instruments) we can shift the PHA peak to the right *completely above* the baseline level, thus ensuring a linear response in our counting electrics.
Here is the PHA scan after adjusting our baseline level and our gain (or bias):
(https://smf.probesoftware.com/gallery/395_14_06_26_10_16_40.png)
Better, but the baseline level still intersects the PHA peak tail a bit on the left. After raising our PHA gain still further, we obtain this PHA scan:
(https://smf.probesoftware.com/gallery/395_14_06_26_10_17_02.png)
This is what we will utilize for our quantitative analyses in the next post. The same PHA tuning procedure was utilized for Fe Ka as seen here:
(https://smf.probesoftware.com/gallery/395_14_06_26_10_38_47.png)
OK, so how does this rather unintuitive PHA tuning method, shown in the previous post actually perform?
Let's start with Ti Ka in SrTiO3 using TiO2 as the primary standard (showing three different matrix correction models) The raw k-ratio for this pairing is around 0.43 so over a 100% difference in count rates:
(https://smf.probesoftware.com/gallery/395_14_06_26_10_19_09.png)
All three models perform quite well and are all within ~1% relative accuracy, though the DAM BSE correction does somewhat better.
Now let's look at Fe Ka in SRM K-411 glass using Fe3O4 as a primary standard:
(https://smf.probesoftware.com/gallery/395_14_06_26_10_19_46.png)
Again, all three models do very well using the integral baseline PHA tuning method, though again, the DAM BSE models is somewhat more accurate. This pair has a raw k-ratio of 0.1405, so an even more extreme extrapolation than the TiO2 example above.
Do you care about EPMA accuracy? Why don't you try this PHA tuning method and do some intensity extrapolations from your primary standard to a secondary standard and see what you learn... send me a private message (or email) if you are too shy to share your results. I'm here to help! :)
Quote from: Probeman on June 14, 2026, 10:46:17 AMStarting a new topic to focus on the correct method to tune one's PHA settings because proper tuning of PHA is a "black box" to most analysts! Including myself until quite recently! >:(
I think one of primary things which should be very much bolded, underlined, SHOUTED, SCREAMED, printed in large font and send all over the earth with paper mails... and I don't know what else... is this:
DO NOT RELY ON OEM AUTO PHA FUNCTION - THOSE ARE MADE BASED ON HISTORICALLY WRONG ASSUMPTIONS AND IT LEADS TO VERY HUGE ERROR!We could ask EMAS, AMAS, MAS and other EPMA-related societies to update their mouse pads, wall-cheat-sheets/posters with this disclamer – maybe it would start changing something...
Quote from: sem-geologist on June 15, 2026, 07:27:28 AMQuote from: Probeman on June 14, 2026, 10:46:17 AMStarting a new topic to focus on the correct method to tune one's PHA settings because proper tuning of PHA is a "black box" to most analysts! Including myself until quite recently! >:(
I think one of primary things which should be very much bolded, underlined, SHOUTED, SCREAMED, printed in large font and send all over the earth with paper mails... and I don't know what else... is this:
DO NOT RELY ON OEM AUTO PHA FUNCTION - THOSE ARE MADE BASED ON HISTORICALLY WRONG ASSUMPTIONS AND IT LEADS TO VERY HUGE ERROR!
We could ask EMAS, AMAS, MAS and other EPMA-related societies to update their mouse pads, wall-cheat-sheets/posters with this disclamer – maybe it would start changing something...
I could not agree more, though I think only the Cameca has such an "auto PHA" button. The JEOL might have it but apparently it's only accessible by the service engineer for running tests.
But regardless, the auto OEM or traditional manual PHA tuning methods basically *force* the user into utilizing "matrix matched" or as I call more properly: "count rate matched" natural standards (with all their documented heterogeneity and inclusions). Because if there is a difference in the count rate between the standard and the unknown, the traditional PHA tuning will cause a non-linear response, due to the baseline/window filtering.
Yup, at this point I think we mostly have a sociological, or at least an educational endeavor (or for some stubborn souls, perhaps a psychological hurdle) to overcome traditional PHA tuning methods. Once people overcome their initial reluctance they will find that they can use high purity synthetic end member mineral standards and still achieve ~1% relative accuracy on their unknown samples.
By the way, if anyone with a JEOL instrument is interested in running PHA tests similar to those in first post above:https://smf.probesoftware.com/index.php?topic=1854.0
I would be very interested in seeing a series screen captures of PHA adjustments where they attempt the integral-baseline PHA tuning method described above.
Then see what quantitative results they get when extrapolating Fe Ka from say Fe3O4 to the NIST glasses or Ti Ka extrapolating from TiO2 to SrTiO3...
Quote from: Probeman on June 15, 2026, 08:21:31 AMBy the way, if anyone with a JEOL instrument is interested in running PHA tests similar to those in first post above:
https://smf.probesoftware.com/index.php?topic=1854.0
I would be very interested in seeing a series screen captures of PHA adjustments where they attempt the integral-baseline PHA tuning method described above.
Then see what quantitative results they get when extrapolating Fe Ka from say Fe3O4 to the NIST glasses or Ti Ka extrapolating from TiO2 to SrTiO3...
Not to put too fine a point on this integral-baseline PHA tuning method, but this next example is pretty graphic. Here is Fe Ka measured at multiple keVs in NIST SRM K-412 mineral glass using Fe3O4 as a primary standard:
(https://smf.probesoftware.com/gallery/395_16_06_26_8_40_07.png)
This measurement yields a raw k-ratio of ~0.97 at 20 at keV, which means that this is a count rate extrapolation of 10x from the primary standard to the secondary standard!
St 160 Set 12 NBS K-412 mineral glass, Results in Elemental Weight Percents
ELEM: Ti Fe Sr Rb Mn Cr Si Mg Ca Al O
TYPE: ANAL ANAL SPEC SPEC SPEC SPEC SPEC SPEC SPEC SPEC SPEC
BGDS: LIN LIN
TIME: 60.00 60.00 --- --- --- --- --- --- --- --- ---
BEAM: 19.94 19.94 --- --- --- --- --- --- --- --- ---
ELEM: Ti Fe Sr Rb Mn Cr Si Mg Ca Al O SUM
1169 .003 7.756 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.094
1170 .000 7.732 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.067
1171 .002 7.713 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.050
1172 .002 7.727 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.064
1173 -.002 7.761 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.094
1174 -.001 7.750 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.085
AVER: .000 7.740 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.076
SDEV: .002 .019 .000 .000 .000 .000 .000 .000 .000 .000 .000 .018
SERR: .001 .008 .000 .000 .000 .000 .000 .000 .000 .000 .000
%RSD: 402.07 .24 .00 .00 .00 .00 .00 .00 .00 .00 .00
PUBL: n.a. 7.742 n.a. n.a. .077 n.a. 21.199 11.657 10.899 4.906 43.597 100.077
%VAR: --- -.03 --- --- --- --- --- --- --- --- ---
DIFF: --- -.002 --- --- --- --- --- --- --- --- ---
STDS: 22 395 --- --- --- --- --- --- --- --- ---
STKF: .5611 .6860 --- --- --- --- --- --- --- --- ---
STCT: 1833.94 1035.67 --- --- --- --- --- --- --- --- ---
UNKF: .0000 .0666 --- --- --- --- --- --- --- --- ---
UNCT: .01 100.60 --- --- --- --- --- --- --- --- ---
UNBG: 2.64 1.38 --- --- --- --- --- --- --- --- ---
ZCOR: 1.1885 1.1615 --- --- --- --- --- --- --- --- ---
KRAW: .0000 .0971 --- --- --- --- --- --- --- --- ---
PKBG: 1.00 73.96 --- --- --- --- --- --- --- --- ---
And here even at 10 keV we are well within 1% relative accuracy:
St 160 Set 1 NBS K-412 mineral glass, Results in Elemental Weight Percents
ELEM: Ti Fe Sr Rb Mn Cr Si Mg Ca Al O
TYPE: ANAL ANAL SPEC SPEC SPEC SPEC SPEC SPEC SPEC SPEC SPEC
BGDS: LIN LIN
TIME: 60.00 60.00 --- --- --- --- --- --- --- --- ---
BEAM: 19.99 19.99 --- --- --- --- --- --- --- --- ---
ELEM: Ti Fe Sr Rb Mn Cr Si Mg Ca Al O SUM
707 .008 7.781 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.124
708 -.015 7.945 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.265
709 .015 7.659 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.009
710 .009 7.778 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.122
711 -.011 7.827 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.152
712 .011 7.800 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.147
AVER: .003 7.798 .000 .000 .077 .000 21.199 11.657 10.899 4.906 43.597 100.136
SDEV: .013 .092 .000 .000 .000 .000 .000 .000 .000 .000 .000 .082
SERR: .005 .038 .000 .000 .000 .000 .000 .000 .000 .000 .000
%RSD: 438.46 1.18 .00 .00 .00 .00 .00 .00 .00 .00 .00
PUBL: n.a. 7.742 n.a. n.a. .077 n.a. 21.199 11.657 10.899 4.906 43.597 100.077
%VAR: --- .73 --- --- --- --- --- --- --- --- ---
DIFF: --- .056 --- --- --- --- --- --- --- --- ---
STDS: 22 395 --- --- --- --- --- --- --- --- ---
STKF: .5446 .6648 --- --- --- --- --- --- --- --- ---
STCT: 317.84 88.25 --- --- --- --- --- --- --- --- ---
UNKF: .0000 .0635 --- --- --- --- --- --- --- --- ---
UNCT: .01 8.42 --- --- --- --- --- --- --- --- ---
UNBG: .96 .34 --- --- --- --- --- --- --- --- ---
ZCOR: 1.1948 1.2290 --- --- --- --- --- --- --- --- ---
KRAW: .0000 .0954 --- --- --- --- --- --- --- --- ---
PKBG: 1.02 25.77 --- --- --- --- --- --- --- --- ---
I encourage you to try this new PHA tuning method and convince yourself. See attached pdf.
What a timely post!
I have a user VERY interested in high precision F and Cl in amphiboles and I am diving headfirst into the PHA settings, a topic which I still haven't had a good explanation of despite running a lab (looks around sheepishly). I think some of the confusion stems from the way PHA is discussed in Cameca vs JEOL software discussions...
I have two questions:
1. Can't we correct for PHA related interferences with interference corrections rather than changing the PHA settings? Not opposed to changing, just wondering
2. What are folks' favorite settings for F in amphibole?
Quote from: dawncruth on June 16, 2026, 11:50:53 AMWhat a timely post!
I have a user VERY interested in high precision F and Cl in amphiboles and I am diving headfirst into the PHA settings, a topic which I still haven't had a good explanation of despite running a lab (looks around sheepishly). I think some of the confusion stems from the way PHA is discussed in Cameca vs JEOL software discussions...
Yes, it's confusing because JEOL only has 2x gain steps, so to fine tune one's PHA, one has to use the bias voltage on JEOL instruments. Whereas Cameca instruments set the bias to the optimum level and then adjust the (fine) gain as needed.
Quote from: dawncruth on June 16, 2026, 11:50:53 AMI have two questions:
1. Can't we correct for PHA related interferences with interference corrections rather than changing the PHA settings? Not opposed to changing, just wondering
Absolutely yes! As I mentioned in this post:
https://smf.probesoftware.com/index.php?topic=1831.msg13974#msg13974
Quote from: Probeman on March 13, 2026, 04:02:19 PMYes, differential mode can help with some higher Bragg order interferences, but it doesn't help at all with *same* Bragg order interferences, and only partially with higher Bragg order interferences. In fact there are only a few rare spectral interference situations I can think of where differential mode might help, such as Na Ka 2nd Bragg order interfering when measuring trace oxygen, because it's difficult to find a standard for the interference correction that contains sodium but no oxygen.
Otherwise it makes much more sense to tune your PHAs to obtain a linear response in count rate over a large range of count rate, and then correct for any spectral interferences using the quantitative interference correction in software:
Donovan, John J., Donald A. Snyder, and Mark L. Rivers. "An improved interference correction for trace element analysis." Proceedings of the Annual Meeting-Electron Microscopy Society of America. San Francisco Press, 1992.
Quote from: dawncruth on June 16, 2026, 11:50:53 AM2. What are folks' favorite settings for F in amphibole?
There is the debate between using TAP which has low sensitivity, and using PC0 (45A 2d) which has excellent sensitivity, but lower spectral resolution. I assume JEOL has a 45A 2d LDE?
Quote from: dawncruth on June 16, 2026, 11:50:53 AMWhat a timely post!
I have a user VERY interested in high precision F and Cl in amphiboles and I am diving headfirst into the PHA settings, a topic which I still haven't had a good explanation of despite running a lab (looks around sheepishly). I think some of the confusion stems from the way PHA is discussed in Cameca vs JEOL software discussions...
I couldn't agree more, maybe we need a good discussion around PHA to make us all understand this a bit better. You're not alone :)
Quote from: dawncruth on June 16, 2026, 11:50:53 AM2. What are folks' favorite settings for F in amphibole?
I haven't measured F in amphibole, but for Fe-bearing volcanic glasses (<1000 ppm F) we use the method of Zhang (2016) https://doi.org/10.1111/j.1751-908X.2015.00390.x, with LDE1 crystal & their F-free glasses. Should be the same for amphiboles. The previous lab manager set this up and fine-tuned PHA etc. successfully on our JEOL system. I have not been able to 'translate' the method into PfE yet, I suspect partially because not fully understanding PHA. It's also not been requested often, so using the 'old' JEOL system if users do want fluorine ;) I did try TAP crystals at some point but even if using two simultaneously it does not seem to capture F. This remains on my to-do-list and I wonder whether it is worth a separate post to gather and compare methods for fluorine? I don't think there is an existing discussion, as I've searched before and not found anything 'concrete'? In theory, I think it would be a mix of utilising interference/blank standards and treating it as a trace element...?
Quote from: KerstinGruender on June 16, 2026, 03:59:10 PMQuote from: dawncruth on June 16, 2026, 11:50:53 AMWhat a timely post!
I have a user VERY interested in high precision F and Cl in amphiboles and I am diving headfirst into the PHA settings, a topic which I still haven't had a good explanation of despite running a lab (looks around sheepishly). I think some of the confusion stems from the way PHA is discussed in Cameca vs JEOL software discussions...
I couldn't agree more, maybe we need a good discussion around PHA to make us all understand this a bit better. You're not alone :)
I've been running a lab for ~40 years and it's only been in the last few years that I think I've finally figured this out! :-[
The good news is that now anyone can properly tune their PHA with a few steps, but before I list them let's consider PHA pulse height depression effects, where the PHA shifts to the left with increasing count rates as seen here:
https://smf.probesoftware.com/index.php?topic=1831.msg13978#msg13978
Now imagine that one has tuned their Fe ka PHA on a unknown mineral with under 10 wt% Fe and gets it nice and centered in the PHA voltage range. When they try to use a primary standard such as magnetite, which has a roughly 10 times the count rate, the peak on the standard shifts to the left, getting vut off by the baseline level, thus yielding a non-linear response from the system. And also obtaining a very inaccurate result.
This in short, is why people have felt compelled to use so called "matrix matched" or what I call "count rate" matched standards for so many years. Thus they rely on problematic natural standards with all their natural variability. But if they instead:
1. Set their PHA to *integral* mode. This way, all photons to the right of the baseline level are counted. Even those photons that no longer plot in the normal PHA range to the right.
2. Tune their PHA on a primary standard with a high concentration of the element, at the highest beam current they expect to use for that element as seen here:
(https://smf.probesoftware.com/gallery/395_27_03_26_10_12_35.png)
Then increasing their gain (Cameca) or bias (JEOL) such that the PHA peak on the primary standard is *completely* above the baseline level. This way, all photons will still be counted in integral mode. And they obtain a PHA peak that will provide a linear response at all lower count rates (unknowns, etc.)
3. Of course since your standard and unknown will have different count rates, we also want to be sure that our dead time calibrations are accurate, and that is why I suggest using the constant k-ratio method here:
https://smf.probesoftware.com/index.php?topic=1466.msg11173#msg11173
along with the logarithmic dead time expression which works up to count rates of ~300 kcps to 400 kcps which are not uncommon on modern large area crystals (the traditional dead time correction fails at count rates above ~30 to 40 kcps).
4. And finally, use high purity synthetic end member standard materials as demonstrated in this topic and also the topic "The Limits of EPMA Accuracy":
https://smf.probesoftware.com/index.php?topic=1831.0
Try it., you'll like it!
Quote from: KerstinGruender on June 16, 2026, 03:59:10 PMQuote from: dawncruth on June 16, 2026, 11:50:53 AM2. What are folks' favorite settings for F in amphibole?
I haven't measured F in amphibole, but for Fe-bearing volcanic glasses (<1000 ppm F) we use the method of Zhang (2016) https://doi.org/10.1111/j.1751-908X.2015.00390.x, with LDE1 crystal & their F-free glasses. Should be the same for amphiboles. The previous lab manager set this up and fine-tuned PHA etc. successfully on our JEOL system. I have not been able to 'translate' the method into PfE yet, I suspect partially because not fully understanding PHA. It's also not been requested often, so using the 'old' JEOL system if users do want fluorine ;) I did try TAP crystals at some point but even if using two simultaneously it does not seem to capture F. This remains on my to-do-list and I wonder whether it is worth a separate post to gather and compare methods for fluorine? I don't think there is an existing discussion, as I've searched before and not found anything 'concrete'? In theory, I think it would be a mix of utilizing interference/blank standards and treating it as a trace element...?
To be fair, trace elements such as F and Cl are subject to different accuracy concerns than major elements as I describe here:
https://smf.probesoftware.com/index.php?topic=1535.msg12121#msg12121
I would also add secondary fluorescence from boundary phases to the trace element slide in the link above.
Another thing to consider for trace background correction is the MAN background correction (Donovan et al., 2016), which when utilized with a blank material can give excellent accuracy. Consider that the variance measured on your blank, when applied to your unknown is now equal to your accuracy, if the blank is truly a blank. Pretty cool.
Remember, you cannot have off-peak interferences with the MAN background correction, because you don't measure off-peak backgrounds at all!
Of course one does also need to consider whether the trace inaccuracy is due to the instrument (trace Ti in SiO2, secondary Bragg diffraction) or the material (trace Au in pyrite, nearby absorption edge) and choose a suitable blank material.
And of course we must also utilize the quantitative interference correction in Probe for EPMA with Cl in apatites and for F in Fe bearing minerals! It works great!
There are several topics on these questions in this forum. Try the search function at the top of the main forum page. Feel free to post to those topics.
Regardless of the approach, looking at the PHA at different count rates is an important activity. The peak shift and doubling and even tripling peaks show up at higher count rates. To include or exclude - that is the question. If you run over a pure material you may even saturate the detector and it is blinded and gives no counts for an appreciable time afterwards.
Quote from: Les Moore on June 16, 2026, 05:53:53 PMRegardless of the approach, looking at the PHA at different count rates is an important activity.
I found it to be very educational!
But the most surprising aspect for me, was discovering that in integral mode all photons to the right of the baseline are counted. Even when they appear to be "cutoff" in the graphical display. That was the "a ha!" moment for me.
Quote from: Les Moore on June 16, 2026, 05:53:53 PMThe peak shift and doubling and even tripling peaks show up at higher count rates. To include or exclude - that is the question. If you run over a pure material you may even saturate the detector and it is blinded and gives no counts for an appreciable time afterwards.
These PHA distributions were acquired at fairly "normal" beam currents, 20, 30 nA or so which makes sense for major and minor elements. Under these conditions I only see the normal peak and sometimes the escape peak if the gas physics permits it.
For trace elements of course one can acquire the primary standard at a lower beam current than the unknown, but then one must be sure to check their picoammeter linearity using the constant k-ratio method:
https://smf.probesoftware.com/index.php?topic=1466.msg11124#msg11124
Quote from: Probeman on June 14, 2026, 10:46:17 AMStarting a new topic to focus on the correct method to tune one's PHA settings because proper tuning of PHA is a "black box" to most analysts! Including myself until quite recently! >:(
This link is to the "Limits of EPMA Accuracy" which explores this topic in broader detail ("peak shift" matching, dead time calibration, and better standards):
https://smf.probesoftware.com/index.php?topic=1831.0
Let's start by analyzing Ti Ka in synthetic SrTiO3 using TiO2 as a primary standard (without "count rate" matching our primary standard to our secondary standard or unknown!).
Running a PHA scan using the default PHA settings we obtain this scan on the TiO2 standard (remember, we always want to adjust our PHA settings on a material with the highest concentration (generally the primary standard) at the highest beam current we expect to utilize (that is, at the highest count rate we expect to see, that is, tuning our PHA to avoid pulse height depression effects which can cause non-linear responses)
(https://smf.probesoftware.com/gallery/395_14_06_26_11_03_22.png)
Note first that we are in "integral" PHA mode. In integral PHA all photons to the right are still counted, even those that plot (invisibly!) to the right of the maximum x axis displayed!
Next we clearly see that the baseline level is too high and is intersecting the PHA peak. Why is that a problem? Because if the peak shifts to the right or left, the baseline level cuts off more or less of the PHA peak and we obtain a non-linear response in our counting electronics!
However, we can make two adjustments to avoid this: first by lowering our baseline level below the PHA peak, and second, increasing our gain (for Cameca instruments) or our bias (for JEOL instruments) we can shift the PHA peak to the right *completely above* the baseline level, thus ensuring a linear response in our counting electrics.
Here is the PHA scan after adjusting our baseline level and our gain (or bias):
(https://smf.probesoftware.com/gallery/395_14_06_26_10_16_40.png)
Better, but the baseline level still intersects the PHA peak tail a bit on the left. After raising our PHA gain still further, we obtain this PHA scan:
(https://smf.probesoftware.com/gallery/395_14_06_26_10_17_02.png)
This is what we will utilize for our quantitative analyses in the next post. The same PHA tuning procedure was utilized for Fe Ka as seen here:
(https://smf.probesoftware.com/gallery/395_14_06_26_10_38_47.png)
Might be missing something but this is how JEOL have always recommended PHA - set to 4 volts. And idealy want to include escape peak, if not exclude escape peak, but ensure baseline is not on peak, it's what Paul Carpenter also has been talking about for decades.
Quote from: Ben Buse on June 17, 2026, 06:15:10 AMMight be missing something but this is how JEOL have always recommended PHA - set to 4 volts. And idealy want to include escape peak, if not exclude escape peak, but ensure baseline is not on peak, it's what Paul Carpenter also has been talking about for decades.
Yes, you are missing something. :)
For one thing these are Cameca plots and the Cameca PHA only goes to 5 volts. So on a JEOL instrument, you would be setting the PHA peak to 8 volts! Do you get it now? :D
In addition, with this integral-baseline method you *always* want to include the escape peak no matter how high one has to amplify the PHA. Not having the escape peak above the baseline means that at some low enough count rate the escape peak could shift to the right, and negating your counting linearity.
The more important point is that we now know that photons that appear "cut off" graphically are still all counted in integral PHA mode. I did not know that until a few years ago, did you?
The final point is that we no longer need to "count rate match" our unknowns to our standards and therefore we can finally begin using globally distributed synthetic end member composition standards.
Combining all these points together will allow us as a global community to finally attain ~1% (or better) relative accuracy throughout the community.
I believe that doing all this (better PHA tuning, better dead time calibrations, better matrix corrections and better globally distributed high purity synthetic standards), as a community, will finally allow us to produce compositions that are in agreement with each other. Because that is certainly not the case today:
Wieser, P. E., Kent, A. J., Till, C. B., Donovan, J., Neave, D. A., Blatter, D. L., & Krawczynski, M. J. (2023).
Barometers behaving badly I: assessing the influence of analytical and experimental uncertainty on clinopyroxene thermobarometry calculations at crustal conditions. Journal of Petrology, 64(2), egac126.
Thanks John for explaining. By "count rate match" you mean changing the beam current so count rate same on standards and unknowns? Might be tricky for some multi element phases.
Quote from: Ben Buse on June 17, 2026, 08:11:21 AMThanks John for explaining. By "count rate match" you mean changing the beam current so count rate same on standards and unknowns? Might be tricky for some multi element phases.
No, I do not.
I mean the widely utilized "practice" of selecting a natural material (no matter how poorly characterized or heterogeneous), to use as a standard to match the count rate observed in an unknown.
The only benefit being that then the dead time and PHA tuning (and matrix corrections) have small effects, but now the accuracy of the standard becomes dominant. But we also know that these natural "standard" materials are not good enough as has been documented by Vicenzi, Fournelle and Nachlas and others.
Of course one can also utilize different beam currents for the standard and unknown as one commonly does for trace element analysis, though accuracy in trace elements then depends on the picoammeter linearity.
Gotcha. Thanks. I need to read more carefully! :)
Has anyone tried it on a JEOL?
Quote from: Ben Buse on June 17, 2026, 08:18:29 AMGotcha. Thanks. I need to read more carefully! :)
No worries. If this PHA tuning method was intuitive, I would have figured it out 40 years ago!
:D
Quote from: Ben Buse on June 17, 2026, 08:21:55 AMHas anyone tried it on a JEOL?
Anette did some testing a while back and found that the JEOL also counts photons above the JEOL 10v graphical limit like the Cameca above the 5v graphical limit.
But it would be great to see some high accuracy tests extrapolating Fe Ka from say Fe3O4 to the NIST glasses.
If one has calibrated their dead times, and their spectrometers are mechanically aligned to give an effective takeoff angle of 40 degrees, you should obtain ~1% relative accuracy even with a 10x difference in count rates. Test your effective takeoff angles using the Bragg order k-ratio tests described here:
https://smf.probesoftware.com/index.php?topic=1739.0
Of course using the logarithmic dead time correction will help with large area Bragg crystals and their higher count rates, and when testing with soft x-rays, e.g., Mg, Al and Si Ka, be sure to use the FFAST MACs. The DAM BSE correction is great for when large atomic number extrapolations are present. I just always use FFAST with the Armstrong/Donovan and Moy matrix correction...
If using SiO2 as an Si Ka standard be sure to defocus the beam to 10 um or so. Do you have the FIGMAS MgO, Al2O3, MgAl2O4 mount? Will Nachlas also has some excellent synthetic Mg2SiO4. It's the Takai Mg2SiO4 recipe, which I have some of the original material from Takai back in the 1980s.
https://www.sciencedirect.com/science/article/abs/pii/0022024874901110
Quote from: Probeman on June 16, 2026, 05:09:21 PMQuote from: KerstinGruender on June 16, 2026, 03:59:10 PMQuote from: dawncruth on June 16, 2026, 11:50:53 AMWhat a timely post!
I have a user VERY interested in high precision F and Cl in amphiboles and I am diving headfirst into the PHA settings, a topic which I still haven't had a good explanation of despite running a lab (looks around sheepishly). I think some of the confusion stems from the way PHA is discussed in Cameca vs JEOL software discussions...
I couldn't agree more, maybe we need a good discussion around PHA to make us all understand this a bit better. You're not alone :)
I've been running a lab for ~40 years and it's only been in the last few years that I think I've finally figured this out! :-[
I really appreciate spreading this "tuning of PHA for integral mode method" by probeman. However as dawncruth and KerstinGruender had noted - the PHA is confusing. I would not blame the "Cameca vs JEOL software discussions", I would not blame anyone, as PHA issue is multidisciplinary and I believe that even authors of different textbooks about microanalysis had no complete understanding about PHA. I, however, want to urge of using proper and precise terminology.
My grin is on using improperly "photon" vs "electronic pulse" and "cutoff" vs "clipped" terms.
PHA have nothing to do with photons. Photons cease to exist somewhere in between the anode and cathode of G(F)PC (Gas (Flow) Proportional Counter) where its energy is converted into bunch of electrons where their sum of energies is proportional to energy of the x-ray photon. (this is a simplification of 1x initial photoelectron -> initial electron cloud, the part where PHA still does not influence that process). This electron cloud becomes a subject of chain of processes which PHA controls directly and indirectly, so PHA begins with electrons and ends with electrons (electronic signal), there is no more photons. While for some of us, who took long discussions with probeman, is clear what his use of "photons" on these plots mean, for some future generations which have no context of these discussion, this could be a source of confusion.
In short – PHA (of GFCP) is about control of amplification of initial electron cloud into measurable electronic signal (setting the height of pulses) AND (optionally) filtering it by height (which is proportional to initial cloud energy – this is where "Analysis" from PHA part-comes into, that "analysis" can be compared to EDS spectral window (i.e. set for mapping of a particular element) - that is a most close comparable thing). If we use "integral" mode we use only the first part, and if we use differential mode - we then use both parts of PHA. It would be so much better if PHA would be renamed into something what would describe both of these functions. I.e. PH&A (Pulse Height AND Analysis)
Short condensed course on X-ray detection, shared paradigms and differencesI want also to present more generalized context of X-ray detection fundamentals, as hitherto to me known EPMA textbooks introduce confusion often by describing EDS and WDS as completely absolutely cardinally different devices. When comparing EDS and GFPC (skipping the diffraction part of WDS) such broader common context can help to understand the differences and, I hope, will easy up the understanding of whole PHA and its place in microanalysis.
So most (excluding some other, like i.e. µ-calorimeter-based EDS) of X-ray and gamma detectors are based on these 3 fundamental parts:
1. semi-conductive (for electric charge) medium
2. voltage bias (gradient) across the medium with cathode and anode
3. measurement system of electron charge at cathode or anode
1. MediumAs for medium it can be made from all 4 states of matter: gas, solid, liquid and even plasma (although these are still in very early-development). Every of these have its pros and cons and are chosen per application basis (required energy resolution, speed/throughput, robustness, cooling requirements, decay (deterioration with age)/long-term stability, maintenance requirements...). The main purpose of medium is to convert photon into photo-electron and then convert that into initial electron cloud. Other optional medium capabilities depend from other 2 parts described below.
2. Voltage BiasThe required minimal voltage bias (for any detection) depends from medium, its size, and requirements of amplification in the medium, it can start from few V and could be up to hundred of thousands of Volts (if not more). Some of mediums transits into amplification region if bias voltage is sufficiently increased. Such amplification makes it easier to measure electron charge at part 3 of the detection system, also lowering its complicated requirements. GFPC is a good example of such amplification, where bias is set at so called "proportional region". IMHO it would be less confusing if it would be called "bias amplification region" instead.
Classical SDD used in common EDS do no amplification in the medium, albeit there are SDD's in development, which would use much higher bias voltages to do some amplification in the medium, and so that would reduce requirements for part 3 of detection (i.e. no cooling needed).
In GFPC we amplify initial electron cloud utilizing increased bias voltage, with that controlling the extent of Townsend's avalanche – the process which amplifies charge of initial electron cloud into much larger collected (and measured) charge at anode. Townsend's avalanche is quite a violent electronic "discharge"-like event (imagine violent avalanche in the mountains, where it could be started by single small dropped snow ball - that is why it is called avalanche; in our case we have electron avalanche instead of snow). GFPC's gas medium is practically "unimpressed" by such violent events and is capable to "repair"/"reset" its state practically instantly after. Trying to achieve such similar electron avalanches on the solid state detector would destroy such solid medium irreparably. This capability of enormous amplification (few orders of magnitude) is the biggest advantage for gas medium compared to other detection mediums, and makes it much easier at part 3 of detection, dropping-off sophisticated cooling and ultra-low-noise electronic design requirements (which are needed i.e. by SDD, because it has no amplification in its medium).
BTW, with some specific gas mixtures and pressure and much higher bias, the gas bias amplification could be "turned up to 11" into "self-quenching streamer" mode (much more faster AND also much more violent discharge-like event compared to Townsend avalanche; for snow avalanche comparison, replace water snow, with some better rolling snow (i.d.k. maybe ammonia, methane...), and replace earth gravity of 9.8 with gravity of 100, while keeping the same mountain height - imagine the result, also add to the picture displaced air upward, faster and more narrow avalanche, more like meteor strike-like). Also do not confuse it with Geiger-Muller mode - that mode would be like you drop a snow ball on the top and, independently from the size of the ball, all snow from whole the mountain collapses to the base reducing the slope of the mountain, and you need to wait for snow to melt down, and evaporate and snow down on the mountain, so the next avalanche would be possible at all.To illustrate the biggest drawback of such gas bias amplification, imagine how difficult task would be to use measured volume of avalanche'd snow at base of the mountain and try to reconstruct how big was initial snowball, which had initiated that avalanche. So, The biggest disadvantage of violent avalanche event is a very huge error in such reconstruction of initial cause (of initial photo-electron energy) - and that is the Achilles heal of PHA diff mode for GFPC. However if we would have ideal mountain (no trees, buildings, valleys, roads, rivers...), with ideal same thickness of snow coverage, the statistics could allow us to get very similar sized avalanches depending from size of initial snow ball dropped on the top, and that would be much more closer comparison to processes going inside our GFPCs. By setting bias we are like adjusting "gravity under such imaginable ideal mountain and controlling size of avalanche proportionally to initial dropped ball".
So to conclude this sub-chapter, we have no control on bias in EDS, as SDD (the solid) do no amplification in the medium. We have bias control for WDS GFPC PHA, because the majority of signal amplification is done within the medium (the gas), and control of such amplification is done by tweaking the bias values.
3. measurement system of electron chargeOn SDD at point of medium (solid) where charge is collected, directly to that point J-FET (very ultra low noise field emission transistor) needs to be attached to amplify very small charge to measurable amount, for following (in the signal pipeline) pre-amplifier. Such J-FET is either directly attached or embedded in the same silicon substrate (i.e. tear-drop shapped SDD). J-FET needs to be as close as possible to point where charge is being collected to minimize the noise introduction.
J-FET amplification is much more smaller when compared with GFPC bias amplification, and so the pre-amplifier construction is a bit different on EDS. Pre-amplifiers in both cases (GFPC and EDS) integrates the sensed collected charge signal (negative short electronic pulse) producing a "stair" or "cascade"-like signal, where step height is proportional to the initial electron cloud energy. Because J-FET amplification is not enough to bring the signal much above the electronic noise floor, the EDS pre-amplifiers feedback loop can't have a bleeding out resistor, and so the feedback loop of integrating OPAMP charges up with integration steps, and continuously due to leakage current (partly J-FET), and so it needs periodic discharge (which adds additional source of dead time). Bleeding out resistor is not used, as resistor on its own would introduce internal resistor noise which would be bigger than signal incoming from J-FET. J-FET itself needs to be cooled down below room temperature to lower internal noise further down and lower leakage current.
On GFPC, because gas bias amplification is so big compared to SDD+J-FET, there is no need for J-FET, and signal is so big that pre-amplifier can use feedback loop with bleeding-out resistor. That means no dead time introduced at pre-amplifier, no charging up of feedback loop, no need to hold detection for its discharge - pre-amplifier is continuously processing the incoming electron charge pulses. There is no need of ultra-low-noise design, and no need of cooling.
In both cases of GFCP and EDS, pre-amplified stair-like signal is further down passed through Shapping amplifiers, which converts the step into
pulse, where its height is a subject for PHA, or EDS.
The difference is that on WDS normally it is a single fixed amplifier (in differentiation configuration), where on EDS systems there are a set of shapping amplifiers each with different shapping time constants, which allows to chose/ balance between either precision and/or throughput, by piping the signal through different shapping amplifiers.
After shapping amplifiers we have the final GAIN amplification which scales the pulse height to fit into specific ADC (analog-digital converter) range. On EDS such GAIN amplification is not accessible directly, it is changed indirectly by calibrating the EDS known line to theoretical position, and after the calibration the GAIN (for given shapping amplifier) stays at that set value during calibration. On WDS GFPC PHA such GAIN is all the time directly accessible and can be set to different values per element or sub-measurement basis. On WDS GFPC gain can be often by default be set smaller than 1.0 (that is the amplitude is downsized). I.e. on CAMECA SX line 1000 equals 1.0. So i.e. when "Auto PHA" sets gain to 350 value it is multiplying previously amplified pulse by 0.35 - shrinking it electronically down.
PHA and pulse counter cutoff and clippingcutoff - is discarding the signals below or above the some thresholds.
clipping - is modifying signal bringing any of its values outside of threshold-set range to values of lower or higher thresholds.
(clipping: the most easy comparison would be overexposure of the photo - you get white pixels - which is information about intense light at that pixel limited at maximum possible value of pixel. cut off would produce NaN pixel - that is no information in the pixel).
WDS systems has much more simple pulse counters than EDS, because on EDS energy discrimination of pulses is primary means to separate the X-rays into different spectral bins (12bit), and on WDS the PHA plot is a secondary mean of separation of X-rays by energy into some bins (8bit).
Precise Pulse height measurement (so the pulse could be added to correct bin in PHA histogram-like plot) requires pulse sensing/detection prior. The amplitude measurement needs a trigger. Both Jeol and Cameca pulse sensing hardware clearly have some cutoff around 0V (in case of Cameca it is ~0.5V) - any pulse which peak is below that value does not pass - it is cutoff. In both hardware pulses with their amplitude close to 0V are cutoff - they are not counted – they are not sensed by counter and they are not measured as they are simply invisible to pulse sensing part.
As for higher values than ADC maximum value, they are clipped. They are very easily sensed with pulse sensing part, but they are clipped to the last maximum pulse size.
for some reason OEM software do not show the last bins of PHA on the graph, or expose it through API, probably as in case of clipping it would produce very strange plots (all clipped values would end in single last bin, and would produce "_|" - shapped plot). Integral mode at Cameca hardware uses only detection of pulses, ignoring the amplitude measurement. As far I had seen crumbs of information, Jeol use amplitude measurement even in integral mode to cutoff the electronic background near 0V.
To conclude PHA:
BIAS controls the primary electron cloud gas amplification inside GFPC
GAIN scales produced pulses to the PHA plot.
Pulses below 0V (or near it) are
cuts-off and does not trigger pulse sensing - can't be counted.
Over-sized pulses are
clipped to the max value of ADC are easy to sense, are counted in integral mode.
OEM PHA plots hide last bin(s) from plot and from API PHA value return, and so hide clipped pulses from the user, but pulses from such bin in the integral mode are still counted by hardware.
Just for comparison, EDS i.e. cuts-off at higher bound value (i.e. when range of EDS is set to 10kV, and using 15kV beam, the EDS will be cut at 10kV). It was natural to think that we would loose counts at higher boundary. Fortunately both Jeol and Cameca hardware designs had limited only on API and plotting limitations, using pulse-sensing (without amplitude information) circuit for counting in integral mode. Finding that out (that PHA on WDS on EPMA just clip, and not cut-off at higher bound) required to question and ignore the prior knowledge presented in textbooks and passed by generations of EPMA operators.
BTW, PHA was one of biggest black box part of EPMA the first day I started working on EPMA 11 years ago. With some luck of events (downtime + covid19) and some spare time, hanging oscilloscope to look into "pulse" directly was my "aha" moment.
Quote from: sem-geologist on Today at 06:24:24 AMI really appreciate spreading this "tuning of PHA for integral mode method" by probeman. However as dawncruth and KerstinGruender had noted - the PHA is confusing. I would not blame the "Cameca vs JEOL software discussions", I would not blame anyone, as PHA issue is multidisciplinary and I believe that even authors of different textbooks about microanalysis had no complete understanding about PHA. I, however, want to urge of using proper and precise terminology.
My grin is on using improperly "photon" vs "electronic pulse" and "cutoff" vs "clipped" terms.
PHA have nothing to do with photons...
Thank-you so much SG for the explanation of these terms. This is a very informative post for those of us (including) myself) that were "lost in the black box".
And just be to clear to everyone, SG was my original source for utilizing integral PHA mode for best accuracy. It just took me a while to realize that we must also make sure our PHA peak is *completely* above the baseline level at the highest count rate we expect to measure. This is the key to being able to quantify materials were very different count rates, e.g., high purity synthetic end member oxides and metals all the way down to trace levels and obtain the highest accuracy for our k-ratios.
Perhaps we can refer to this as "pulse counting of x-rays"? We are after all, counting them one by one! :)