Starting a new topic on Bragg order k-ratio testing as previously discussed here:
https://smf.probesoftware.com/index.php?topic=1718.msg13333#msg13333
These tests (suggested by Pete McSwiggen), are where one measures element/x-ray k-ratios at two or more different Bragg orders of reflections on a spectrometer/crystal. Because whatever the two materials are,
we should obtain the same k-ratio (within statistics) for all the Bragg order reflections of that emission line. Also we generally want to chose an element/x-ray and two materials that are significantly absorbed, in order to be significantly affected by variations in the effective take off angle. For example, measuring Al Ka in MgAl2O4 using Al2O3 as a primary standard or measuring Mg Ka in MgCr2O4 using Mg2SiO4 as a primary standard. These materials have relatively large matrix effects as described in the posts linked above.
Note that these Bragg order k-ratio tests can be performed with any EPMA software, but below I will describe how it can be done easily and automatically in the Probe for EPMA software.
Meanwhile, this last weekend I decided to run some Bragg order k-ratio tests on my Cameca SX100, just to compare with what Joe Boesenberg found on his JEOL instrument, and it appears that the UofO Cameca instrument is in pretty good shape for a 20 year old instrument, but it seems at least one spectrometer could do with an mechanical re-alignment after all these years.
I say that because we did perform simultaneous k-ratio tests when we accepted the instrument in 2005, and again a year later, and all spectrometers agreed with each other within ~2% relative at that time:
https://epmalab.uoregon.edu/reports/Additional%20Specifications%20New.pdf
And the simultaneous k-ratio test is great, but it can only compare k-ratios from one spectrometer to another (or another instrument).
But what's cool about the Bragg order k-ratio test is that it tells us if a
single spectrometer is aligned consistently over its range (though all spectrometers regardless of the spectrometer/crystal should yield the same k-ratios). So I ran the tests last weekend at 20 keV on the FIGMAS-1 (MgO-Al2O3-MgAl2O4) mount from Will Nachlas, using the setup below for the 1st order Bragg reflections for Mg Ka and Al Ka on spectrometers 1 (TAP), 2 (LTAP) and 4 (TAP):
On and Off Peak Positions:
ELEM: mg ka mg ka mg ka al ka al ka al ka
CRYST: TAP LTAP TAP TAP LTAP TAP
ONPEAK 38593.0 38262.0 38402.0 32556.5 32255.3 32381.0
OFFSET -93.723 237.277 97.2773 -90.529 210.670 84.9707
HIPEAK 39724.5 39392.8 39533.5 33781.9 33486.7 33613.1
LOPEAK 37461.5 37131.2 37270.5 31331.1 31023.9 31148.8
HI-OFF 1131.50 1130.80 1131.50 1225.40 1231.40 1232.10
LO-OFF -1131.5 -1130.8 -1131.5 -1225.4 -1231.4 -1232.2
PHA Parameters:
ELEM: mg ka mg ka mg ka al ka al ka al ka
DEAD: 2.850 2.800 3.000 2.850 2.800 3.000
BASE: .32 .32 .37 .30 .30 .30
WINDOW 4.00 4.00 4.00 4.00 4.00 4.00
MODE: INTE INTE INTE INTE INTE INTE
GAIN: 2963. 2589. 2300. 2250. 2330. 1863.
BIAS: 1320. 1320. 1320. 1320. 1320. 1320.
Last (Current) On and Off Peak Count Times:
ELEM: mg ka mg ka mg ka al ka al ka al ka
BGD: OFF OFF OFF OFF OFF OFF
BGDS: LIN LIN LIN LIN LIN LIN
SPEC: 1 2 4 1 2 4
CRYST: TAP LTAP TAP TAP LTAP TAP
ORDER: 1 1 1 2 2 2
Note that the Bragg orders are not listed above because all the lines are first order.
I then tuned the peak centers and checked the PHAs, setting the bias voltage the same for all elements (for improved stability) and adjusting the gain on MgO and Al2O3 to ensure that the PHA peaks were all above the baseline. Then I ran a wavescan on MgAl2O4 to check for off-peak interferences because indeed, there are satellite lines to be avoided.
After the off-peak backgrounds were adjusted they looked like this:
On and Off Peak Positions:
ELEM: mg ka mg ka mg ka al ka al ka al ka
CRYST: TAP LTAP TAP TAP LTAP TAP
ONPEAK 38593.0 38262.0 38402.0 32556.5 32255.3 32381.0
OFFSET -93.723 237.277 97.2773 -90.529 210.670 84.9707
HIPEAK 40216.1 40074.6 40241.9 34419.4 34186.5 34025.8
LOPEAK 36811.7 36464.3 36588.7 30370.1 30009.1 30195.5
HI-OFF 1623.13 1812.64 1839.86 1862.91 1931.18 1644.84
LO-OFF -1781.3 -1797.7 -1813.4 -2186.4 -2246.2 -2185.5
I then changed all the
Mg and Al emission lines to 2nd Bragg order from the Elements/Cations dialog (note that doing this changes the PHA parameters back to their defaults, so you will need to edit the PHA parameters by hand to make sure they are the same as the 1st order PHA parameters), and obtained these values after peaking (the PHAs being set the same) and setting the off-peak bgds again from the Plot! window:
On and Off Peak Positions:
ELEM: mg ka mg ka mg ka al ka al ka al ka
CRYST: TAP LTAP TAP TAP LTAP TAP
ONPEAK 76934.9 76569.0 76757.3 64905.0 64534.0 64710.8
OFFSET -62.305 303.594 115.297 -79.281 291.719 114.918
HIPEAK 78307.7 77938.0 78159.1 66292.2 65923.3 66216.5
LOPEAK 75527.1 75167.1 75312.8 63635.9 63040.2 63262.6
HI-OFF 1372.79 1368.98 1401.80 1387.18 1389.26 1505.65
LO-OFF -1407.8 -1401.9 -1444.5 -1269.1 -1493.8 -1448.2
PHA Parameters:
ELEM: mg ka mg ka mg ka al ka al ka al ka
DEAD: 2.850 2.800 3.000 2.850 2.800 3.000
BASE: .32 .32 .37 .30 .30 .30
WINDOW 4.00 4.00 4.00 4.00 4.00 4.00
MODE: INTE INTE INTE INTE INTE INTE
GAIN: 2963. 2589. 2300. 2250. 2330. 1863.
BIAS: 1320. 1320. 1320. 1320. 1320. 1320.
Last (Current) On and Off Peak Count Times:
ELEM: mg ka mg ka mg ka al ka al ka al ka
BGD: OFF OFF OFF OFF OFF OFF
BGDS: LIN LIN LIN LIN LIN LIN
SPEC: 1 2 4 1 2 4
CRYST: TAP LTAP TAP TAP LTAP TAP
BRAGG: 2 2 2 2 2 2
ORDER: 1 1 1 2 2 2
Note that the Bragg orders are now listed here because they are order = 2. Here are the sequence of events documented using empty unknown samples in Probe for EPMA:
(https://smf.probesoftware.com/gallery/395_01_04_25_2_00_03.png)
Then you simply save both these 1st order and 2nd order samples as sample setups (from the Analyze! window Add to Sample Setups button) and then assign those sample setups to the MgO, Al2O3 and MgAl2O4 standards in the Automate! window (using the Sample Setups or Multiple Setups buttons), and then acquire these samples using automation!
By the way, I found a small bug where Probe for EPMA was not re-loading the primary standard intensities for samples with different Bragg orders and so that is fixed in the most recent version of Probe for EPMA v. 14.1.3. Please update as usual using the Help menu to fix this bug.
To be continued...
Continuing from the above post...
Once your Mg (and Al) (primary and secondary) standard intensities are acquired for both the 1st order and 2nd order reflections, you can go to the Output | Output Standard and Unknown XY Plots menu and select your two MgAl2O4 secondary standards and export the k-ratio data to a plot (or file) for one or more spectrometers as seen here:
(https://smf.probesoftware.com/gallery/395_02_04_25_2_07_09.png)
Next selecting the "Scatter" plot option (no lines between points), we output the data as seen here:
(https://smf.probesoftware.com/gallery/395_02_04_25_2_07_30.png)
As you can see, spectrometer 1 has about a 6% difference between the 1st and 2nd order k-ratios, while the other spectrometers look pretty reasonable.
Note that one can also view your k-ratios from the Analyze! window. Here is a screen shot of the k-ratios for the MgAl2O4 (secondary) standard using the first order lines. This is displayed by clicking the Analyze button followed by the Kraws button as seen here:
(https://smf.probesoftware.com/gallery/395_02_04_25_2_07_54.png)
I then used the Copy button to paste the output to an Excel spreadsheet, though one can also output k-ratios to a tab delimited file by using the User Specified Output menu by right clicking the sample list:
https://smf.probesoftware.com/index.php?topic=8.msg427#msg427
And if you export the data you can plot these k-ratios up in your favorite plotting app. Here are all three spectrometers for both Mg ka and Al ka using Golden Software's Grapher software:
(https://smf.probesoftware.com/gallery/395_02_04_25_2_08_09.png)
As you can see, our spectrometer 1 would appear to need a re-alignment!
Joe and I would be really interested to see Bragg order k-ratio data from other instruments... again, thanks to Pete McSwiggen for coming up with the most excellent test!
At first I thought this is some kind of April 1st joke :o . But seeing it being continued on 2nd April, I looked closer what is this all about.
Quote from: Probeman on April 01, 2025, 02:16:56 PMBut what's cool about the Bragg order k-ratio test is that it tells us if a single spectrometer is aligned consistently over its range (though all spectrometers regardless of the spectrometer/crystal should yield the same k-ratios).
AT first I could not get it what alignment have to do with k-ratios... Do you mean crystal movement misalignment from perfect 40° takeoff angle, so that crystal at low theta and high theta focus X-rays escaping the analytical spot at slightly different angles? And such difference would cause the observed differences in k-ratios between different orders of same material?
Sounds interesting and I am looking forward conducting such tests (Especially that I have also the same synthetic standards). Albeit I quickly checked your measurement setup on my own wave-scans and I see other potential sources for your observed discrepancies.
Background position selection - it seems for me potentially inconsistent in your experiment. For 1st order your sin theta-low background position cross over Mg absorption edge, where 2nd order is measured better – not crossing over the absorption edge. Because of that, for 1st order the interpolated background position will be underestimated, where for 2nd order a little bit overestimated. This whole situation is a bit more complicated by different spectral resolution for 1st and 2nd orders. For 2nd order the Low-background can be placed between second order Kβ1 and Kα10 (or Kα10 and Kα9, they convolve into single little peak), and as spectral resolution is excellent there, the measurement of background there will be measurement of background and not some peak-tail. For 1st order placing the low-background between 1st order Kβ1 and Kα10,9 will give overestimated background as it will be on the tail of these much worse resolution peaks, thus escaping such clear disadvantage people tend to move the LOW background position further behind Kβ1 and thus behind the absorption edge – which is "from the pan to the fire" kind of situation.
Thus said – by using two background measurement method this test becomes comparing "apples" and "oranges" (as 1st order Mg Ka is impossible to measure precisely with 2 background method) and its outcome is highly at mercy of spectral resolution differences between particular XTAL's. I would redo test with single background method, with background measured only from HIGH position, with precise slope (which can be estimated comparing artifact free other element wavescans of different Z, i.e. SiO2, NiO, Cr, Al2O3 (albeit there is a small slope introduced by Al KLL RAE lines-continuum)).
Quote from: sem-geologist on April 02, 2025, 03:46:40 PMAt first I thought this is some kind of April 1st joke :o . But seeing it being continued on 2nd April, I looked closer what is this all about.
Very funny! I wish it were a joke, but it correlates with what Joe is seeing on his spectrometers.
Quote from: sem-geologist on April 02, 2025, 03:46:40 PMQuote from: Probeman on April 01, 2025, 02:16:56 PMBut what's cool about the Bragg order k-ratio test is that it tells us if a single spectrometer is aligned consistently over its range (though all spectrometers regardless of the spectrometer/crystal should yield the same k-ratios).
AT first I could not get it what alignment have to do with k-ratios... Do you mean crystal movement misalignment from perfect 40° takeoff angle, so that crystal at low theta and high theta focus X-rays escaping the analytical spot at slightly different angles? And such difference would cause the observed differences in k-ratios between different orders of same material?
Yes. We are essentially attempting to measure the effective take-off angle over the range of the spectrometers.
Quote from: sem-geologist on April 02, 2025, 03:46:40 PMSounds interesting and I am looking forward conducting such tests (Especially that I have also the same synthetic standards). Albeit I quickly checked your measurement setup on my own wave-scans and I see other potential sources for your observed discrepancies.
Background position selection - it seems for me potentially inconsistent in your experiment. For 1st order your sin theta-low background position cross over Mg absorption edge, where 2nd order is measured better – not crossing over the absorption edge. Because of that, for 1st order the interpolated background position will be underestimated, where for 2nd order a little bit overestimated. This whole situation is a bit more complicated by different spectral resolution for 1st and 2nd orders. For 2nd order the Low-background can be placed between second order Kβ1 and Kα10 (or Kα10 and Kα9, they convolve into single little peak), and as spectral resolution is excellent there, the measurement of background there will be measurement of background and not some peak-tail. For 1st order placing the low-background between 1st order Kβ1 and Kα10,9 will give overestimated background as it will be on the tail of these much worse resolution peaks, thus escaping such clear disadvantage people tend to move the LOW background position further behind Kβ1 and thus behind the absorption edge – which is "from the pan to the fire" kind of situation.
Thus said – by using two background measurement method this test becomes comparing "apples" and "oranges" (as 1st order Mg Ka is impossible to measure precisely with 2 background method) and its outcome is highly at mercy of spectral resolution differences between particular XTAL's. I would redo test with single background method, with background measured only from HIGH position, with precise slope (which can be estimated comparing artifact free other element wavescans of different Z, i.e. SiO2, NiO, Cr, Al2O3 (albeit there is a small slope introduced by Al KLL RAE lines-continuum)).
Sure, the background measurements need to be carefully placed and for this experiment I attempted to place them at relatively similar positions. And these first and second order measurements are all using the same Bragg crystal on each spectrometer, so the change in resolution is minor.
And besides, why would one spectometer's k-ratios be so different from the others as they all used similar background offsets? But I suspect it is a moot point as the peak to background ratios for these elements (even for 2nd order reflections) are very large, e.g.,:
STKF: .4220 .4220 .4220 .3997 .3997 .3997 ---
STCT: 63.66 177.66 80.22 84.60 204.61 94.12 ---
UNKF: .1212 .1152 .1129 .2198 .2233 .2214 ---
UNCT: 18.28 48.52 21.46 46.51 114.31 52.13 ---
UNBG: .06 .18 .08 .10 .25 .09 ---
ZCOR: 1.2233 1.2233 1.2233 1.6221 1.6221 1.6221 ---
KRAW: .2872 .2731 .2675 .5497 .5587 .5538 ---
PKBG: 301.21 269.95 282.24 459.31 467.16 677.37 ---
I don't think the k-ratios for these major elements are going to change 6% just from a slight difference in the background placement. But please go ahead and make your own measurements, we would be very interested in seeing them.
And for my part I will re-scan the backgrounds again and re-run next weekend...
Quote from: Probeman on April 02, 2025, 04:39:33 PMSure, the background measurements need to be carefully placed and for this experiment I attempted to place them at relatively similar positions. And these first and second order measurements are all using the same Bragg crystal on each spectrometer, so the change in resolution is minor.
If that change is minor, when I would like to know how "huge" change would looks like? :)
(https://smf.probesoftware.com/gallery/1607_03_04_25_6_02_54.png)
Different sections of MgO wavescan made with same spectrometer, same XTAL, same conditions. X axes got scaled so that it would span similar comparable region ( Kb and Ka juxtaposed vertically). Y got scaled to 20% of maximum of Mg Ka peak in both cases. Now to make a point – look to the Ka3,4 peaks, and please notice twice the amplitude on 1st order, than on second order. In 1st order measurements of main peak, we also partially measure effect of Ka3,4 (its tail overlaps with Ka1,2), on second order such tail of Ka3,4 won't overlap on main Ka1,2 peak in case of that XTAL. Why it is important? Ka3,4 depends from crystallography - depends from phase, thus including and excluding it from measurement can impact the k-ratio. how much it is included/excluded is directly controlled by resolution of particular XTAL.
I am not telling that experiment is not worth to pursuit, I just want to point out that there is very easy way to measure "apples" and "oranges" and needs very careful approach. If only there would be much simpler - single X-ray line like element for the same region...
Where are your background positions? Let's see the k-ratios!
And more to the point, if these problems with the background are so large,
why do they only manifest on one of the spectrometers for both Mg and Al, and not on the other spectrometers?
But to your point, I suspect the effect of backgrounds are minor on these k-ratios because the background positions I selected are well away from those secondary peaks, and the peak to background ratios are very large, so the background intensities have only a minor effect on major elements. In fact the peak to background ratios on spec 1 for Mg Ka is higher than for spec 2 and 3 (as pointed out above):
STKF: .4220 .4220 .4220 .3997 .3997 .3997 ---
STCT: 63.66 177.66 80.22 84.60 204.61 94.12 ---
UNKF: .1212 .1152 .1129 .2198 .2233 .2214 ---
UNCT: 18.28 48.52 21.46 46.51 114.31 52.13 ---
UNBG: .06 .18 .08 .10 .25 .09 ---
ZCOR: 1.2233 1.2233 1.2233 1.6221 1.6221 1.6221 ---
KRAW: .2872 .2731 .2675 .5497 .5587 .5538 ---
PKBG: 301.21 269.95 282.24 459.31 467.16 677.37 ---
Also note that the background is only 0.3% of the peak intensity for spec 1, so even doubling the background intensity would not equate to a ~6% change in the k-ratio! Here are the two scans normalized and plotted as keV on the x-axis:
(https://smf.probesoftware.com/gallery/395_03_04_25_7_31_40.png)
Where the magenta vertical lines are the default off-peak peak positions, and the green vertical lines are the off-peak positions actually utilized.
This weekend, I will scan further out and place the backgrounds even further away, so we'll see. And/or I'll utilize MAN backgrounds (e.g., add SiO2 into the acquisition) where no off-peaks are utilized!
In the meantime you should measure these Mg and Al k-ratios yourself also. The actual compositions don't matter so much as long as the materials are homogeneous and you measure at least 4 or more points per material.
Show me the data! :)
Although there are a few degrees of freedom to the JEOL spectrometer plate within the WDS housing*, it would be good to see what happens to the Mg Ka I and Mg Ka II K-ratios from SP1 (MgAl2O3 vs MgO) when you vary the take off angle in the probewin.ini file (or might be easier to replicate the .mdb file multiple times and change the take off in each e.g. _38.MDB for a 38 degree TOA for SP1). I'm wondering whether you could determine a more appropriate take off angle to use for that spectrometer.
*meaning the axis of movement for the crystal might not actually point at the exact spot on the sample where the X-ray emission is occurring, in which case the take off angle will actually be a variable dependent on spectrometer L value. That'll be fun...
Also, another way to check for spectrometer alignment is to do a low magnification beam scan map over a perfectly flat and homogeneous sample. The idea is that you want to see the Bragg defocusing on the map, where the band of peak emission should run through the middle of the mapped area. You can even work out if your plate is either too high or too low dependent on which way off-centre the band of maximum intensity runs.
Quote from: JonF on April 03, 2025, 07:56:05 AMAlthough there are a few degrees of freedom to the JEOL spectrometer plate within the WDS housing*, it would be good to see what happens to the Mg Ka I and Mg Ka II K-ratios from SP1 (MgAl2O3 vs MgO) when you vary the take off angle in the probewin.ini file (or might be easier to replicate the .mdb file multiple times and change the take off in each e.g. _38.MDB for a 38 degree TOA for SP1). I'm wondering whether you could determine a more appropriate take off angle to use for that spectrometer.
*meaning the axis of movement for the crystal might not actually point at the exact spot on the sample where the X-ray emission is occurring, in which case the take off angle will actually be a variable dependent on spectrometer L value. That'll be fun...
Good point. In fact that's one reason I suggest running a calculation using the Calculate Effective Takeoff Angle K-Ratios menu dialog in CalcZAF:
https://smf.probesoftware.com/index.php?topic=598.msg12062#msg12062
That is, you want to make sure you have the largest absorption correction possible from your primary to secondary standard to ensure you have maximum sensitivity to the spectrometer alignment.
That is why I like the MgCr2O4 synthetic that Joe Boesenberg obtained from Oak Ridge Nat'l Lab:
Effective K-Ratios for Primary Standard: 3012 MgO FIGMAS
Secondary Standard: 41 MgCr2O4
Emission line: Mg ka at 15 keV
Absorption Correction Method: Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS
MAC File: LINEMU Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV
Absolute k-ratio change per degree at 40 degrees: .000968
Percent (relative) k-ratio change per degree at 40 degrees: .666299
Takeoff Angle: 35.0000, K-Ratio: .138970
Takeoff Angle: 35.5000, K-Ratio: .139547
Takeoff Angle: 36.0000, K-Ratio: .140113
Takeoff Angle: 36.5000, K-Ratio: .140669
Takeoff Angle: 37.0000, K-Ratio: .141214
Takeoff Angle: 37.5000, K-Ratio: .141750
Takeoff Angle: 38.0000, K-Ratio: .142275
Takeoff Angle: 38.5000, K-Ratio: .142791
Takeoff Angle: 39.0000, K-Ratio: .143298
Takeoff Angle: 39.5000, K-Ratio: .143795
Takeoff Angle: 40.0000, K-Ratio: .144284
Takeoff Angle: 40.5000, K-Ratio: .144763
Takeoff Angle: 41.0000, K-Ratio: .145234
Takeoff Angle: 41.5000, K-Ratio: .145695
Takeoff Angle: 42.0000, K-Ratio: .146149
Takeoff Angle: 42.5000, K-Ratio: .146594
Takeoff Angle: 43.0000, K-Ratio: .147031
Takeoff Angle: 43.5000, K-Ratio: .147460
Takeoff Angle: 44.0000, K-Ratio: .147881
Takeoff Angle: 44.5000, K-Ratio: .148294
Takeoff Angle: 45.0000, K-Ratio: .148699
The relative change of 0.6% per degree in the k-ratio ensures good sensitivity. And at 20 keV (which is what I used for these above measurements), the effect is even larger:
Effective K-Ratios for Primary Standard: 3012 MgO FIGMAS
Secondary Standard: 41 MgCr2O4
Emission line: Mg ka at 20 keV
Absorption Correction Method: Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS
MAC File: LINEMU Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV
Absolute k-ratio change per degree at 40 degrees: .000919
Percent (relative) k-ratio change per degree at 40 degrees: .755964
Takeoff Angle: 35.0000, K-Ratio: .115711
Takeoff Angle: 35.5000, K-Ratio: .116236
Takeoff Angle: 36.0000, K-Ratio: .116754
Takeoff Angle: 36.5000, K-Ratio: .117265
Takeoff Angle: 37.0000, K-Ratio: .117769
Takeoff Angle: 37.5000, K-Ratio: .118266
Takeoff Angle: 38.0000, K-Ratio: .118756
Takeoff Angle: 38.5000, K-Ratio: .119239
Takeoff Angle: 39.0000, K-Ratio: .119715
Takeoff Angle: 39.5000, K-Ratio: .120184
Takeoff Angle: 40.0000, K-Ratio: .120647
Takeoff Angle: 40.5000, K-Ratio: .121103
Takeoff Angle: 41.0000, K-Ratio: .121553
Takeoff Angle: 41.5000, K-Ratio: .121996
Takeoff Angle: 42.0000, K-Ratio: .122432
Takeoff Angle: 42.5000, K-Ratio: .122862
Takeoff Angle: 43.0000, K-Ratio: .123286
Takeoff Angle: 43.5000, K-Ratio: .123703
Takeoff Angle: 44.0000, K-Ratio: .124114
Takeoff Angle: 44.5000, K-Ratio: .124519
Takeoff Angle: 45.0000, K-Ratio: .124917
Quote from: JonF on April 03, 2025, 07:56:05 AMI'm wondering whether you could determine a more appropriate take off angle to use for that spectrometer.
As you know, one can specify an effective takeoff angle in PFE based on a measured sample tilt (using the sample z focus values) and your spectrometer orientation:
https://smf.probesoftware.com/index.php?topic=1579.0
But I hesitate to make this a user editable parameter... though it can be specified in the SCALERS.DAT file for each spectrometer/crystal combination if absolutely necessary! As documented in the PFE User's Reference Manual/Help file.
And it might come to that if the mechanical alignment cannot be improved upon... >:(
Quote from: JonF on April 03, 2025, 08:02:06 AMAlso, another way to check for spectrometer alignment is to do a low magnification beam scan map over a perfectly flat and homogeneous sample. The idea is that you want to see the Bragg defocusing on the map, where the band of peak emission should run through the middle of the mapped area. You can even work out if your plate is either too high or too low dependent on which way off-centre the band of maximum intensity runs.
Your suggestion reminds me of the "alignment peak center" test in the StartWin application:
https://smf.probesoftware.com/index.php?topic=953.msg6136#msg6136
originally suggested by Paul Carpenter...
Basically, it performs a number of automated peak center scans, and one plots the highest intensity from each peak scan to see how well it correlates to the stage optical Z focus.
Yeah, I guess its similar.
In my case, I was doing some beam scan maps at the transition region between stage scan and beam scan maps and noticed a gradient across one of the spectrometers that I didn't think came from the sample.
I ran a low magnification beam scan map ("400x", or 300 microns across with a 1.2 micron step size) over a perfectly flat, optically focussed V metal standard and got the result below. I've labelled (roughly) the peak intensity (diagonal red line running perpendicular to the direction to the spectrometer, which is labelled by the black arrow). The green vertical line is the mid point of the map (in the X plane) and the black dashed line shows the direction you can offset the maximum intensity by moving the spectrometer plate up and down.
(https://smf.probesoftware.com/gallery/796_04_04_25_9_37_12.jpeg)
I had the engineer come in and realign that spectrometer, and that line of maximum intensity now intersects the midpoint of the map.
PS I apologise to any colourblind people trying to figure out what I'm on about above!
Quote from: JonF on April 04, 2025, 09:45:43 AMI had the engineer come in and realign that spectrometer, and that line of maximum intensity now intersects the midpoint of the map.
Was this a TAP spectrometer/crystal?
It would be cool if you could run these Bragg order k-ratio tests using Mg and Al Ka as described above. It's a pretty straight forward measurement and provides a quantitative test over the range of the spectrometer.
Quote from: Probeman on April 04, 2025, 10:52:36 AMQuote from: JonF on April 04, 2025, 09:45:43 AMI had the engineer come in and realign that spectrometer, and that line of maximum intensity now intersects the midpoint of the map.
Was this a TAP spectrometer/crystal?
It would be cool if you could run these Bragg order k-ratio tests using Mg and Al Ka as described above. It's a pretty straight forward measurement and provides a quantitative test over the range of the spectrometer.
This was a PET crystal, although that spectrometer does have a TAP crystal and I ran these maps a couple of years ago. I used V metal as I could see it on all spectrometers with the somewhat unusual crystal configuration our 8530F has.
I plan on testing out the Bragg order K-ratio tests with the FIGMAS block as soon as our instrument is back up and running.
We have a mystery that I need your help with...
I ran the MgO, Al2O3 and MgAl2O4 standards again this last weekend on my Cameca instrument to compare to what Joe Boesenberg is seeing on his instrument:
https://smf.probesoftware.com/index.php?topic=1718.15
We got some more results, and they confirm what I saw a week ago. However, in thinking about the difference in k-ratios for Mg Ka on spec 1, I just can't believe that this is a problem with the spectrometer alignment, at least so far as the effective take off angle is concerned.
Let me first discuss the new results. I re-peaked Mg and Al ka, and then re-checked the background positions, changing them to be even further out from the peak as seen here:
(https://smf.probesoftware.com/gallery/395_15_04_25_1_35_58.png)
These improved peak to background ratios are now even better than the previous measurements, so the background correction is now even less of a possible issue as SG wondered above.
STKF: .4220 .4220 .4220 .3997 .3997 .3997 ---
STCT: 61.69 178.02 78.97 80.23 206.72 93.69 ---
UNKF: .1187 .1140 .1151 .2199 .2222 .2217 ---
UNCT: 17.36 48.10 21.53 44.14 114.92 51.96 ---
UNBG: .06 .14 .06 .12 .21 .09 ---
ZCOR: 1.2237 1.2237 1.2237 1.6212 1.6212 1.6212 ---
KRAW: .2814 .2702 .2726 .5502 .5559 .5546 ---
PKBG: 318.69 343.39 380.35 408.47 558.35 584.23 ---
Then there's the dead time correction question which could be spectrometer dependent, but the other spectrometers have higher count rates and both 1st and 2nd order k-ratios are within statistics for those spectrometers. And in any case all these count rates are under 20K cps, and we're using the log dead time correction so I don't think the dead time correction is the issue either.
So what is causing the Mg Ka k-ratios on spectrometer 1 to be so different for the 1st and 2nd order measurements?
To be continued...
Quote from: Probeman on April 15, 2025, 01:38:25 PMWe have a mystery that I need your help with...
My preliminary calculation from wavescan taken at 25kV some time ago on our SXFiveFE for Mg 2nd order K-ratio in MgO/MgAl2O4 is
0.267 which seems to be close in agreement what you got with 1st order and second order for 3rd and 4th spectrometers.
Again, You are right – the background positions should not influence k-ratios up to 6%. I still think there could be some spectrometer resolution differences between those which could cause your observations. At 1st order all the measurements from all spectrometers will be similar as KA1 and KA2 will be convolved into visible and mathematically indistinguishable single peak (also amplitude includes the tail from KA3). On 2nd order the Mg KA peak asymmetry is starting to show up due to KA1 and KA2 small energy difference (there is still not clearly observable 2 peaks, but shape of the peak (a buldge) starts to show up, depending from resolution and lack of segmentation of TAP).
Proposition for experiment: Instead of calculating k-ratios on measurements made with Pk-bkgd method I would suggest try doing k-ratios from measured integral/area of the peak.
My other experiences (which somehow is connected with issue):
* Some time ago due to extreme overlap-hell (42+ measured elements) (before Peaksight introduced possibility of negative interference correction) I was for some time measuring Si Ka on the second order line to get away with it. It however appeared to be much much much less stable than the first order, and required constant re-calibration, thus I had dropped that completely after upgrading to Peaksight 6.5. As far I could remember, both amplitude and peak shift was very unstable.
* fluorine measurement on TAP vs PC0, or "when worse spectral resolution "is better"". The major problem with fluorine on TAP is that its shape will change from measured phase to phase, and pk-bkgd measurement method is not reliable (CaF2, Topaz-F, Biotite-F, Apatite-F – every phase would have different shape and standardization based on pk-bkgd would not work). On PC0 standardization works as expected and i.e. flourine can be mesured in CaF2 and Biotite-F and Apatite-F using the same Topaz-F standard. That is thanks to worse spectral resolution, where all those minute details of F KA shape observed on TAP is merged/convolved into single Voigt function shape on PC0 - and thus pk-bkgd due to worse resolution then works correctly on PC0, where due to too good spectral resolution on TAP does not work. TAP could work in limited cases for Florine if there is possibility to use peak/area method.
Quote from: sem-geologist on April 16, 2025, 05:21:51 AMProposition for experiment: Instead of calculating k-ratios on measurements made with Pk-bkgd method I would suggest try doing k-ratios from measured integral/area of the peak.
My other experiences (which somehow is connected with issue):
* Some time ago due to extreme overlap-hell (42+ measured elements) (before Peaksight introduced possibility of negative interference correction) I was for some time measuring Si Ka on the second order line to get away with it. It however appeared to be much much much less stable than the first order, and required constant re-calibration, thus I had dropped that completely after upgrading to Peaksight 6.5. As far I could remember, both amplitude and peak shift was very unstable.
* fluorine measurement on TAP vs PC0, or "when worse spectral resolution "is better"". The major problem with fluorine on TAP is that its shape will change from measured phase to phase, and pk-bkgd measurement method is not reliable (CaF2, Topaz-F, Biotite-F, Apatite-F – every phase would have different shape and standardization based on pk-bkgd would not work). On PC0 standardization works as expected and i.e. flourine can be mesured in CaF2 and Biotite-F and Apatite-F using the same Topaz-F standard. That is thanks to worse spectral resolution, where all those minute details of F KA shape observed on TAP is merged/convolved into single Voigt function shape on PC0 - and thus pk-bkgd due to worse resolution then works correctly on PC0, where due to too good spectral resolution on TAP does not work. TAP could work in limited cases for Florine if there is possibility to use peak/area method.
I will do the integrated area measurement, but I very much doubt there's a peak shape change because the bonding physics is the same in both measurements.
More importantly, if the change between 1st and 2nd order Bragg k-ratios is due to a change in spectrometer resolution, why does this effect only appear in one spectrometer?
Continuing from the previous post...
So what is causing the Mg Ka k-ratios on spectrometer 1 to be so different for the 1st and 2nd order measurements? Using the CalcZAF effective angle k-ratio calculator I get these results for Mg Ka at 20 keV for MgAl2O4 as the secondary standard and MgO as the primary standard:
Effective K-Ratios for Primary Standard: 3012 MgO FIGMAS
Secondary Standard: 3100 MgAl2O4 FIGMAS
Emission line: Mg ka at 20 keV
Absorption Correction Method: Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS
MAC File: LINEMU Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV
Absolute k-ratio change per degree at 40 degrees: .000294
Percent (relative) k-ratio change per degree at 40 degrees: .107318
Takeoff Angle: 35.0000, K-Ratio: .271588
Takeoff Angle: 35.5000, K-Ratio: .271767
Takeoff Angle: 36.0000, K-Ratio: .271943
Takeoff Angle: 36.5000, K-Ratio: .272115
Takeoff Angle: 37.0000, K-Ratio: .272283
Takeoff Angle: 37.5000, K-Ratio: .272448
Takeoff Angle: 38.0000, K-Ratio: .272609
Takeoff Angle: 38.5000, K-Ratio: .272767
Takeoff Angle: 39.0000, K-Ratio: .272922
Takeoff Angle: 39.5000, K-Ratio: .273073
Takeoff Angle: 40.0000, K-Ratio: .273221
Takeoff Angle: 40.5000, K-Ratio: .273367
Takeoff Angle: 41.0000, K-Ratio: .273509
Takeoff Angle: 41.5000, K-Ratio: .273648
Takeoff Angle: 42.0000, K-Ratio: .273784
Takeoff Angle: 42.5000, K-Ratio: .273918
Takeoff Angle: 43.0000, K-Ratio: .274049
Takeoff Angle: 43.5000, K-Ratio: .274177
Takeoff Angle: 44.0000, K-Ratio: .274302
Takeoff Angle: 44.5000, K-Ratio: .274425
Takeoff Angle: 45.0000, K-Ratio: .274546
The thing is, if I plot this range of Bragg (1st and 2nd) order k-ratios from the new data as seen here:
(https://smf.probesoftware.com/gallery/395_16_04_25_9_02_58.png)
there's no reasonable change in effective takeoff angle that could explain this much of a variation in the k-ratios for the 1st and 2nd order reflections on spectrometer 1 for Mg Ka.
Note: the absolute values of the calculated k-ratios (e.g., the horizontal green lines), will depend on the specific matrix corrections and MAC tables selected.
And from a quant perspective, my spectrometer 1 shows a ~3.5% difference for Mg Ka, which is similar to what Joe Boesenberg at Brown is seeing on both his TAP spectrometers, but I'm seeing only on one of my three TAP spectrometers...
So what could be causing this? Ideas?
Here's the complete data from both sets of Bragg order k-ratio testing I did a few weeks ago...
To review, we've all known about the simultaneous k-ratio tests, which attempts to determine if the k-ratios produced from our spectrometers agree with each other within statistics. And the physics indicates that these 1st and 2nd order k-ratios should be statistically similar.
And of course that extends to comparisons with spectrometers on other instruments in other labs! That is the essence of the "consensus k-ratio" tests that have been proposed by several of us:
https://smf.probesoftware.com/index.php?topic=1239.0
https://smf.probesoftware.com/index.php?topic=1415.0
For such testing of the consistency of spectrometer k-ratios on your own instrument, I suggest running the "constant k-ratio" test which tests three separate aspects: dead time, picoammeter linearity and (if you measure your k-ratios on more than one spectrometer) also simultaneous k-ratios, depending on how you assign the primary standards to your data:
https://smf.probesoftware.com/index.php?topic=1466.msg11102#msg11102
But how do we know if a single spectrometer is producing consistently accurate k-ratios? Well, Peter McSwiggen suggested we measure k-ratios for both 1st order reflections and also the 2nd order reflections as described here at the beginning of this topic:
https://smf.probesoftware.com/index.php?topic=1739.0
Because regardless of the Bragg reflection, we should obtain the same k-ratios within statistics. And there's two things to consider: first the consistency between the 1st and 2nd order k-ratios, but also, how do the k-ratios we measure compare to our physics models in an absolute accuracy sense? Yes, it's a bit circular...
Here is a plot for Mg Ka at 20 keV, again showing the range of k-ratios from PAP/FFAST k-ratios from 35 to 45 degrees:
(https://smf.probesoftware.com/gallery/395_03_05_25_3_14_08.png)
Clearly Spec 1 has a problem with Mg, but the other two are quite reasonable. And here for Al Ka also at 20 keV:
(https://smf.probesoftware.com/gallery/395_03_05_25_3_14_29.png)
The upper range for Al Ka is off the plot (45 degrees = ~ 0.570, but the measured data is mostly within the 35 degree limit. As to the accuracy of the analytical calculations, that is the question...
What surprises me though, is how much these k-ratios vary, if the effective takeoff angle is the only variable here!
John
For your post of April 2, for the first and second order Al results, you get a value of about 0.562. I get a value of about 0.605 for all of my Bragg tests with spinel all the way back to March. Are we using such different conditions and correction procedures? Seems like this is really big difference.
Joe
Quote from: Joe Boesenberg on June 25, 2025, 07:16:48 PMFor your post of April 2, for the first and second order Al results, you get a value of about 0.562. I get a value of about 0.605 for all of my Bragg tests with spinel all the way back to March. Are we using such different conditions and correction procedures? Seems like this is really big difference.
Good eye! Yes, the expected 15 keV k-ratio for Al Ka (Al2O3/MgAl2O4) is around 0.60:
QuoteEffective K-Ratios for Primary Standard: 3013 Al2O3 FIGMAS
Secondary Standard: 3100 MgAl2O4 FIGMAS
Emission line: Al ka at 15 keV
Absorption Correction Method: Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS
MAC File: LINEMU Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV
Absolute k-ratio change per degree at 40 degrees: .001716
Percent (relative) k-ratio change per degree at 40 degrees: .281803
Takeoff Angle: 35.0000, K-Ratio: .597463
Takeoff Angle: 35.5000, K-Ratio: .598536
Takeoff Angle: 36.0000, K-Ratio: .599585
Takeoff Angle: 36.5000, K-Ratio: .600608
Takeoff Angle: 37.0000, K-Ratio: .601606
Takeoff Angle: 37.5000, K-Ratio: .602581
Takeoff Angle: 38.0000, K-Ratio: .603534
Takeoff Angle: 38.5000, K-Ratio: .604464
Takeoff Angle: 39.0000, K-Ratio: .605373
Takeoff Angle: 39.5000, K-Ratio: .606261
Takeoff Angle: 40.0000, K-Ratio: .607128
Takeoff Angle: 40.5000, K-Ratio: .607976
Takeoff Angle: 41.0000, K-Ratio: .608804
Takeoff Angle: 41.5000, K-Ratio: .609614
Takeoff Angle: 42.0000, K-Ratio: .610405
Takeoff Angle: 42.5000, K-Ratio: .611178
Takeoff Angle: 43.0000, K-Ratio: .611934
Takeoff Angle: 43.5000, K-Ratio: .612674
Takeoff Angle: 44.0000, K-Ratio: .613396
Takeoff Angle: 44.5000, K-Ratio: .614103
Takeoff Angle: 45.0000, K-Ratio: .614795
But for 20 keV the expected k-ratio for Al Ka (Al2O3/MgAl2O4) is around 0.56:
QuoteEffective K-Ratios for Primary Standard: 3013 Al2O3 FIGMAS
Secondary Standard: 3100 MgAl2O4 FIGMAS
Emission line: Al ka at 20 keV
Absorption Correction Method: Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS
MAC File: LINEMU Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV
Absolute k-ratio change per degree at 40 degrees: .002098
Percent (relative) k-ratio change per degree at 40 degrees: .372878
Takeoff Angle: 35.0000, K-Ratio: .548901
Takeoff Angle: 35.5000, K-Ratio: .550176
Takeoff Angle: 36.0000, K-Ratio: .551424
Takeoff Angle: 36.5000, K-Ratio: .552647
Takeoff Angle: 37.0000, K-Ratio: .553845
Takeoff Angle: 37.5000, K-Ratio: .555019
Takeoff Angle: 38.0000, K-Ratio: .556169
Takeoff Angle: 38.5000, K-Ratio: .557295
Takeoff Angle: 39.0000, K-Ratio: .558398
Takeoff Angle: 39.5000, K-Ratio: .559480
Takeoff Angle: 40.0000, K-Ratio: .560539
Takeoff Angle: 40.5000, K-Ratio: .561577
Takeoff Angle: 41.0000, K-Ratio: .562594
Takeoff Angle: 41.5000, K-Ratio: .563590
Takeoff Angle: 42.0000, K-Ratio: .564567
Takeoff Angle: 42.5000, K-Ratio: .565524
Takeoff Angle: 43.0000, K-Ratio: .566462
Takeoff Angle: 43.5000, K-Ratio: .567381
Takeoff Angle: 44.0000, K-Ratio: .568282
Takeoff Angle: 44.5000, K-Ratio: .569165
Takeoff Angle: 45.0000, K-Ratio: .570029
Yes, my measurements here:
https://smf.probesoftware.com/index.php?topic=1739.msg13407#msg13407
were performed at 20 keV...
Why? Because the 20 keV measurement is more sensitive to the effective takeoff angle, e.g., at 15 keV:
Percent (relative) k-ratio change per degree at 40 degrees: .281803
and at 20 keV:
Percent (relative) k-ratio change per degree at 40 degrees: .372878
As some of you may know, Joe Bosenberg had some trouble getting quantitative results on his TAP spectrometers on his new JEOL iHP200F instrument:
https://smf.probesoftware.com/index.php?topic=1718.0
After six months of continued efforts by him and his local JEOL service engineer without resolution of the problem, Joe was able to get JEOL service engineer John Glass to come out to take a look. John was able to determine the problem and get Joe's spectrometers properly aligned:
https://smf.probesoftware.com/index.php?topic=1718.msg13502#msg13502
I wrote to John to ask him what exactly he did to get Joe's spectrometers aligned and I here post here (with permission) what he said:
QuoteHi John,
The baseplate alignment is done using an alignment script, where it will defocus the stage, peak, and measure. Plots the measured counts out and fits a curve to determine where to adjust the baseplate.
The crystal is usually done with the alignment script in the same way. But I prefer to align the crystal without the script because I find it's faster, and improves reproducibility at the upper middle and upper end of the spectrometer.
I will focus on the standard (Si Metal for PET, Ti Metal for LiF, Mg Metal for TAP). I will then peak the spectrometer. I open up the chart recorder and adjust the count rate to at least 20kcps, usually shooting for the range of 20k-40kcps. I usually use 25kV for this.
Looking at the chart recorder, I will then defocus the stage, going +100um from just focus (I use +50um for LiF), and observe the count rate. Then I go -100um from just focus (-50um for LiF) and observe the count rate. I want to see less than a 1000 cps difference between the defocused count rates. If not, I will adjust the crystal at the -100um (-50um LiF) from focus spot and try to split the difference (usually need to go over a little bit). Then I repeak at just focus, and check again until I'm satisfied. If a large adjustment was done, I will redo the baseplate alignment.
It's also important to check the belt linearity, as this affects the alignment of the spectrometer between the baseplate and the crystal. The spec is a delta Z of 40um for standard spectrometers, and 60um for H type. But the better you get this, the better the performance and reproducibility will be. So even though the belt linearity passed on Joe's CH-3 spectrometer, I tweaked the belt length to get it a little bit better.
I find the problems with the alignment scripts is sometimes there will be an outlier in the measurements (like a noise spike) and it will include that in its calculations. If the engineer is not familiar with interpreting the data, they will end up just following the script's adjustment instructions and end up in a loop where they are chasing their tails. Sometimes the script will fail in peaking, and it's not smart enough yet to know that, and so the count rates will be much different since it will use the previous peak position from the previous step's measurement. The scripts have gotten better, but they are not perfect.
I tend to see a bit of difference aligning the TAP manually compared to the scripts. PET and LiF not so much, where the results between script and manual adjustment is similar.
Hope that makes sense.
Regards,
John
To help perform these Bragg order k-ratio calibrations on your EPMA spectrometers, we added a document to the Probe for EPMA Help menu:
(https://smf.probesoftware.com/gallery/1_27_01_26_1_35_57.png)
Remember, that these tests can be performed with any materials containing the same element as long as they are beam stable and homogeneous. For the most sensitive Bragg order k-ratio measurements, consider running these tests at a higher beam energy, e.g., 20 or 25 keV in materials with relatively high absorption absorption characteristics. The goal being to obtain the same k-ratio within statistics at all Bragg orders if ones spectrometer is properly aligned.
Note that one can calculate k-ratios for specific primary and secondary standards as a function of effective takeoff angles in CalcZAF as described here:
https://smf.probesoftware.com/index.php?topic=598.msg12062#msg12062
Here is the calculation for SiO2 as the primary standard, Mg2SiO4 as the secondary standard at 25 keV. Note there is a 0.6% change in the k-ratio as a function of effective takeoff angle:
(https://smf.probesoftware.com/gallery/1_28_01_26_9_10_20.png)
This is helpful to test your spectrometer effective takeoff angles on TAP Bragg crystals using three Bragg orders:
Spectro position for si ka on TAP (2d=25.745 A) (Spc=140 mm), is 77.67373 (with refractive index correction, k= 0.00218)
Spectro position for si ka (II) on TAP (2d=25.745 A) (Spc=140 mm), is 155.0933 (with refractive index correction, k= 0.00218)
Spectro position for si ka (III) on TAP (2d=25.745 A) (Spc=140 mm), is 232.5695 (with refractive index correction, k= 0.00218)
Update Probe for EPMA (and CalcZAF) from the Help menu or download the latest apps from our web site for free:
https://www.probesoftware.com/resources/