If you have a Thermo NSS or Bruker Esprit EDS system on your EPMA instrument, you can specify that Probe for EPMA acquires a full EDS spectrum for every WDS analysis. These EDS spectra can subsequently be simply browsed to investigate low totals or possible sample charging, but they can also be quantified along with the WDS elements, so as long as there are appropriate EDS spectra acquired on suitable standards for the EDS elements that have been specified for quantitative analysis. This is full quant EDS with *standards*! Fortunately Probe for EPMA automatically also acquires a full EDS spectra on every specified standard, so the task is made significantly easier...
After specifying the elements by WDS acquisition, we go to the Acquisition Options button in the Acquire! window and select the Acquire EDS Spectrum Intensities option, followed by specifying the EDS acquisition time which can be the default in NSS or Esprit or user specified as shown here:
(https://smf.probesoftware.com/oldpics/i42.tinypic.com/wgw28.jpg)
In addition you'll want to check that the EDS and WDS counting times are roughly equal so there is less "slack time" in the acquisition as seen here:
(https://smf.probesoftware.com/oldpics/i40.tinypic.com/9s77uh.jpg)
Finally, we can start the integrated WDS-EDS acquisition as usual from the Acquire! or Automate! windows. The EDS acquisition display will be shown with the current spectra as seen here:
(https://smf.probesoftware.com/oldpics/i41.tinypic.com/r953ww.jpg)
The acquired EDS spectra can be viewed from the Run | Display and Export EDS Spectra menu dialog as seen here:
(https://smf.probesoftware.com/gallery/1_20_10_18_9_44_46.png)
The selected samples and data lines can be selected as shown here and the individual spectra can be displayed in a re-sizable window if desired:
(https://smf.probesoftware.com/oldpics/i43.tinypic.com/10h7q7r.jpg)
Elements by EDS are entered in the Elements/Cations dialog as seen here:
(https://smf.probesoftware.com/gallery/1_20_02_19_8_08_51.png)
In addition we can optionally display the calculated net intensities for the specified EDS quant elements as seen here:
(https://smf.probesoftware.com/oldpics/i44.tinypic.com/efo28x.jpg)
Finally, we click the Analyze button in the Analyze! window and the log window output is seen here, with trace elements by WDS and major elements by EDS:
(https://smf.probesoftware.com/oldpics/i39.tinypic.com/2aklksy.jpg)
I caught myself looking for a "Like" button. Awesome feature.
Be sure to check out these new improvements to integrated EDS-WDS in PFE:
https://smf.probesoftware.com/index.php?topic=482.msg2826#msg2826
To prevent the software from re-calculating the EDS net intensities (for example, until you are ready for quantitative analysis results), simply select your samples in the Analyze! window and click the Calculation Options button and turn off the EDS processing as seen here:
(https://smf.probesoftware.com/oldpics/i58.tinypic.com/21crr4n.jpg)
This will not affect your subsequent acquisition of EDS spectra, and when you are ready to reprocess EDS data, simply select the samples again and this time apply the Use EDS Element Data option.
The Thermo and Bruker EDS WDS integration in Probe for EPMA is constantly being improved. One can now access all EDS spectra acquired in a run from the Run | Display and Export EDS Spectra menu dialog as seen here:
(https://smf.probesoftware.com/oldpics/i58.tinypic.com/nyhhs1.jpg)
Note that EDS elements can now be quantitatively corrected for interferences just as has been the case for WDS elements as described here:
https://smf.probesoftware.com/index.php?topic=482.msg2826#msg2826
I wanted to show the new Acquisition Options and Elements/Cations dialog windows because they have been changed extensively since this topic was last updated. Here is the new Acquisition Options dialog:
(https://smf.probesoftware.com/gallery/1_19_09_16_3_35_50.png)
And here is the new Elements/Cations dialog:
(https://smf.probesoftware.com/gallery/1_19_09_16_3_38_00.png)
Note that the WDS and EDS elements (and unanalyzed elements by specification) are specified in the same window now. This means that one can perform interference corrections between WDS by WDS, WDS by EDS, EDS by EDS and EDS by WDS.
And here is a screen shot of the new graphics for displaying EDS spectra in Probe for EPMA:
(https://smf.probesoftware.com/gallery/1_27_04_17_9_05_16.png)
The cool thing is that because PFE acquires and stores the full EDS spectrum for every analysis, one can add or remove elements by EDS in post processing for quantification with the WDS elements.
In fact many Probe for EPMA users are now routinely acquiring all their major elements with EDS and just using WDS for the trace elements which really speeds things up. Note that Probe Software currently supports complete integration with both Thermo (NSS and Pathfinder) and Bruker (Esprit) EDS systems.
Attached (please login to see attachments) is my 2016 EPMA Topical Conference talk (Madison, WI) on integrated EDS-WDS with Thermo and Bruker systems.
john
I recently modified the EDS acquisition code to utilize a "sample counting time" option. It used to be called a "preset count time" option which utilized the EDS integration time of the EDS software, but Bruker doesn't have an API call for this, and I've personally never seen a good reason for using the EDS software integration time as opposed to a "user specified count time" option which was already there.
So now with this new option the software will automatically calculate how long the WDS elements will take to acquire and simply sets the EDS integration time to that number (minus a correction for deadtime, since the EDS acquisition time is in "live time" units.
(https://smf.probesoftware.com/gallery/1_16_08_17_2_52_23.png)
I believe that Karsten Goemann mentioned this as an idea some time ago and I only just gotten around to implementing it because I finally managed to think of a reasonable method to get it working. :-[
Anyway, it's all working now. Update from the Help menu and give it a whirl!
john
Hi John
Any update on doing this with a "JEOL" EDS detector?
Richard
Hi Richard,
Vern Robertson (JEOL USA) wrote this to us a few days ago:
QuoteI received confirmation from our factory that they will release the final version of the API at around M&M time frame (so early-mid August).
Sorry for the delay. I know that the original date was sometime May-June of this year.
Once we get the new API from Japan it will need to be tested again by Glenn Poirior in Ottawa. We tested the beta JEOL EDS API last year and it worked, but had some glitches that JEOL needed to fix. If it all looks good, we will make an announcement and release a new PFE sometime after that.
A colleague of ours contacted us recently about a problem they were having performing EDS analyses in PFE. That is, acquiring only EDS spectra and no WDS elements. They had this method working great for them when they had been using Thermo NSS, but they recently upgraded to the new Thermo Pathfinder software, and now they are just seeing zero intensities when displaying the raw data (by double-clicking on the sample) as seen here:
EDS Spectrum Parameters (for datarow=1):
Time Constant= 0, Sample Time= 60.0
Elapsed Time= 75.3, Dead Time(%)= 20.4
Live Time= 60.0, Channels= 2048
Ev Per Chan= 10, Max Counts= 69277
On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: Al ka Si ka Ca ka Mg ka Fe ka BEAM1 BEAM2
BGD: EDS EDS EDS EDS EDS
SPEC: 0 0 0 0 0
CRYST: EDS EDS EDS EDS EDS
ORDER: 1 1 1 1 1
5G .00 .00 .00 .00 .00 19.970 19.970
AVER: .00 .00 .00 .00 .00 19.970 19.970
SDEV: .00 .00 .00 .00 .00 .000 .000
1SIG: .00 .00 .00 .00 .00
SIGR: .00 .00 .00 .00 .00
SERR: .00 .00 .00 .00 .00
%RSD: .00 .00 .00 .00 .00
This made us wonder if there was an issue with the new Thermo Pathfinder software, but as it turns out, it was working fine. I should mention that the new Thermo Pathfinder software is really awesome, but you want to be at v. 1.3.22 or higher.
If our colleague had been acquiring both EDS and WDS elements, the actual problem would have been more obvious as you will see. The other clue was that we could see the net intensities properly displayed in the EDS spectra display dialog in Probe for EPMA (from the Run menu) as seen here:
(https://smf.probesoftware.com/gallery/1_20_10_18_9_47_02.png)
and *also* in the Thermo Pathfinder software. But when we clicked the Analyze button in the Analyze! window it displayed this message:
(https://smf.probesoftware.com/gallery/1_20_10_18_9_44_19.png)
Huh, I thought. That's weird. Then scrolling up the log window output a bit we discovered this message:
EDS Acquisition (user specified) Time: 60.00
Number of Data Lines: 1 Number of 'Good' Data Lines: 1
First/Last Date-Time: 10/19/2018 02:45:13 PM to 10/19/2018 02:45:13 PM
WARNING- EDS Spectrum Data Analysis is disabled
Wait, what? What is this "WARNING- EDS Spectrum Data Analysis is disabled" message?
It turns out that Probe for EPMA is very flexible, one can acquire EDS spectra with WDS elements, or just WDS elements, or just EDS spectra elements, but if you want to include them in your quant calculations, one needs to "turn them on" using the Calculation Options dialog from the Analyze! window as seen here:
(https://smf.probesoftware.com/gallery/1_20_10_18_9_55_28.png)
Now you might say "Why is there an option for this? Why not have it turned on all the time?". Well, we often acquire EDS spectra routinely with our WDS data just to check for missing elements or for checking sample charging (observing the Duane-Hunt limit). Also sometime we want to switch back and forth between a WDS acquired element and an EDS acquired element.
Also, sometimes we don't want to have to fire up the EDS software, if we are not interested in seeing EDS intensities (we utilize the Bruker and Thermo software obtain the EDS net intensities because, well, they know what they are doing with EDS spectra!). Once we have the net intensities from our standards and our unknowns we can run them through the matrix and interference, etc., corrections with or without the WDS elements. Pretty cool!
If our colleague had been analyzing some WDS elements also, this problematic option would have been more obvious because the WDS element intensities would have been properly displayed, and only the EDS elements would have had zero intensities.
So we realized that we needed to make that warning about the missing standard intensities more explicit, if the missing standard intensity is an EDS element. So now the error dialog (as soon we upload the next version) will show this message:
(https://smf.probesoftware.com/gallery/1_20_10_18_9_44_33.png)
We also now display the "EDS Spectrum Data Analysis is disabled" warning in the log window using a magenta font color! So now, once the Use EDS Element Data option is selected, we obtain these EDS net intensities:
EDS Spectrum Parameters (for datarow=1):
Time Constant= 0, Sample Time= 60.0
Elapsed Time= 75.3, Dead Time(%)= 20.4
Live Time= 60.0, Channels= 2048
Ev Per Chan= 10, Max Counts= 69277
On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: Al ka Si ka Ca ka Mg ka Fe ka BEAM1 BEAM2
BGD: EDS EDS EDS EDS EDS
SPEC: 0 0 0 0 0
CRYST: EDS EDS EDS EDS EDS
ORDER: 1 1 1 1 1
5G .00 293.49 .44 491.10 25.28 19.970 19.970
AVER: .00 293.49 .44 491.10 25.28 19.970 19.970
SDEV: .00 .00 .00 .00 .00 .000 .000
1SIG: .00 .49 .02 .64 .15
SIGR: .00 .00 .00 .00 .00
SERR: .00 .00 .00 .00 .00
%RSD: .00 .00 .00 .00 .00
And these quant results:
St 539 Set 1 Olivine - San Carlos, Results in Elemental Weight Percents
ELEM: Al Si Ca Mg Fe Mn Ni O
TYPE: ANAL ANAL ANAL ANAL ANAL SPEC SPEC SPEC
BGDS: EDS EDS EDS EDS EDS
TIME: 60.00 60.00 60.00 60.00 60.00 --- --- ---
BEAM: 19.97 19.97 19.97 19.97 19.97 --- --- ---
ELEM: Al Si Ca Mg Fe Mn Ni O SUM
5 .000 19.398 .046 29.780 7.423 .108 .291 43.593 100.639
AVER: .000 19.398 .046 29.780 7.423 .108 .291 43.593 100.639
SDEV: .000 .000 .000 .000 .000 .000 .000 .000 .000
SERR: .000 .000 .000 .000 .000 .000 .000 .000
%RSD: .00 .00 .00 .00 .00 .00 .00 .00
PUBL: n.a. 19.076 .007 29.802 7.423 .108 .291 43.593 100.300
%VAR: --- 1.69 547.87 (-.07) (.00) .00 .00 .00
DIFF: --- .322 .039 (-.02) (.00) .000 .000 .000
STDS: 510 510 524 539 539 --- --- ---
Note that the olivine standard was assigned for Fe and Mg, and the Si (and other elements) were analyzed using a secondary standard. This is the best thing about performing EDS analyses in Probe for EPMA- one *must* utilize actual, honest, got to love 'em, standards! ;D
Edit by John: the latest PFE update now includes improved warning messages regarding this issue.
Quote from: John Donovan on July 27, 2018, 09:41:55 AM
Hi Richard,
Vern Robertson (JEOL USA) wrote this to us a few days ago:
QuoteI received confirmation from our factory that they will release the final version of the API at around M&M time frame (so early-mid August).
Sorry for the delay. I know that the original date was sometime May-June of this year.
Once we get the new API from Japan it will need to be tested again by Glenn Poirior in Ottawa. We tested the beta JEOL EDS API last year and it worked, but had some glitches that JEOL needed to fix. If it all looks good, we will make an announcement and release a new PFE sometime after that.
Just FYI, we're still waiting for JEOL to release the final version of their EDS API. Last we heard from Vern it will be sometime this fall.
Once the JEOL API is all up and running will PfEPMA be able to integrate multiple EDS analyses from multiple spectrometers? For example, my new 8530F+ has both a JEOL EDS and a Thermo EDS. It would be interesting to see if integrating the spectra from both detectors is possible and useful.
Hi Dave,
Nice idea but unfortunately that simply can't be done! :(
We can combine EDS intensities from more than one EDS spectrometer if they are the same vendor, for example two Thermo EDS detectors, but not if they are from different vendors.
The 8530 at Exxon NJ has two Thermo detectors that can be utilized separately or together and that works great with both the Thermo software and our software.
Sorry.
john
Quote from: DavidAdams on October 22, 2018, 07:56:16 AM
Once the JEOL API is all up and running will PfEPMA be able to integrate multiple EDS analyses from multiple spectrometers? For example, my new 8530F+ has both a JEOL EDS and a Thermo EDS. It would be interesting to see if integrating the spectra from both detectors is possible and useful.
Since you will have both a Thermo EDS detector and a JEOL EDS detector on your 8530 instrument, one thing you *will* be able to do is to use Probe for EPMA with the Thermo detector for combined WDS and EDS analyses, and then switch to the JEOL detector (again) for combined WDS and EDS analyses. That is, once JEOL releases their final EDS API.
It will be interesting to directly compare the two detector systems and their peak stripping capabilities on the same instrument on the same samples. Sounds like a presentation in the making! :)
Today I was acquiring some integrated EDS and WDS point analyses and ran into the same problem that another user (Emma Bullock) reported to me a couple of weeks ago, where PFE was complaining that the EDS intensities were zero even though the Get EDS Net Intensities button in the Display EDS Spectra dialog worked fine.
When I looked at her data file I found that she had not checked the Use EDS Element Data checkbox in the Calculation Options dialog. So I let her know that and all was well.
Then today I proceeded to run into *exactly* the same issue because I also forgot to check that damn Use EDS EDS Element Data checkbox in the Calculation Option dialog. So you know what this means? It means I'm going to modify the code to automatically set that flag whenever someone adds an element by EDS for quant. ::)
This post is primarily intended for the students in Julie's EPMA class, but there is an interesting twist at the end so even experts might be amused to read through.
The new EDS flags in PFE that are automatically enabled in Probe for EPMA when Bruker or Thermo EDS acquisitions are performed seem to be working great for the students. Using EDS quant with WDS quant in PFE is quite easy now.
In fact we even discovered another helpful bit of code when the students were setting up a quant lab practical yesterday doing trace elements on WDS and major elements by EDS when we added our trace elements by WDS first, and then we added an element by EDS before we had even acquired an EDS spectrum. The software then popped up a little message saying that we had forgotten to turn on the "acquire EDS spectra" checkbox, and telling us that it turned it on for us automatically!
Such a nice software! :D
So here are the results of our integrated EDS-WDS lab practical measuring Rb and Ti in a synthetic quartz. The idea being to measure Rb and Ti as trace elements using EDS and Si using WDS just to obtain a decent matrix correction. Specifically: how accurately can we measure "zero" Rb when there is a significant interference of Si Ka on Rb La? First lets look at the wavescan on Rb La:
(https://smf.probesoftware.com/gallery/395_13_11_18_1_58_08.png)
One can see that the tail of the Si Ka peak intrudes on the peak position of the Rb La line mostly due to "polygonization" of the Bragg crystals during manufacturing, which causes these extended tails (from Goldstein et al.) due to micro domain mis-orientation during the thermal cycling utilized to re-crystallize the plastically deformed Bragg crystal to improve reflectivity:
(https://smf.probesoftware.com/gallery/395_13_11_18_2_07_05.png)
Meanwhile, here are the quant results *without* the interference correction running the SiO2 as an unknown (using standards SiO2 for Si by EDS, and RbTiOPO4 for Rb, and TiO2 for Ti using WDS):
Un 4 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si
TYPE: ANAL ANAL ANAL
BGDS: LIN EXP EDS
TIME: 80.00 80.00 70.00
BEAM: 49.71 49.71 49.71
ELEM: Rb Ti Si SUM
118 .148 .001 40.921 41.071
119 .156 -.002 40.989 41.143
120 .156 -.003 40.977 41.130
121 .149 -.002 40.995 41.143
122 .145 .000 40.973 41.118
AVER: .151 -.001 40.971 41.121
SDEV: .005 .002 .029 .030
SERR: .002 .001 .013
%RSD: 3.22 -143.58 .07
STDS: 1023 22 14
First of all we note that besides the interference on Rb by Si of around 1500 PPM, the totals are quite low, because although we added Si by EDS, we forgot to add oxygen by EDS. And because it's an unknown sample, the software does not know that oxygen is present. So we could either turn on oxygen by stoichiometry as seen here:
Un 4 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL CALC
BGDS: LIN EXP EDS
TIME: 80.00 80.00 70.00 ---
BEAM: 49.71 49.71 49.71 ---
ELEM: Rb Ti Si O SUM
118 .171 .001 46.634 53.149 99.954
119 .180 -.002 46.711 53.236 100.125
120 .179 -.003 46.698 53.220 100.095
121 .172 -.002 46.718 53.244 100.133
122 .167 .000 46.692 53.215 100.075
AVER: .174 -.001 46.691 53.213 100.076
SDEV: .006 .002 .034 .038 .072
SERR: .003 .001 .015 .017
%RSD: 3.22 -143.58 .07 .07
STDS: 1023 22 14 ---
Or, we could leave it as elemental and just add oxygen by EDS using the SiO2 standard as the oxygen standard, since we acquired an EDS spectra automatically on each standard like this:
Un 4 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL ANAL
BGDS: LIN EXP EDS EDS
TIME: 80.00 80.00 70.00 70.00
BEAM: 49.71 49.71 49.71 49.71
ELEM: Rb Ti Si O SUM
118 .171 .001 46.656 53.679 100.507
119 .180 -.002 46.745 54.002 100.925
120 .180 -.003 46.738 54.104 101.018
121 .172 -.002 46.756 54.080 101.006
122 .167 .000 46.732 54.092 100.992
AVER: .174 -.001 46.725 53.991 100.890
SDEV: .006 .002 .040 .179 .217
SERR: .003 .001 .018 .080
%RSD: 3.22 -143.58 .09 .33
STDS: 1023 22 14 14
Either way we get a decent total and more importantly as I will show below, a better matrix correction (and why would a matrix correction matter for a minor element you might ask? See below).
Now it should also be pointed out that the net intensities for Si and O by EDS were obtained from the default Thermo software profile without any special processing for background fitting or peak stripping so this is quite good actually for oxygen. Now let's turn on the interference for Rb La by Si as seen here:
(https://smf.probesoftware.com/gallery/395_13_11_18_1_59_26.png)
Un 4 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL ANAL
BGDS: LIN EXP EDS EDS
TIME: 80.00 80.00 70.00 70.00
BEAM: 49.71 49.71 49.71 49.71
ELEM: Rb Ti Si O SUM
118 .002 .001 46.665 53.588 100.256
119 .012 -.002 46.754 53.911 100.674
120 .012 -.003 46.746 54.013 100.768
121 .005 -.002 46.765 53.989 100.758
122 .002 .000 46.741 54.002 100.744
AVER: .007 -.001 46.734 53.901 100.640
SDEV: .005 .002 .040 .179 .218
SERR: .002 .001 .018 .080
%RSD: 77.68 -143.58 .09 .33
STDS: 1023 22 14 14
Now that looks better! 70 PPM +/- 50 PPM (one sigma) with only 80 seconds of counting time (15 keV, 50 nA), so essentially zero. Here's another analysis of the synthetic SiO2 as an unknown, where we obtained 40 PPM +/- 30 PPM, again essentially zero:
Un 5 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL ANAL
BGDS: LIN EXP EDS EDS
TIME: 80.00 80.00 70.00 70.00
BEAM: 50.46 50.46 50.46 50.46
ELEM: Rb Ti Si O SUM
153 .004 -.001 47.988 55.251 103.242
154 .003 .003 46.401 53.169 99.575
155 .000 -.003 46.745 53.566 100.309
157 .008 .002 47.002 54.375 101.388
AVER: .004 .001 47.034 54.090 101.128
SDEV: .003 .003 .682 .922 1.594
SERR: .002 .001 .341 .461
%RSD: 88.93 458.16 1.45 1.71
STDS: 1023 22 14 14
STKF: .3028 .5547 .4101 .2664
STCT: 5506.7 32081.8 48240.1 16388.5
UNKF: .0000 .0000 .4125 .2712
UNCT: .5 .3 48522.6 16683.3
UNBG: 41.0 45.9 .0 .0
ZCOR: 1.1959 1.2024 1.1402 1.9948
KRAW: .0001 .0000 1.0059 1.0180
PKBG: 1.01 1.01 .00 .00
INT%: -97.89 ---- ---- ----
Now here's the interesting thing about the matrix correction in this analysis. Let's go back to the Un 4 SiO2 as unk sample and this time I'll turn off the oxygen by EDS and so we obtain this result for the Rb:
Un 4 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL ANAL
BGDS: LIN EXP EDS EDS
TIME: 80.00 80.00 70.00 ---
BEAM: 49.71 49.71 49.71 ---
ELEM: Rb Ti Si O-D SUM
118 .000 .001 40.929 --- 40.931
119 .009 -.002 40.997 --- 41.004
120 .009 -.003 40.985 --- 40.991
121 .003 -.002 41.003 --- 41.005
122 .000 .000 40.980 --- 40.980
AVER: .004 -.001 40.979 --- 40.982
SDEV: .004 .002 .029 --- .031
SERR: .002 .001 .013 ---
%RSD: 105.09 -143.58 .07 ---
STDS: 1023 22 14 ---
STKF: .3028 .5547 .4101 ---
STCT: 5490.5 32240.2 48315.1 ---
UNKF: .0000 .0000 .4098 ---
UNCT: .7 -.6 48279.9 ---
UNBG: 40.5 46.1 .0 ---
ZCOR: 1.0380 1.1985 1.0000 ---
KRAW: .0001 .0000 .9993 ---
PKBG: 1.02 .99 .00 ---
INT%: -97.25 ---- ---- ---
Notice that we obtain 40 PPM of Rb without oxygen in the matrix and also notice that the matrix correction for Rb La in this matrix is calculated as 1.038. Now we turn oxygen by EDS back on and we obtain this result:
Un 4 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL ANAL
BGDS: LIN EXP EDS EDS
TIME: 80.00 80.00 70.00 70.00
BEAM: 49.71 49.71 49.71 49.71
ELEM: Rb Ti Si O SUM
118 .002 .001 46.665 53.588 100.256
119 .012 -.002 46.754 53.911 100.674
120 .012 -.003 46.746 54.013 100.768
121 .005 -.002 46.765 53.989 100.758
122 .002 .000 46.741 54.002 100.744
AVER: .007 -.001 46.734 53.901 100.640
SDEV: .005 .002 .040 .179 .218
SERR: .002 .001 .018 .080
%RSD: 77.68 -143.58 .09 .33
STDS: 1023 22 14 14
STKF: .3028 .5547 .4101 .2664
STCT: 5490.5 32240.2 48315.1 16364.3
UNKF: .0001 .0000 .4098 .2704
UNCT: 1.0 -.6 48279.9 16614.5
UNBG: 40.5 46.1 .0 .0
ZCOR: 1.1961 1.2024 1.1404 1.9931
KRAW: .0002 .0000 .9993 1.0153
PKBG: 1.02 .99 .00 .00
INT%: -96.25 ---- ---- ----
Now we obtain 70 PPM of Rb! Just by adding oxygen into the matrix correction we raised the Rb content (a trace element since it's probably close to zero in the synthetic SiO2), from 40 PPM to 70 PPM!
Then we were able to have the students think on this and observe that the Rb La line cannot fluoresce the Si Ka edge since the Rb La = 1.694 keV and Si K edge = 1.84 keV. But Rb La *can* fluoresce the O K edge, so Rb La is significantly more absorbed by oxygen than Si and the matrix correction goes from 1.038 to to 1.1961!
Now just to prolong the agony of the above quite tedious trace element analysis posting, I thought I would mention something else. Even though the Rb concentrations we obtained after the interference correction are just over one standard deviation from zero, I thought to myself, we should have performed a blank correction!
But I had figured we could only assume that the SiO2 had zero Rb since I thought that we didn't have a value for Rb in this synthetic SiO2, but then I remembered that we had an ICP-MS measurement from Alan Konig for this standard material from about 8 years ago, and when I found the Excel file, it says 11 PPM of Rb!
So since we have two samples of the SiO2 run as an unknown and therefore applicable as a blank measurement, I assigned the first SiO2 unk as a blank for the second SiO2 unknown and obtained the following result:
Un 5 SiO2 as unk, Results in Elemental Weight Percents
ELEM: Rb Ti Si O
TYPE: ANAL ANAL ANAL ANAL
BGDS: LIN EXP EDS EDS
TIME: 80.00 80.00 70.00 70.00
BEAM: 50.46 50.46 50.46 50.46
ELEM: Rb Ti Si O SUM
153 -.002 -.001 47.989 55.248 103.234
154 -.003 .003 46.401 53.166 99.566
155 -.005 -.003 46.745 53.563 100.301
157 .002 .002 47.003 54.372 101.379
AVER: -.002 .001 47.034 54.087 101.120
SDEV: .003 .003 .682 .922 1.594
SERR: .002 .001 .341 .461
%RSD: -162.27 458.16 1.45 1.71
STDS: 1023 22 14 14
So negative 20 PPM average with a 30 PPM one sigma variance. Now that is again statistically still a zero, but I thought it worth mentioning. For more on the blank correction for WDS spectrometer artifacts, see this paper:
https://epmalab.uoregon.edu/pdfs/3631Donovan.pdf
and this paper:
https://epmalab.uoregon.edu/publ/A%20new%20EPMA%20method%20for%20fast%20trace%20element%20analysis%20in%20simple%20matrices.pdf
Anyway, the whole point of this exercise was to demonstrate to the students that if we are primarily interested in trace elements, we can dedicate our WDS spectrometers to the trace elements of interest, and just utilize the EDS quant for a matrix correction. The accuracy of major elements by EDS may not always be as good as using WDS, but they are probably more than good enough for the purposes of obtaining a matrix correction for the trace elements.
I think it's worth mentioning whenever discussing trace elements, that statistics are your friend. :D
We routinely utilize detection limit statistics when evaluating trace WDS elements, but what about "trace" EDS elements? Well of course statistics are also our friend, but there is a rub. Not only are trace element statistics generally significantly worse than WDS, but not all vendors can provide background intensities, which are normally the basis for detection limits statistics (of course other methods can be applied to obtain a reproducibility measure of detection).
So currently, Bruker and JEOL both provide background intensities from their "net intensity" EDS API interfaces to allow us to calculate detection statistics just as we do for WDS elements (but not Thermo). In Probe for EPMA, we can turn on detection limit statistics for all elements (WDS and EDS) as seen here:
(https://smf.probesoftware.com/gallery/1_10_03_20_12_52_57.png)
Here is an example from a Bruker EDS detector (data provided by Karsten Goeman on his SX100) showing the resulting output in his log window:
(https://smf.probesoftware.com/gallery/1_10_03_20_12_53_12.png)
and of course this data can be exported using the "user specified" output from the Output menu or by right clicking selected samples from the Analyze! window as seen here also saved to an Excel spreadsheet:
(https://smf.probesoftware.com/gallery/1_10_03_20_12_53_27.png)
Now, if one is looking closely one will notice that a few of the elements (K, Mn, and Ti) are reported as zero statistics and also zero concentrations. This is for a very good reason and is because the returned net intensities for these elements, in these particular cases, were zero. And one cannot calculate statistics on zeros!
Now it may be that these zero net intensities could be avoided by choosing a different background (and peak fitting) fitting method in their EDS software, and I encourage everyone to learn how to optimize the processing of their spectra in their EDS software for optimum results.
Hi All,
Just wanted to show some data collected with the final JEOL API and PFE software for using the JEOL EDS system on 8230 and 8530 machines.
The beta software has been able to talk to the JEOL EDS for a year or so now but there were various issues (the biggest problems were related to the locking of the interface after the analysis was done and putting the beam into scanning mode during the analyses) that needed to be worked out in the JEOL API.
The latest version works well and I haven't seen any issues.
A picture is worth a thousand words, so here it is:
(https://smf.probesoftware.com/gallery/537_04_08_20_11_58_55.png)
Everything worked as expected and reanalysis of standards as unknowns produced good results. (Just have to remember to check "Use EDS Spectra for Quant" box in the calculations Options menu. I see from other post in the forum that I'm not the only one who forgets to do this!).
As a test I re-analysed some anorthoclase and acquired Si, Al, Fe, Mg and Ca with EDS and the rest using MAN correction. EDS acquisition was 40s livetime, using TI pulse processor and the largest detector aperture (#1).
(https://smf.probesoftware.com/gallery/537_04_08_20_12_01_22.png)
The EDS acquired elements are in yellow. As you can see the results are very close (I didn't analyse the exact same spots so the differences are probably real).
Note how close the Ca and Fe results are despite only being in the thousands of PPM range.
Great to be able to do combined WDS/EDS finally! It'll be interesting to see how this affects workflow.
Cheers
Glenn
Hi Glenn, that's awesome. Great news for many people.
Cheers, Karsten
I was hoping that others with JEOL 8530s could help me. My eds/wds integration is working except for one issue: PfEPMA isn't retaining any spectral data.
Everything else works. I can change the aperture, start an acquisition.. all that. When I ask PfEPMA to use EDS to quantify an element it says there's no spectrum collected, yet during acquisition the EDS window pops up and I can watch the detector view all the x-rays in real time.
My JEOL engineer suggests that this might have something to do with permissions between different versions of Windows, so that JEOL may indeed be collecting a spectrum, but it's putting it somewhere where PfEPMA cant see it or doesn't have permission to read it. The probe is running WinXP and PfEPMA is running on Win7 64x.
So, am I on the right trail? Or is there a check box in PfEPMA I'm missing?
Hi Ben,
Are you getting an error in PFE during the acquisition? If you go to the Run | Display and Export EDS Spectra menu, do you see any EDS spectra there?
Yes. And when I use the "Display Net Intensities" button, I get a message that says "No EDS elements specified for analysis in Sample 67 Set 2 Ge".
Yes, what? Yes, you are getting an error in PFE or yes you can see spectra in the Run menu?
Sorry! Yes, I'm able to see spectra for each of the standards and unknowns I've acquired. When I quantify, though, there are no raw counts (even with the "Use EDS for quant" box checked).
So it is acquiring EDS spectra and saving it to PFE OK.
Are you entering EDS elements in the Elements/Cations dialog?
I've entered elements once each in the E/C dialog.
Did you select the EDS (vs. WDS) option? Does it list the EDS elements in the Elements/Cations dialog?
Maybe we should discuss this off-line. Please send me the MDB file and call me at Probe Software.
OK, so John and I did some testing and found that JEOL eds is not returning any net intensities to PfEPMA, or rather the data file is not in the place it's supposed to be on the JEOL PC. Either way, I'll be doing some more investigation into 1) making sure the JEOL eds is functioning properly to begin with and 2) looking to see (with JEOL engineer) where the intensity files are kept.
Stay tuned!
Quote from: bgarcia on January 07, 2021, 01:50:48 PM
OK, so John and I did some testing and found that JEOL eds is not returning any net intensities to PfEPMA, or rather the data file is not in the place it's supposed to be on the JEOL PC. Either way, I'll be doing some more investigation into 1) making sure the JEOL eds is functioning properly to begin with and 2) looking to see (with JEOL engineer) where the intensity files are kept.
Stay tuned!
To clarify a bit, the JEOL EDS interface is returning the EDS spectra as expected, but subsequently returns zero value intensities for net intensity requests (and no errors are reported). At least for oxygen k-alpha. Ben will next try to get net intensities for other elements to see if it's a general issue.
Any ideas on what might be causing this?
Update: I've gotten the WDS/EDS integration package to successfully return intensities in PFE. JEOL installed a software update (1.19.0.1) for PC_EPMA.
I'm currently working through setting up my first "real" file with EDS enabled.
I just got the EDS-WDS integration with my JEOL OEM EDS. So for clarity, when I get EDS net intensities back, where are the backgrounds coming from?
That is are the default net intensities from the JEOL software correct?
Both the EDS net intensities and EDS background intensities are returned by the JEOL get EDS net intensity function call.
As to how accurate these net and background intensities are, I would have to refer you to someone who has tested the JEOL EDS system. I believe Changkun Park at Korea Polar Reseach Institute has done some testing on his JEOL EDS system. Also Glenn Poirier at the University of Ottawa.
This is a new feature that we just added which allows one to plot WDS and EDS spectra together when using the integrated EDS and WDS acquisition feature in Probe for EPMA.
First acquire some WDS wavescans with the EDS acquisition turned on (see Acquisition Options dialog from the Acquire! window). Might as well set the EDS acquisition time to use the sample acquisition time for the EDS acquisition runs the full time of the wavscan.
Then in the Plot! window check the Plot EDS Spectrum checkbox and for a WDS element, select corresponding Kilovolts for that element as shown here:
(https://smf.probesoftware.com/gallery/1_07_07_22_12_52_42.png)
Then click the output menu:
(https://smf.probesoftware.com/gallery/1_07_07_22_12_52_22.png)
Still a new feature, so let us know if there's anything that doesn't look right. To see the WDS peak better you can check the No Peak Markers checkbox.
I'm finally getting to integrating the Thermo EDS and WDS setup, partially because one of our spectrometers went down. What better time to do this?
Three questions -- for now.
1. My EDS count times are longer than the Use Sample Counting time option. For example: I set up an olivine run which runs 264 seconds (PFE estimate), and the estimate given for EDS is 207 seconds. When I run the sample Thermo runs it for almost 6.5 minutes, so considerably longer. I looked through the forum and couldn't find anything to explain that.
Note it also did this for my standards, which should only take 20 seconds total.
Note, I'm using a 20% deadtime
2. I started an automated olivine run with Si and Mg on EDS and the rest of the elements on WDS. It started great and then Si tanked by about 10 wt%. I re-standardized and cps/nA remained the same from my previous standard run. Usually, I'd repeak Si, but am not sure how to troubleshoot this as I didn't peak. I'm re-running the points to see what happens. Any thoughts?
3. I can't seem to specify O for stoichiometry calculations, when it was measured with EDS. I only have the EDS option.
Quote from: dawncruth on July 29, 2022, 11:14:33 AM
I'm finally getting to integrating the Thermo EDS and WDS setup, partially because one of our spectrometers went down. What better time to do this?
Three questions -- for now.
1. My EDS count times are longer than the Use Sample Counting time option. For example: I set up an olivine run which runs 264 seconds (PFE estimate), and the estimate given for EDS is 207 seconds. When I run the sample Thermo runs it for almost 6.5 minutes, so considerably longer. I looked through the forum and couldn't find anything to explain that.
Note it also did this for my standards, which should only take 20 seconds total.
Note, I'm using a 20% deadtime
The acquisition time is just an estimate and when EDS is involved the clock time is completely dependent on the actual dead times that occur.
One very important note: always use a *fixed* pulse processing time for EDS quant (that is, non-zero). If you have the "auto" pulse processing time selected in Thermo or PFE it will auto adjust based on the current count rate regardless of whether the faraday cup is in or out. So when the cup comes out the pulse processing shifts to match the count rate, which messes everything up for EDS quant.
In other words be sure to set a fixed pulse processing time in PFE, then go to a sample, unblank the beam and set what the dead time in Pathfinder is. Then enter that value when it asks you for the estimated dead time from the Automate window.
In practice is almost impossible to estimate this acquisition time accurately for EDS because the dead time depends on the sample and even more so on the beam current.
Quote from: dawncruth on July 29, 2022, 11:14:33 AM
2. I started an automated olivine run with Si and Mg on EDS and the rest of the elements on WDS. It started great and then Si tanked by about 10 wt%. I re-standardized and cps/nA remained the same from my previous standard run. Usually, I'd repeak Si, but am not sure how to troubleshoot this as I didn't peak. I'm re-running the points to see what happens. Any thoughts?
I have absolutely no idea.
Quote from: dawncruth on July 29, 2022, 11:14:33 AM
3. I can't seem to specify O for stoichiometry calculations, when it was measured with EDS. I only have the EDS option.
Are you trying to measure oxygen or calculate it by stoichiometry? You can't do both things.
That said you might be able to disable quant for measured oxygen and then add it in as an unanalyzed element for calculating by stoichiometry.
Quote from: John Donovan on July 29, 2022, 12:45:36 PM
The acquisition time is just an estimate and when EDS is involved the clock time is completely dependent on the actual dead times that occur.
One very important note: always use a *fixed* pulse processing time for EDS quant (that is, non-zero). If you have the "auto" pulse processing time selected in Thermo or PFE it will auto adjust based on the current count rate regardless of whether the faraday cup is in or out. So when the cup comes out the pulse processing shifts to match the count rate, which messes everything up for EDS quant.
In other words be sure to set a fixed pulse processing time in PFE, then go to a sample, unblank the beam and set what the dead time in Pathfinder is. Then enter that value when it asks you for the estimated dead time from the Automate window.
In practice is almost impossible to estimate this acquisition time accurately for EDS because the dead time depends on the sample and even more so on the beam current.
Ok, that makes sense. We have a Thermo and the Time Constant (what I think you mean by pulse processing time) was set to auto. I'll have to play with it to see how to manage that.
Thermo users -- if y'all have tips on integrating EDS/WDS, I'd be most grateful!
Quote from: John Donovan on July 29, 2022, 12:45:36 PM
Are you trying to measure oxygen or calculate it by stoichiometry? You can't do both things.
That said you might be able to disable quant for measured oxygen and then add it in as an unanalyzed element for calculating by stoichiometry.
That's exactly what I tried to do, disable quant. But when you disable quant - it doesn't allow you to select specify in the E/C properties window.
Quote from: dawncruth on July 29, 2022, 01:39:13 PM
Quote from: John Donovan on July 29, 2022, 12:45:36 PM
Are you trying to measure oxygen or calculate it by stoichiometry? You can't do both things.
That said you might be able to disable quant for measured oxygen and then add it in as an unanalyzed element for calculating by stoichiometry.
That's exactly what I tried to do, disable quant. But when you disable quant - it doesn't allow you to select specify in the E/C properties window.
Did you click on an empty row in the Elements/Cations dialog?
Quote from: dawncruth on July 29, 2022, 11:14:33 AM
1. My EDS count times are longer than the Use Sample Counting time option. For example: I set up an olivine run which runs 264 seconds (PFE estimate), and the estimate given for EDS is 207 seconds. When I run the sample Thermo runs it for almost 6.5 minutes, so considerably longer. I looked through the forum and couldn't find anything to explain that.
Note it also did this for my standards, which should only take 20 seconds total.
Note, I'm using a 20% deadtime
2. I started an automated olivine run with Si and Mg on EDS and the rest of the elements on WDS. It started great and then Si tanked by about 10 wt%. I re-standardized and cps/nA remained the same from my previous standard run. Usually, I'd repeak Si, but am not sure how to troubleshoot this as I didn't peak. I'm re-running the points to see what happens. Any thoughts?
Hi Dawn,
I am happy to look at the Pathfinder data for items 1 and 2, if you want to zip the project and send it to me.
I may be able to discern what is going on.
-Steve
Quote from: SteveSeddio on July 31, 2022, 07:52:03 AM
Quote from: dawncruth on July 29, 2022, 11:14:33 AM
1. My EDS count times are longer than the Use Sample Counting time option. For example: I set up an olivine run which runs 264 seconds (PFE estimate), and the estimate given for EDS is 207 seconds. When I run the sample Thermo runs it for almost 6.5 minutes, so considerably longer. I looked through the forum and couldn't find anything to explain that.
Note it also did this for my standards, which should only take 20 seconds total.
Note, I'm using a 20% deadtime
2. I started an automated olivine run with Si and Mg on EDS and the rest of the elements on WDS. It started great and then Si tanked by about 10 wt%. I re-standardized and cps/nA remained the same from my previous standard run. Usually, I'd repeak Si, but am not sure how to troubleshoot this as I didn't peak. I'm re-running the points to see what happens. Any thoughts?
Hi Dawn,
I am happy to look at the Pathfinder data for items 1 and 2, if you want to zip the project and send it to me.
I may be able to discern what is going on.
-Steve
I think the issue she was seeing is because she was using the "auto" time constant, which causes problems when doing quant and the faraday cup is being inserted and removed repeatedly. Basically, the time constant is always changing during the acquisition and therefore the quant is affected. The solution is to pick a fixed time constant for Pathfinder from the Probe for EPMA Acquisition Options dialog.
Quote from: bgarcia on December 13, 2021, 03:03:10 PMUpdate: I've gotten the WDS/EDS integration package to successfully return intensities in PFE. JEOL installed a software update (1.19.0.1) for PC_EPMA.
I'm currently working through setting up my first "real" file with EDS enabled.
Update Update:
I know this thread is long dead but I thought I'd put this here for posterity.
I was mistaken in that I posted the earlier message (below) just a little too quickly.. I DID NOT get the EDS to work using PfEPMA on our 8530. I had just gotten PfEPMA to show the peak it was scanning over, however, it did not return any net intensities besides zeros. :-\
I never really got beyond this point. Everything on the JEOL side worked fine; there were backgrounds and intensities galore. Eventually our JEOL guy ran out of things to try (he did a lot!), even after talking to other SEs and The Factory. The Factory just never really devoted much time to pursuing this so it died with them.
We're unfortunately unable to pursue this now as our 8530 hasn't worked in about 2 years. JEOL service in our region underwent experienced-staffing changes and they have been unable to devote someone knowledgeable to working on this full time. :-X When we do get the probe up and running again, I hope a solution for the issue at hand will have been found!
Quote from: bgarcia on March 25, 2025, 10:26:45 AMQuote from: bgarcia on December 13, 2021, 03:03:10 PMUpdate: I've gotten the WDS/EDS integration package to successfully return intensities in PFE. JEOL installed a software update (1.19.0.1) for PC_EPMA.
I'm currently working through setting up my first "real" file with EDS enabled.
Update Update:
I know this thread is long dead but I thought I'd put this here for posterity.
I was mistaken in that I posted the earlier message (below) just a little too quickly.. I DID NOT get the EDS to work using PfEPMA on our 8530. I had just gotten PfEPMA to show the peak it was scanning over, however, it did not return any net intensities besides zeros. :-\
Thanks for confirming this.
We did not learn about this issue until this last month when the Univ Toronto JEOL 8230 had a hard drive failure on their JEOL computer.
When JEOL replaced the hard drive and re-installed their software, Yanan found that she could connect to the JEOL EDS using Probe for EPMA, and even acquire an EDS spectrum, but the EDS element net intensities always came back as zeros.
That this appears to be caused by the JEOL software being updated is confirmed by Glenn Poirier who wrote to me, that he used to be able to obtain EDS net intensities from the JEOL EDS system in Probe for EPMA, but after his JEOL software was updated he no longer could get actual EDS element net intensities for quantification.
However, Julien Allaz at ETH Zurich, who has
not updated his JEOL software, can still obtain EDS net intensities, so apparently JEOL broke something at some point in their 8230/8530 EDS interface.
That this is caused on the JEOL server side can be seen by using the JEOL provided test application: TestEDSLibIS.exe and the associated DLL: LibbEDSIS.dll. Which can be found in the Probe for EPMA application folder (see below).
Glenn did notice an error message when using the JEOL test app as seen here:
(https://smf.probesoftware.com/gallery/1_25_03_25_1_00_28.png)
One thought occurs to me for those affected by this issue. Please search your JEOL hard drive and see if you can find more recent versions of the JEOL TestLibEDSIS.exe and LibEDSIS.dll files.
The files we have are dated from 08/17/2020. If you find more recent versions on your JEOL hard drive, please copy both files to the Probe for EPMA application folder, usually C:\Programs Files (x86)\Probe Software\Probe for EPMA, and overwrite the exiting files.
Then try again to acquire an EDS spectrum, and obtain net intensities.
Quote from: bgarcia on March 25, 2025, 10:26:45 AMWe're unfortunately unable to pursue this now as our 8530 hasn't worked in about 2 years. JEOL service in our region underwent experienced-staffing changes and they have been unable to devote someone knowledgeable to working on this full time. :-X When we do get the probe up and running again, I hope a solution for the issue at hand will have been found!
Your probe has been offline for two YEARS?!
For the other two instruments, has anything changed on the Probe for EPMA computers? I'm assuming these are the PfE computers that are running the TestLibEDSIS.exe and trying to communicate with the JEOL PCs over LAN (with the updated JEOL software).
Reason I ask is that I was googling the MSCOMCTL.OCX error that you mention and an interesting post on Stack Overflow (Stack Overflow (https://stackoverflow.com/questions/39251880/mscomctl-ocx-missing-windows-10)) suggests this is a problem with a component of the Visual Basic 6.0 IDE that is no longer routinely distributed and needs to be installed and registered manually.
I checked on my JEOL PfE PC which
does return EDS net intensities and the MSCOMCTL.OCX file is where it should be.
You can get the MSCOMCTL.OCX file from the (still available) IDE directly from Microsoft here: Microsoft website (https://www.microsoft.com/en-us/download/details.aspx?id=7030)
And extract the required .OCX file by unzipping the .msi file using 7zip.
You then place the .OCX file in C:/Windows/SystemWOW64/ and register the component via an administrative console with
regsvr32 C:\Windows\SysWOW64\MSCOMCTL.OCX It could of course also be something to do with one of the dependencies for this file (which might hopefully also be in the .msi file above), or something completely different!
Quote from: JonF on March 26, 2025, 10:11:41 AMYou can get the MSCOMCTL.OCX file from the (still available) IDE directly from Microsoft here: Microsoft website (https://www.microsoft.com/en-us/download/details.aspx?id=7030)
And extract the required .OCX file by unzipping the .msi file using 7zip.
You then place the .OCX file in C:/Windows/SystemWOW64/ and register the component via an administrative console with
regsvr32 C:\Windows\SysWOW64\MSCOMCTL.OCX
It could of course also be something to do with one of the dependencies for this file (which might hopefully also be in the .msi file above), or something completely different!
Update: Yanan Liu at Univ Toronto, recently tried these steps on her JEOL 8230 and is still not able to obtain non-zero net intensities. But it was certainly worth a try! :)
JEOL Japan is continuing looking into this issue... so if your 8230/8530 EDS interface is still returning non-zero net intensities, you might want to wait to upgrade your JEOL software until this is fixed.
One additional observation is that JEOL added this get net intensity function call towards the end of the development of the LibEDSIS.dll file, so maybe at some point these late changes were not included in the latest JEOL PC-SEM software?
But again, please note this zero net intensities issue does NOT affect the newer JEOL iSP100/iHP200F instruments which use a completely different interface for EDS integration.
That might explain why the get spectrum calls all work, but just not the get net intensity call.
Ryan McAleer makes some suggestions for getting the best results from the JEOL EDS interface on iSP100/iHP200F instruments:
Quote1. You should run a single EDS spectrum acquisition in the JEOL software prior to any EDS acquisitions with Probe for EPMA. Doing seems to get the JEOL software interface into a correct state. Just one EDS acquisition for each time starting the JEOL software.
2. To avoid issues with the Faraday cup inserting before the WDS acquisitions are finished, you must uncheck the "Insert PCD after reservation execution is completed" [PFE will prompt you about this once per run]
3. The user should run a single EDS acquisition after they change the EDS time constant in Probe for EPMA. This is to ensure that these EDS conditions are properly saved for subsequent EDS element analyses. Or one can just set the EDS time constant they want in both JEOL (Analysis-->EDS analysis basic conditions) and Probe for EPMA. Otherwise the documented time constant on that first point will be incorrectly saved [we are looking into why this occurs].
4. If there is any hangup during EDS comm, RESTART the JEOL COMPUTER. If you just restart the software (either through "ResetEPMA" or through the task manager) the "reservation" of the EDS will not clear and you will run into a variety of problems.
John
Given my continuing issues with my TAP crystals, I was trying to do a mini WDS-EDS run yesterday for olivine. Just Fe and Mn on WDS and Si and Mg on EDS. A couple questions since Scott B. is out in the field.
1) PfE asks a question about "Do I want to output the EDS data?" just before starting the Standards analysis. I said yes, but am not sure this is correct?
2) As far as the EDS correction procedure, I want the Bruker phi-rho-z procedure, correct? This is what is recommended by Bruker when using standards, but I am not sure if PfE is doing the analysis of the spectra independently or is Bruker doing the analysis and then outputting it to PfE.
3) Also, to process the data in Analyze, why does PfE need to connect to the EDS? If that connection is not established, PfE doesn't do any calculation of the data and I seem to lose whatever EDS data I had after I try to reconnect. Is there a specific option in PfE that should be check marked to save the spectra other than "Acquire EDS data".
4) Where is the saved EDS spectra for an individual run (mdb file) located? Is the spectra saved within the mdb file?
Thanks.
Joe
Quote from: Joe Boesenberg on May 29, 2025, 08:32:21 AMGiven my continuing issues with my TAP crystals, I was trying to do a mini WDS-EDS run yesterday for olivine. Just Fe and Mn on WDS and Si and Mg on EDS. A couple questions since Scott B. is out in the field.
1) PfE asks a question about "Do I want to output the EDS data?" just before starting the Standards analysis. I said yes, but am not sure this is correct?
Good questions.
As you know, when PFE runs automated data acquisition it outputs the raw data for every point automatically to the log window. This takes only a fraction of a second for WDS data, but when EDS data is being acquired, it calls the EDS interface (JEOL, Thermo or Bruker) to obtain the EDS net intensities. This takes a bit longer since the EDS software has to do a peak deconvolution.
Also since all the data in the sample is output for each new data point, all the EDS points in the current sample are output each time, which, if the sample contains hundreds of points, can take a few seconds or many more depending on the number of points. During a long automated run these repeated EDS net intensity calculations can add up to increase the automated acquisition time.
So this question is just asking if you really want to run these EDS net intensity calculations during the automated acquisition, so you can reduce the amount of time it takes to run the automated acquisition with EDS elements.
If you say "Yes" it outputs the EDS net intensities for each point acquisition which takes a bit longer. If you say "No", it won't hurt anything, but the EDS net intensities won't get automatically calculated and stored in your probe database. You might also want to read this topic from the beginning as it has lots of information on this topic:
https://smf.probesoftware.com/index.php?topic=79.0
After writing all the above I found this post:
https://smf.probesoftware.com/index.php?topic=42.msg8432#msg8432
Quote from: Joe Boesenberg on May 29, 2025, 08:32:21 AM2) As far as the EDS correction procedure, I want the Bruker phi-rho-z procedure, correct? This is what is recommended by Bruker when using standards, but I am not sure if PfE is doing the analysis of the spectra independently or is Bruker doing the analysis and then outputting it to PfE.
When PFE asks for net intensities from the EDS interface, the EDS software calculates the composition depending on the vendor model for deconvolution. Some vendors use a filter fit, some vendors model the continuum and the latter method does depend on the quantification used by the EDS vendor, but only to the extent that the composition affects the continuum modeling.
In other words, the matrix correction model in the EDS software doesn't affect the EDS net intensity calculations much at all. Of course once PFE obtains the EDS net intensities, then both the WDS and EDS net intensities are calculated using the matrix corrections selected in Probe for EPMA. See here:
https://smf.probesoftware.com/index.php?topic=482.msg2826#msg2826
Finally I should note that because Probe for EPMA handles the matrix corrections for both EDS and WDS elements, it can perform spectral interference corrections from EDS on WDS elements or WDS on EDS elements:
https://smf.probesoftware.com/index.php?topic=482.0
Quote from: Joe Boesenberg on May 29, 2025, 08:32:21 AM3) Also, to process the data in Analyze, why does PfE need to connect to the EDS? If that connection is not established, PfE doesn't do any calculation of the data and I seem to lose whatever EDS data I had after I try to reconnect. Is there a specific option in PfE that should be check marked to save the spectra other than "Acquire EDS data".
Your EDS data is still there if you don't have a connection to the EDS interface on your data re-processing computer, but you'll want to turn on the Use Stored EDS Net Intensities option here from the Analytical | Analysis Options menu dialog:
(https://smf.probesoftware.com/gallery/1_29_05_25_9_40_06.png)
That of course assumes that the EDS net intensities have already been calculated and stored.
So for example, if you answer "No" to the question: "Do I want to output the EDS data?" when acquiring your automated EDS (and WDS) elements, the EDS net intensities will not have been calculated and stored in the probe database during the automated acquisition.
That's not an issue when you're still connected to the EDS interface and start calculating analyses from say the Analyze! window, because the EDS net intensities will be automatically obtained from the EDS interface, stored in your probe database and the composition calculated.
But if you finish your automated acquisition and then immediately take the MDB file to another computer that does not have the EDS interface, there will be no EDS net intensities stored for the EDS elements. So if you answered "No" to that question, what you want to do when the automation is finished is to select all your samples in the Analyze! window and click the "Raw Data" button while you are still connected to the EDS interface.
Then the software will calculate net intensities for all your points and store them in the MDB probe database. Once that is done you can move the MDB file to another computer (that doesn't have the JEOL/Thermo/Bruker EDS software installed), and then go to the Analytical | Analysis Options menu dialog and select the Use Stored EDS Net Intensities as described above...
Then the software will utilize the already stored EDS net intensities even if the EDS interface is no longer present. Of course the best thing is to install the Thermo/Bruker software in "demo" mode on your off-line computers and then you can interface to the Bruker EDS software for off-line re-processing (the JEOL software cannot be installed off-line).
Quote from: Joe Boesenberg on May 29, 2025, 08:32:21 AM4) Where is the saved EDS spectra for an individual run (mdb file) located? Is the spectra saved within the mdb file?
The EDS spectra data is stored in the probe MDB data for your run. You can view it any time from the Run | Display and Export EDS Spectra menu dialog:
https://smf.probesoftware.com/index.php?topic=40.msg8739#msg8739
Let us know if you have further questions.
Hi, very interesting reading how PFE incorporates EDS signal. Given the EDS manufacturer provides the net intensity do we see some EDS manufacturers provide better net intensity? How much does the accuracy of the data vary from manufacturer to manufacturer?
Quote from: Ben Buse on June 02, 2025, 02:11:41 AMHi, very interesting reading how PFE incorporates EDS signal. Given the EDS manufacturer provides the net intensity do we see some EDS manufacturers provide better net intensity? How much does the accuracy of the data vary from manufacturer to manufacturer?
Great question. Maybe we could do a study?
Quote from: John Donovan on March 28, 2025, 01:53:40 PMJEOL Japan is continuing looking into this issue... so if your 8230/8530 EDS interface is still returning non-zero net intensities, you might want to wait to upgrade your JEOL software until this is fixed.
One additional observation is that JEOL added this get net intensity function call towards the end of the development of the LibEDSIS.dll file, so maybe at some point these late changes were not included in the latest JEOL PC-SEM software?
But again, please note this zero net intensities issue does NOT affect the newer JEOL iSP100/iHP200F instruments which use a completely different interface for EDS integration.
That might explain why the get spectrum calls all work, but just not the get net intensity call.
As quoted above, several of our customers who had their JEOL EDS software updated on their 8230/8530 instrument lost the ability to obtain net intensities for data processing of integrated WDS and EDS in Probe for EPMA.
Thanks to efforts by Yanan Liu at the Univ of Toronto and her JEOL support team, they were finally able to figure out what the what was causing zero EDS net intensities to be returned:
QuoteSome good news our end: our EDS net intensity problem seems to be resolved! Thanks to our local service team and the field service engineer Tong, we are now able to get EDS intensities back and can conduct EDS-WDS combined analyses in PFE again as before!
I was told that the key adjustment was in the standard data folder setting. In PC-SEM, under Energy Calibration → Configuration → Folders tab, the "Standard data" should be set to "DrySC40E(SD30)" (screenshot attached).
Here is the screenshot:
(https://smf.probesoftware.com/gallery/1_17_06_25_2_46_19.png)
In hindsight the solution is completely obvious... just kidding! :D
I can confirm that the fix reported by Yunan solved the problem on my JEOL 8230 (2011 vintage). The computer was upgraded in 2022 but I only notice the net intensity problem a few months ago.
One thing to note is that you have to start the JEOL software in administrator mode to change the standard folder.
On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM: Ca ka Mg ka Si ka O ka BEAM1 BEAM2
BGD: EDS EDS EDS EDS
SPEC: 0 0 0 0
CRYST: EDS EDS EDS EDS
ORDER: 1 1 1 1
6G 172.01 123.05 322.33 62.54 20.050 20.060
AVER: 172.01 123.05 322.33 62.54 20.050 20.060
SDEV: .00 .00 .00 .00 .000 .000
1SIG: .00 .00 .00 .00
SIGR: .00 .00 .00 .00
SERR: .00 .00 .00 .00
%RSD: .00 .00 .00 .00
DEAD: ---- ---- ---- ----
DTC%: 11.5 11.5 11.5 11.5
Trouble adding unanalyzed elements if EDS has been collected:
Now that the JEOL WDS/EDS integration is working pretty well (Thanks!) I'd like to collect EDS (with no elements quantified) with every WDS analysis—just to have a record, so later I could check if I missed elements, possibly use EDS for certain elements etc. This has created a minor problem with adding specified concentrations. If an EDS analysis has been collected—I can't figure out how to add an "unanalyzed element." What am I missing! :P
For example, if I add Carbon in the Analyze! window after an analysis where EDS was collected, the EDS radio button is automatically selected. I couldn't figure out how to add Carbon as unanalyzed. If there is no EDS analysis collected, then WDS/EDS radio buttons are both greyed out, I can add Carbon as unanalyzed and then specify the concentration--but if EDS is selected you get "you can't specify an analyzed element"
Is it possible to add unanalyzed elements if you have collected an EDS spectrum?
Also, unrelated, is there a way to output high and low background intensities separately vs. the single calculated off peak intensity from the 2 pts?
Thanks!
Quote from: Ryan McAleer on July 28, 2025, 07:52:03 AMTrouble adding unanalyzed elements if EDS has been collected:
Now that the JEOL WDS/EDS integration is working pretty well (Thanks!) I'd like to collect EDS (with no elements quantified) with every WDS analysis—just to have a record, so later I could check if I missed elements, possibly use EDS for certain elements etc. This has created a minor problem with adding specified concentrations. If an EDS analysis has been collected—I can't figure out how to add an "unanalyzed element." What am I missing! :P
For example, if I add Carbon in the Analyze! window after an analysis where EDS was collected, the EDS radio button is automatically selected. I couldn't figure out how to add Carbon as unanalyzed. If there is no EDS analysis collected, then WDS/EDS radio buttons are both greyed out, I can add Carbon as unanalyzed and then specify the concentration--but if EDS is selected you get "you can't specify an analyzed element"
Is it possible to add unanalyzed elements if you have collected an EDS spectrum?
Yes. In the dropdown list for the x-ray line, scroll all the way down and select the blank line.
Quote from: Ryan McAleer on July 28, 2025, 07:52:03 AMAlso, unrelated, is there a way to output high and low background intensities separately vs. the single calculated off peak intensity from the 2 pts?
I'm sure there is. Just check the PFE User's Reference manual and check the various "custom" output formats. I think there's several of them that output the raw high and low intensity data.
Excellent! I was not aware of the blank line. That works!... and custom data #7 (NIST) includes the Raw high off peak AND Raw low off peak vs the calculated off peak from the two measurements. Thanks!
Hi John,
I noticed that when doing TDI with an integrated EDS/WDS collection there is a significant lag (8s in this case) in the time of the first TDI measurement.
Is this lag a function of the initialization sequence required by the JEOL EDS--or is a similar lag present on other EDS detectors. Any way to reduce this? Thanks!
USGS TDI.png
Quote from: Ryan McAleer on December 15, 2025, 06:09:13 AMHi John,
I noticed that when doing TDI with an integrated EDS/WDS collection there is a significant lag (8s in this case) in the time of the first TDI measurement.
Is this lag a function of the initialization sequence required by the JEOL EDS--or is a similar lag present on other EDS detectors. Any way to reduce this? Thanks!
Looks like the EDS initialization.
Does this only occur on the first point with EDS elements or for every point with EDS elements?
Does anyone see a similar delay using the Bruker (or Thermo) EDS?
It is with every point
Quote from: Ryan McAleer on December 15, 2025, 09:09:02 AMIt is with every point
In the JEOL PC-SEM software, if you switch from the JEOL EDS window to the JEOL video imaging window it disconnects the JEOL EDS interface (I guess that's a feature?). Are you doing that?
Maybe try putting PFE into DebugMode with the Time Stamp option and see if there's any EDS disconnections occurring.
While Ryan McAleer and I were looking into how we might decrease the time it takes to start an EDS acquisition using the JEOL MEC EDS interface, when using the TDI acquisition feature in Probe for EPMA:
https://smf.probesoftware.com/index.php?topic=79.msg13791#msg13791
we found another "interesting" behavior of the JEOL EDS software.
Previously we found that the JEOL EDS software automatically inserts the Faraday cup (PCD) when the EDS acquisition is complete. Of course when one is still acquiring WDS elements, this is not a good thing. So in addition to item #2 listed here:
Quote from: John Donovan on April 07, 2025, 07:59:33 AMRyan McAleer makes some suggestions for getting the best results from the JEOL EDS interface on iSP100/iHP200F instruments:
Quote1. You should run a single EDS spectrum acquisition in the JEOL software prior to any EDS acquisitions with Probe for EPMA. Doing seems to get the JEOL software interface into a correct state. Just one EDS acquisition for each time starting the JEOL software.
2. To avoid issues with the Faraday cup inserting before the WDS acquisitions are finished, you must uncheck the "Insert PCD after reservation execution is completed" [PFE will prompt you about this once per run]
3. The user should run a single EDS acquisition after they change the EDS time constant in Probe for EPMA. This is to ensure that these EDS conditions are properly saved for subsequent EDS element analyses. Or one can just set the EDS time constant they want in both JEOL (Analysis-->EDS analysis basic conditions) and Probe for EPMA. Otherwise the documented time constant on that first point will be incorrectly saved [we are looking into why this occurs].
4. If there is any hangup during EDS comm, RESTART the JEOL COMPUTER. If you just restart the software (either through "ResetEPMA" or through the task manager) the "reservation" of the EDS will not clear and you will run into a variety of problems.
we have to add a new item because the JEOL EDS software also seems to change the beam mode once the EDS acquisition is completed, even if WDS elements are still being acquired!
Here are Ryan's observations:
QuoteDuring EDS analysis: JEOL software indicates scan coils on and spot mode--equivalent of pfe digital spot mode I think.
(https://smf.probesoftware.com/gallery/1_19_12_25_10_35_08.png)
After EDS ends (but WDS still going), changes to this configuration: pfe equivalent of scan mode. I think when EDS run ends JEOL reverts to a standard state, which is probe scan, note that the beam stays defocused if you have that set, so if the Mag is set to 270K for analysis then maybe there is little practical effect. Becomes an issue if you want to make a valiant attempt to measure something smaller than FOV at 270K (<500nm).
(https://smf.probesoftware.com/gallery/1_19_12_25_10_35_28.png)
So, just FYI.