Performing Integrated WDS and EDS Acquisition in PFE

[John Donovan]

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:



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:



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:



The acquired EDS spectra can be viewed from the Run |  Display and Export EDS Spectra menu dialog as seen here:



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:



Elements by EDS are entered in the Elements/Cations dialog as seen here:



In addition we can optionally display the calculated net intensities for the specified EDS quant elements as seen here:



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:

[ericwgh]

I caught myself looking for a "Like" button. Awesome feature.

[John Donovan]

Be sure to check out these new improvements to integrated EDS-WDS in PFE:

https://probesoftware.com/smf/index.php?topic=482.msg2826#msg2826

[John Donovan]

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:



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.

[John Donovan]

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:



Note that EDS elements can now be quantitatively corrected for interferences just as has been the case for WDS elements as described here:

https://probesoftware.com/smf/index.php?topic=482.msg2826#msg2826

[John Donovan]

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:



And here is the new Elements/Cations dialog:



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.

[John Donovan]

And here is a screen shot of the new graphics for displaying EDS spectra in Probe for EPMA:



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.

[John Donovan]

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

[John Donovan]

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.



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

[UoL EPMA LAB]

Hi John

Any update on doing this with a "JEOL" EDS detector?

Richard

[John Donovan]

Hi Richard,
Vern Robertson (JEOL USA) wrote this to us a few days ago:

I 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.

[John Donovan]

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:



and *also* in the Thermo Pathfinder software. But when we clicked the Analyze button in the Analyze! window it displayed this message:



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:



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:



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!   

Edit by John: the latest PFE update now includes improved warning messages regarding this issue.

[John Donovan]

Hi Richard,
Vern Robertson (JEOL USA) wrote this to us a few days ago:

I 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.

[DavidAdams]

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.

[John Donovan]

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