Latest version changes for Probe for EPMA (and CalcImage) v. 13.8.3

[John Donovan]

To enable the automated acquisition of constant k-ratios we implemented a new option which will increment the Y stage axis when acquiring multiple sample setups. This option is available from the Multiple Setups button in the Automate! window as seen here:



The constant k-ratio test for checking the instrument dead times and picoammeter accuracy is discussed here:

https://probesoftware.com/smf/index.php?topic=1466.0

This new Y stage increment option works for both the original multiple sample setups acquisitions (each position sample for all (multiple) sample setups), and the new "one at a time" multiple sample setups acquisitions, which can be used for the constant k-ratio testing if ones samples are susceptible to beam damage.

And it works for all position samples with multiple sample setups (standards, unknowns and wavescans!). Check it out.

[John Donovan]

We have been working with Philipp Poeml recently adding some new features in CalcImage (e.g., a new filter for blanking pixel with bad analytical totals) and have found that a version uploaded in last last two weeks has a few minor bugs that have now been fixed.

So if you've updated your Probe for EPMA software in the last two weeks, please update again and all should be good.

Sorry for any inconvenience.

[John Donovan]

There is now a new button in the Analytical | Update Dead Time Constants menu dialog as seen here:



This allows one to update all the dead time constants in an old probe run (or new probe run using older element setups from the element setup database), by using the dead time constants stored in the SCALERS.DAT file (which normally should be the most recent dead time constants that have been determined).

[John Donovan]

Latest version of Probe for EPMA now notes the dead time correction expression type utilized in the Report output format:

[John Donovan]

The latest version of Probe for EPMA now includes the exponential dead time correction expression for those that might want to try it out:



It does not appear to work well on Cameca instruments, at least when typical Cameca dead times are ~3 usec or so, because the product of deadtime * cps is often greater than 1/e as explained in this post:

https://probesoftware.com/smf/index.php?topic=1489.msg11245#msg11245

But further evaluations of JEOL intensities using these expressions are most welcome. Please note that when acquiring constant k-ratios on JEOL (and Cameca for that matter) instruments, be sure to record your PHA scans at both the lowest *and* highest count rates to be sure that no PHA shifting is occurring that could bias the results. Normally this should be performed on your primary standard, e.g., pure Ti or pure Si. See here for more details:

https://probesoftware.com/smf/index.php?topic=1466.msg11247#msg11247

What we want to avoid is PHA shifting as seen here from Anette's SiO2/Si constant k-ratio run:



If necessary one might need to modify the PHA settings for the high current acquisitions to avoid such extreme PHA shifting...

[John Donovan]

We added some additional output in Probe for EPMA that might be helpful for those evaluating the various dead time correction expressions. Specifically the dead time constant for each element (DEAD) and also the percent dead time correction (DTC%) as shown here:

On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM:    si ka   si ka   si ka   si ka   si ka   BEAM1   BEAM2
BGD:       OFF     OFF     OFF     OFF     OFF
SPEC:        1       2       3       4       5
CRYST:     TAP    LTAP    LPET     TAP     PET
ORDER:       1       1       1       1       1
  102G  223.63  663.19   72.31  238.14   23.34   7.727   7.727
  103G  223.49  665.10   73.30  235.02   23.13   7.730   7.727
  104G  223.19  666.12   73.15  233.68   23.34   7.729   7.727
  105G  225.02  667.15   71.75  235.16   23.55   8.406   8.438
  106G  224.17  667.77   71.12  232.59   23.64   8.190   8.200
  107G  224.53  664.00   71.57  230.58   23.35   7.402   7.396
  108G  223.26  666.34   74.89  231.33   23.80   8.422   8.438
  109G  223.63  655.35   72.00  229.94   23.64   8.188   8.200

AVER:   223.87  664.38   72.51  233.30   23.47   7.974   7.982
SDEV:      .65    3.96    1.22    2.75     .22    .375    .387
1SIG:      .68    1.18     .39     .70     .22
SIGR:      .95    3.37    3.12    3.94     .99
SERR:      .23    1.40     .43     .97     .08
%RSD:      .29     .60    1.68    1.18     .94
DEAD:     2.85    2.65    3.00    2.76    3.10
DTC%:       .5     1.4      .2      .5      .1

Typically, the dead time correction percentages are less than 1%, but we thought it was worth displaying when outputting raw intensities using the Raw data button in Probe for EPMA.  Of course when running Si Ka on a large TAP crystal at high beam currents one is going see much larger corrections. Here is one such example:

On-Peak (off-peak corrected) or EDS (bgd corrected) or MAN On-Peak X-ray Counts (cps/1nA) (and Faraday/Absorbed Currents):
ELEM:    si ka   si ka   si ka   si ka   si ka   BEAM1   BEAM2
BGD:       OFF     OFF     OFF     OFF     OFF
SPEC:        1       2       3       4       5
CRYST:     TAP    LTAP    LPET     TAP     PET
ORDER:       1       1       1       1       1
  350G 1529.94 3069.74  684.65 1607.96  197.11 200.568 200.568
  351G 1527.25 3076.57  684.89 1611.71  197.30 200.629 200.598
  352G 1531.49 3076.92  685.27 1609.49  197.70 200.598 200.598
  353G 1529.87 3077.09  685.17 1611.09  197.27 200.598 200.583
  354G 1527.81 3080.52  685.17 1612.68  197.33 200.583 200.583
  355G 1530.51 3078.64  685.65 1609.84  197.46 200.568 200.552
  356G 1529.83 3077.20  685.69 1609.11  197.13 200.583 200.583
  357G 1527.66 3078.21  685.60 1606.19  196.80 200.629 200.537

AVER:  1529.29 3076.86  685.26 1609.76  197.26 200.594 200.575
SDEV:     1.53    3.15     .37    2.09     .26    .024    .022
1SIG:      .24     .28     .20     .25     .12
SIGR:     6.26   11.25    1.90    8.38    2.19
SERR:      .54    1.11     .13     .74     .09
%RSD:      .10     .10     .05     .13     .13
DEAD:     2.85    2.65    3.00    2.76    3.10
DTC%:    112.8   227.4    48.4   115.2    13.0

Note the 227% correction!   

Also worth mentioning that if one exceeds the valid range of dead time * cps product, the software will warn you that the correction cannot be applied as shown here:



Although all the dead time expressions will fail mathematically at high enough dead time constants and count rates, the only time this error should ever become visible is when applying the exponential dead time correction on a Cameca instrument with its typically ~3 usec dead times.

[John Donovan]

This is a very small change to the software and I'm not sure how many will find it useful, but it was requested by Chi Ma at Cal Tech, so we added the capability.

So of you may have noticed that Probe for EPMA controls the optical light automatically on several occasions. For example:

The light is turned off:
1. Before automated image acquisition
2. Before PI is being run during automation
3. At the end of automation
4. Before manual sample acquisition from Acquire! if using EDS or CL

The light is turned on:
1. Auto-focus
2. After sample acquisition for manual sample acquisition or if automated and confirm positions is specified
3. If automation is canceled

But Chi requested that we add an option to not allow PFE to control the reflected and/or transmitted light temporarily. So we implemented the following new checkbox control in the stage map window:



When this checkbox is checked PFE will no longer control the reflected or transmitted light on or off commands (automatically or manually).  The only time the light will be automatically controlled is during auto-focus of stage Z position.

[John Donovan]

I got a strange feature request from Probeman, but the more I thought about it, the more reasonable it sounded.

Anyway, here's the deal: in Probe for EPMA we can integrate JEOL or Cameca WDS EPMA instruments with EDS systems from Thermo, Bruker or JEOL. However, Probe for EPMA does not connect to the EDS system until it is needed. That could be because one starts an EDS acquisition (from an existing WDS-EDS run), or one needs to extract EDS net intensities for quantification, or maybe just because one decides to open the Acquisition Options dialog from the Acquire! window.

When the Acquisition Options dialog is opened, Probe for EPMA checks the current EDS pulse process time in the EDS system and updates the value displayed in the dialog. If the EDS interface is not already connected, it tries to connect to the EDS system which might be on the same computer as Probe for EPMA (e.g., Thermo or Bruker) or on a remote computer (e.g., JEOL 8230/8530 and  iSP100/iHP200F).  The Bruker and Thermo EDS systems can also be on a remote computer depending on how your computer network is arranged.

For example, when the Acquisition Options dialog is opened and a Thermo NSS or Pathfinder system is present, this dialog would previously be displayed:



to prompt you to either click OK to attempt to connect to the Thermo system *or* to click Cancel to exit and not open the Acquisition Options dialog. This means that the Acquisition Options dialog cannot be opened unless the Thermo EDS software is up and running on a local or remote computer.  But what if you don't want to use the integrated WDS-EDS acquisition in Probe for EPMA?  Or even worse, what if there's a problem with the Thermo software or computer and you can't run the Thermo software at all?

One could close the application and edit the Probewin.ini file to indicate that no EDS system is present (EDSSpectraInterfacePresent=0), or perhaps we could just temporarily disable the EDS interface just for this session? That was Probeman's thought and so we've implemented that so, when being prompted for attempting a connection to the Thermo (or Bruker or JEOL) EDS software, we are now presented with this dialog:



A slightly different message appears if the Thermo system is on another computer, but the key point is that when one clicks Cancel, instead of exiting and not opening the Acquisition Options dialog, it merely temporarily disables the EDS interface (for the duration of this session) and displays the dialog as seen here with the EDS controls disabled:



Of course you'll probably want to add some elements by WDS...  but the point being you can proceed and open the Acquisiiton Options dialog without having to get the Thermo EDS software up and running just to analyze some WDS elements.

Now what happens if you then decide to start an EDS acquisition (for a run that already contains EDS data)?  Well you'll get this dialog:



And what about if you already have some EDS element acquired and try to quant them?  Well, you'll get this dialog:



Note that you can re-start the software and then have the EDS software up and running and then connect to it in order to obtain new net intensities, *or* you could simply open the Analysis Options dialog from the Analytical menu and check the following checkbox:



This forces Probe for EPMA to utilize EDS net intensities that have been previously stored in the user's current probe database.  This, by the way, is also a neat way to process data off-line from Thermo, Bruker or JEOL EDS systems.  Though remember, one can install an off-line version of the Thermo and Bruker software on any computer for the purposes of obtaining net intensities.

Note that JEOL does not have an "off-line" version of their software so this "Only Use Stored Intensities" option is very handy when you want to process WDS-EDS analyses on another computer not connected to the microprobe private network.

[John Donovan]

The latest version of Probe for EPMA 13.3.0 now includes display and output of intensity units to clarify any confusion of whether the displayed/output intensities are normalized to beam current or not in the Output | Output Standard and Unknown XY Plots menu window as shown here:



If, for example, the Use Beam Drift Correction flag is turned on (as it is by default) in the Analytical | Analysis Options menu dialog, the units will be cps/X nA where X is the nominal beam current which is displayed (and edited) in the Count Times dialog.  If the beam drift correction is turned off, the units displayed will be cps. If displaying "raw" intensities, those will be counts per nA or simply counts (if the beam drift correction is turned off) to indicate that the intensities are de-normalized to time.

[John Donovan]

Some of you may have noticed that we have not released a new version of Probe for EPMA since v. 13.3.1 in early June. But not because we haven't been working hard on new features and capabilities in the software!

There's been a number of significant improvements to the software since then, but we wanted to be sure everything was tested and working before we released a new version. Our beta testers have been working with these new versions all summer and they say the new software appears to be working well in their labs.

So starting today we've uploaded the latest v. 13.5.2 of Probe for EPMA to our usual download sites so you can update your software using the Help | Update Probe for EPMA menu dialog as usual. And over the next few weeks I (and others) will be posting about these changes and provide descriptions of these new features and other modifications.

We will start with the oldest changes starting back in June, which was when we added the ability for users to specify different atomic weights for elements in their standards and/or in their unknowns as mentioned here in the version.txt file which is distributed with Probe for EPMA:

06/21/23  Modify Standard and Probe for EPMA to handle different atomic weights for standards
v. 13.3.2        and unknowns. Lots of code changes- needs to be tested. Note: Isotopes of the same
                      element should always produce the same x-ray intensities, but the concentrations and
                      stoichiometries will be different if the atomic weights are different.
                      E.g. Si28 vs. Si29.

Interestingly the use of different atomic weights in our calculations doesn't affect our matrix corrections (except for the backscatter corrections- more on that later!) because for the absorption correction, we utilize mass normalized absorption coefficients and for energy loss calculations we normalize to mass thickness (though for absolute rigor we really should be normalizing our absorption coefficients to the actual densities of enriched atomic weights involved- yeah, we really should be utilizing atomic fractions for all our physics calculations as is done in Penepma).

But it does affect how the mass fraction results are reported!  Now we may wonder why this capability has not been implemented in the JEOL or Cameca software (as far as I know), but for actinide materials the difference between say, U235 and U238 is fairly small at around 1.2% relative and I guess might be ignored. But for an element such as Si28 vs. Si29 the difference is larger at around 3.5% relative, and even larger for Si30, at least for those of you using isotopes in your silicate experiments...

Anyway, we started by adding an extra text field to allow the user to specify different atomic weights in the Standard application as shown here:



When the standard is displayed in the log window, the atomic weights are reported as seen here:



Note that the atomic weights for standard elements can only be edited in the Standard application. We also added an atomic weight field in the Probe for EPMA Elements/Cations dialog as shown here for unknown samples:



These values (for unknown samples) can be edited directly in Probe for EPMA. When the raw data is displayed in the log window, the atomic weights are displayed as seen here:



And when results are calculated for samples with different atomic weights between the standards and unknown, the atomic weights are also displayed for both:



Ok, that's enough for today.  Lots of other new features to be described over the next few weeks but you can get a preview here:

https://probesoftware.com/smf/index.php?topic=40.0

Or download to the latest Probe for EPMA v. 13.5.2 update and see for yourselves.

[John Donovan]

07/14/23    Add code to read "effective takeoff angles" from SCALERS.DAT file and save to MDB database based on
v. 13.4.2         spectrometer/crystal combination.

This next implemented feature in Probe for EPMA allows one to calibrate the "effective" takeoff angles for each spectrometer and crystal combination on their instruments, document those values in the SCALERS.DAT file, and utilize these takeoff angles in the absorption matrix corrections.

Although we assume that our WDS spectrometer take off angles are *exactly* 40 degrees, it is evident that the "effective" takeoff angle on some spectrometer/crystals are quite different from the nominal values, as evidenced from k-ratio measurements from multiple spectrometers, referred to sometimes as "simultaneous" k-ratios (by Paul Carpenter and John Armstrong) previously.

That is, k-ratio of measurements on multiple spectrometers should yield the same k-ratios within statistics. Now some of these differences in k-ratios could result from miscalibration of the dead time constant, especially on large area crystals with high count rates as described in our 2023 paper "A New Method for Dead Time Calibration and a New Expression for Correction of WDS Intensities for Microanalysis".

https://doi.org/10.1093/micmic/ozad050

But once the dead time constants (and picoammeter linearity) are calibrated properly, and it is determined that the electron beam is perpendicular to the sample surface, any remaining differences in these "simultaneous" k-ratios should be due to differences in the "effective" takeoff angle of the spectrometer/crystal combination. These calibrations are discussed in this topic:

https://probesoftware.com/smf/index.php?topic=1535.msg11937#msg11937

Here's an example of consistently different k-ratios from multiple spectrometers:

https://probesoftware.com/smf/index.php?topic=1466.msg11329#msg11329

For example, the spectrometer could be misaligned internally or relative to the electron column, or the crystal diffracting asymmetrically (as was the case for the EPMA instrument at Caltech).

We will discuss how one might go about calibrating these "effective" takeoff angles, but assuming that one has determined what these "effective" takeoff angle actually are, we have introduced a new flag in Probe for EPMA, that allows one to compare analytical results using the nominal takeoff angle versus these "effective" takeoff angles as seen here:



To utilize these "effective" takeoff angles, one must edit their SCALERS.DAT file. Previously the SCALERS.DAT file appeared like this near the bottom of this text file:

1300.    1290.    1890.    1300.    1800. "default detector bias1"
 1300.    1300.    1850.    1300.    1850. "default detector bias2"
 1500.    0.       0.       1480.    0.    "default detector bias3"
 1500.    0.       0.       1460.    0.    "default detector bias4"
 0.       0.       0.       0.       0.    "default detector bias5"
 0.       0.       0.       0.       0.    "default detector bias6"
 1        1        1        1        1     "default PHA inte/diff modes1"
 1        1        1        1        1     "default PHA inte/diff modes2"
 1        0        0        1        0     "default PHA inte/diff modes3"
 1        0        0        1        0     "default PHA inte/diff modes4"
 0        0        0        0        0     "default PHA inte/diff modes5"
 0        0        0        0        0     "default PHA inte/diff modes6"
 0        0        0        0        0     "default detector deadtimes1"
 0        0        0        0        0     "default detector deadtimes2"
 0        0        0        0        0     "default detector deadtimes3"
 0        0        0        0        0     "default detector deadtimes4"
 0        0        0        0        0     "default detector deadtimes5"
 0        0        0        0        0     "default detector deadtimes6"
 0        1        1        0        0     "Cameca large area crystal flag1"
 0        1        1        0        0     "Cameca large area crystal flag2"
 0        0        0        0        0     "Cameca large area crystal flag3"
 0        0        0        0        0     "Cameca large area crystal flag4"
 0        0        0        0        0     "Cameca large area crystal flag5"
 0        0        0        0        0     "Cameca large area crystal flag6"
0        0        0        0        0     "unused"
 0        0        0        0        0     "unused"
 0        0        0        0        0     "unused"
 0        0        0        0        0     "unused"
 0        0        0        0        0     "unused"
 0        0        0        0        0     "unused"
0        0        0        0        0      "unused"

However, you will need to edit the bolded lines for your spectrometer/crystal "effective" takeoff angles for each spectrometer and crystal as shown here, where it is assumed that all the "effective" takeoff angles are 40 degrees:

1674.    1764.    1750.    1650.    1790. "default detector bias1"
 1750.    1800.    1800.    1700.    1770. "default detector bias2"
 0.       0.       1740.    0.       0.    "default detector bias3"
 0.       0.       1740.    0.       0.    "default detector bias4"
 0.       0.       0.       0.       0.    "default detector bias5"
 0.       0.       0.       0.       0.    "default detector bias6"
 -1      -1       -1       -1       -1     "default PHA inte/diff modes1"
 -1      -1       -1       -1       -1     "default PHA inte/diff modes2"
 0        0       -1        0        0     "default PHA inte/diff modes3"
 0        0       -1        0        0     "default PHA inte/diff modes4"
 0        0        0        0        0     "default PHA inte/diff modes5"
 0        0        0        0        0     "default PHA inte/diff modes6"
 1.23     1.31     1.56     1.32     1.04  "default detector deadtimes1"
 1.21     1.16     1.31     1.14     1.03  "default detector deadtimes2"
 0        0        1.23     0        0     "default detector deadtimes3"
 0        0        1.18     0        0     "default detector deadtimes4"
 0        0        0        0        0     "default detector deadtimes5"
 0        0        0        0        0     "default detector deadtimes6"
 0        0        0        0        0     "Cameca large area crystal flag1"
 0        0        0        0        0     "Cameca large area crystal flag2"
 0        0        0        0        0     "Cameca large area crystal flag3"
 0        0        0        0        0     "Cameca large area crystal flag4"
 0        0        0        0        0     "Cameca large area crystal flag5"
 0        0        0        0        0     "Cameca large area crystal flag6"
40       40       40       40       40     "effective take off angles1"
40       40       40       40       40     "effective take off angles2"
 0        0       40        0        0     "effective take off angles3"
 0        0       40        0        0     "effective take off angles4"
 0        0        0        0        0     "effective take off angles5"
 0        0        0        0        0     "effective take off angles6"
0        0        0        0        0     "unused"

We will go into the calibration and testing of these "effective" takeoff angles later, but in the meantime, it is something to think about.

[John Donovan]

The next new feature we've added to Probe for EPMA this summer is an interesting one:

07/17/23   Enable secondary fluorescence from boundary code in PFE. Needs testing.
v. 13.4.3

I will discuss this new method in the topic specifically for this feature:

https://probesoftware.com/smf/index.php?topic=1545.0

Please note that we fixed a small bug in this feature yesterday (9/11/2023), so please update your Probe for EPMA using the Help menu as usual if you have an older version of the software.

[John Donovan]

Continuing with changes since June, we added a new backscatter correction called the DAM (Donovan and  Moy) backscatter correction as described in the latest version.txt file:

07/29/23   Add new matrix correction code for Donovan and Moy BSC/BKS corrections (modified from PAP).

This deserves its own topic here:

https://probesoftware.com/smf/index.php?topic=1566.msg12044#msg12044

Why did we name it the DAM backscatter correction?  Well. perhaps because that was better than the MAD backscatter correction...   

Be sure to update your Probe for EPMA using the Help menu as we had to make some minor tweaks (today) to fix some display issues.

[John Donovan]

Another change we made earlier this summer:

07/31/23   Add output of variable Z fraction exponent for MAN parameters. Add two more references to AnalyzeTypeReport.
v. 13.4.5   Add variable exponent to Z fraction backscatter exponent code. Add new
      Z fraction backscatter parameter to GetZAF form and code.

07/30/23   Modify MAN Z fraction zbar calculation to accept a zero for dynamically calculated
v. 13.4.4   Zbar exponents based on emission line energy.

These two changes are slightly related.

The variable exponent in the MAN Z-bar calculation allows the user to have a "optimized" Z fraction exponent based on each MAN element's emission line energy.  For example, see this topic for more details:

https://probesoftware.com/smf/index.php?topic=4.msg12050#msg12050

The variable exponent for the Donovan and Moy (DAM) backscatter correction is discussed here in more detail:

https://probesoftware.com/smf/index.php?topic=1566.msg12051#msg12051

[John Donovan]

      Modify Calculation Options dialog to fit on screen better (Nachlas).

We modified the Calculation Options dialog to fit better on smaller (laptop) screens: