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Discussion of General EPMA Issues / Re: Generalized dead times
« Last post by Probeman on Today at 09:31:52 AM »
Maybe we can test some of these ideas regarding paralyzable/non-paralyzable with just looking at the raw data?  I plotted raw count (observed) rates from my LTAP and Anette's TAPL on Si metal and of course the Cameca is "topping out" at a lower count rate due to its higher nominal dead times (JEOL = ~1.5 usec vs. Cameca = ~3 usec) but perhaps if we keep going...



Clearly this graph doesn't take it far enough, but perhaps if we continue to increase the beam current we can see if the behavior at even higher count rates produces a different response?

But remember, one must carefully adjust their PHA settings to keep their PHA peak above the baseline to avoid affecting the measurement.  I suggest performing PHA scans at several beam currents over the range being utilized for these tests.  The JEOL seems to be more susceptible to pulse height depression so it is especially important for that instrument to monitor the PHA peak as the beam current is increased.

Another problem specific to JEOL instruments is that if one is adjusting the bias voltage to compensate for pulse height depression (as is usually the case) we have to ask ourselves, could different bias voltages produce different dead times, or are these effects minor compared to the dead times of the pulse processing electronics?
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Discussion of General EPMA Issues / Re: Generalized dead times
« Last post by Probeman on Today at 08:53:42 AM »
First, I believe the Jeol has "enforced" dead time - the difference from Cameca is that on Jeol it is "cut-in-the-stone", where on Cameca it is "user-settable" with low boundary of 1µs (to prevent from "floating" dead time by multiplexing) and high 255µs (max of 8-bits). Anyway, as by default it is set to 3µs and most user don't change it -- that will produce less of PHA shift than on Jeol. Other reason is Jeol gain circuit looks rubish (sorry), and setting the PHA peak position centrally by changing the bias is not the best idea (the countermeasures of PHA shift by increasing bias just increase the very cause of the shift). Lastly I am not sure about that, I am near ready to test it out, but I think Jeol has "pseudo"-integral mode, where Cameca has real integral mode for counting, and that would do the huge difference introducing the paralysable behaviour for Jeol and no paralysable behaviour observed on Cameca.

The biggest confusion comes from mixing the "extending" and "non-extending" with "paralysing" and "non-paralysing" terminology. It is not synonimous, but misunderstanding originates due to extending deadtime producing paralyzable behaviour. But it is not the same other way arround!

If it goes about mathematics: extendable dead time will revert the input count rate vs observed count rate curve at some point, and it will drop and drop untill will reach the 0 output counts at extremely high input count rate - which would be 100% dead time on the EDS. Clearly this is extendable and paralysing.

Thank-you for your thoughts on this very complicated topic.  It will be interesting to see further results from your investigations. 

We have additional recent PHA data from Anette's JEOL instrument that I will be posting soon.  This data should be compared to the PHA data from my Cameca instrument which is here:

https://probesoftware.com/smf/index.php?topic=1466.msg11271#msg11271

But would be nice to see some PHA data from your instrument as well as some constant k-ratio measurements!

As for the fact that Cameca users tend to adjust their PHAs by setting the bias to a fixed number and adjusting the gain to center the PHA peak, while JEOL users tend to do the opposite (set the gain and adjust the bias to center the PHA peak- I don't know how to modify that behavior as the gain settings on the JEOL are in 2x increments which is very coarse.

Anette is also going to post more detailed information on JEOL PHA behavior as she tried centering her PHA peaks at various gain settings.  She has a lot of data to share.
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Discussion of General EPMA Issues / Re: Generalized dead times
« Last post by sem-geologist on Today at 03:45:12 AM »
So you agree that WDS dead time is non-extending? I agree this would seem to be true by definition, since all WDS systems count only for exactly as long as the specified count time.  But then why does Brian make this claim:

It is not that I agree or don't agree (That is not a matter of an agreement).
1) on Cameca instruments I am 100% sure it is non-extendable as I am fully aware how the hardware is built, and on Jeol I argue that by seeing secondary observations (strong shifts of PHA) that it is designed with very similar hardware (and missing hardware part which is needed for extension of dead time - else there would be no PHA shifts). However, probably on Jeol it does have some unintended pralysable behavior misidentified as "extension" by some mechanisms/processes, which are not on Cameca instrument.
2) Before we dwell further we need to distinguish that most of dead time we observe on these instruments is intentionally designed to be there and it cover-over (with huge overlap) the unintentional dead-time (the missing counts from other processes which creeps into signal process depending from count rate)... I think confusion comes from that all (EDS and WDS) systems enforce some dead time in different ways, but I think it does that for a bit different reasons and thus it is more (EDS) or less (WDS) complicated/advanced.
3) lets look to EDS "enforced" dead time. The main reason for EDS enforced dead time is energy accuracy. The counting system looks for all pulses (with very fast but low resolution pulse shapping amplifier) in parallel to the main (high resolution) shapping amplifier and rejects the currently processed pulse if any (accepted or rejected) pulse was close enough before to overlap anyhow with currently processed pulse. As such counter is keeping track of all incoming pulses it will keep rejecting pulses perpetually, unless there is enough of space before the current pulse and its amplitude then can be guaranteed to be accurate. That ability to keep rejecting pulses, unless the height of incoming pulse can be guaranteed to be accurate, - that is what makes the dead time extendable by hardware design.
4) WDS could look similar on the first glimpse, as it "enforces" some dead time. But, it does it differently: a) it enforces dead time after the sensing pulse and blinds itself from sensing any incoming pulses during the dead time (see the difference: EDS does not blind itself at the fast track - so it could keep a note of all incoming pulse, where WDS blinds itself completely) b) it could look that the reason is similrar to EDS: a simplified attempt to prevent to count the pulse coming after the sensed pulse (As there is normally negative tail of pulse, thus preventing overlapped pulse with tail) - thus only the pulse with accurate height would be counted. I initially thought that would be the reason - but, it fails completely, as system have no idea what happened before the sensed pulse (and thus we see PHA shifts on both Cameca and Jeol). Basically if it sees a pulse it holds the pulse and blinds itself (it is accepted or rejected by PHA) for "enforced" amount of time. c) I think the main reason for WDS "enforced" dead time is not accuracy (which we know fails miserable) but to have predictable dead time and overcome the bottleneck of sharing the part of pipeline by few spectrometers. In example on Cameca SX old WDS boards that is up to 3 spectrometers, where analog pulse signal is multiplexed to single shared ADC - The multiplexer requires 1µs for switch! setting dead time anything below 3µs with all three spectrometers on high count rate would not decrease the dead time! On new WDS boards multiplexing is shifted to digital domain (switching can be done at 50 MHz) on single digital bus (all five spectrometers); There setting the "enforced" dead time below 3µs shows the huge difference in count rates, even when all spectrometers are near fully saturated. Still because of multiplexing it should not be set below 1µs (and thus it is blocked from doing that) as the dead time would start to "float" depending from count rate of other spectrometers.

So it is not that "WDS systems count only for exactly as long as the specified count time" - You actually can force most of EDS systems to count for realtime and not live time, which would make it the same from that perspective. No, it is so because of the different counting design and hardware. But, why Brian brings in extending dead time? probably there is misunderstanding what is extending vs non-extending and paralyzing vs non-paralyzing. I think Jeol is at disadvantage and I think You had uncovered the reason in your other thread showing that Jeol is much more affected with PHA shifts than Cameca instruments, which introduce paralysable behavior where more and more pulses are rejected by baseline of PHA. I actually could simulate paralysable behavior at my Monte-Carlo simulation for diff mode (which demonstrates it (diff mode) is very unsuitable for high count rates), --the rejection by baseline would be a similar.

How can pulse pileup in a (JEOL) WDS system equate to an extending dead time model when the count time is fixed? Is the (JEOL) pulse processing electronics "saving" pulses to be counted later?  But then you go on to say:

Again "fixing counting time" has nothing to do with extending - non-extending. As JEOL sees more rejected pulses by PHA baseline with increasing count rate, due to severe broadening and shifting of the PHA it starts to observe paralysable behaviour. It have nothing to do with extension of dead time as hardware is blind for any pulse-pileup and don't care (same as I had wrote before).

I agree with this, but then why does Brian say the JEOL WDS system is extending?  How could it be different from the Cameca?  Because of the "enforced" dead time of the Cameca electronics?  I am somewhat confused by these seemingly conflicting statements.

First, I believe the Jeol has "enforced" dead time - the difference from Cameca is that on Jeol it is "cut-in-the-stone", where on Cameca it is "user-settable" with low boundary of 1µs (to prevent from "floating" dead time by multiplexing) and high 255µs (max of 8-bits). Anyway, as by default it is set to 3µs and most user don't change it -- that will produce less of PHA shift than on Jeol. Other reason is Jeol gain circuit looks rubish (sorry), and setting the PHA peak position centrally by changing the bias is not the best idea (the countermeasures of PHA shift by increasing bias just increase the very cause of the shift). Lastly I am not sure about that, I am near ready to test it out, but I think Jeol has "pseudo"-integral mode, where Cameca has real integral mode for counting, and that would do the huge difference introducing the paralysable behaviour for Jeol and no paralysable behaviour observed on Cameca.

The biggest confusion comes from mixing the "extending" and "non-extending" with "paralysing" and "non-paralysing" terminology.
It is not synonimous, but misunderstanding originates due to extending deadtime producing paralyzable behaviour. But it is not the same other way arround!

If it goes about mathematics: extendable dead time will revert the input count rate vs observed count rate curve at some point, and it will drop and drop untill will reach the 0 output counts at extremely high input count rate - which would be 100% dead time on the EDS.
Clearly this is extendable and paralysing.
To compare with EDS, on WDS with non-extendable deadtime, we can also see paralyzable behaviour at some point - in particular if using diff PHA mode. However, that paralyzable behaviour won't lead to 0 cps at very extremely high input count rates - it will never drop there, as that is only additional mechanism blocking some but not all pulses. It will start dropping but after some time then will go into plato. If paralysing behaviour is noted on any detector, going above that point is absolutely bad as it is not possible to calculate the real count rate (as it can be from both sides of parabolic curve). EDS gets away with that as due to tracking dead time (as it measures all incoming pulses) it knows on which side of such parabolic curve it is. WDS by not tracking the total number of pulses is blind and resolution is impossible.

As for experiment, I have access only for Cameca instruments. As soon I will have something to share I will do, hopefully someone owning Jeol probe will feel adventurous and knowledgeable enough (connecting the earth/ground clip of oscilloscope to wrong place can instantly fry the boards! be warned!) to do such experiments for Jeol.

P.S. above described "double track" pipelines on EDS was on previous detectors. Newest generation of EDS detectors most probably has no more of double tracking but resolve the pileups with terrific beefy Digital Signaling Processors on FPGA's (I am aware that some EDS vendors had moved there - the outcome is terrific: You wont see any pulse-pile ups even with 90% dead time!!!). That is what I would like to go with for WDS too.
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Discussion of General EPMA Issues / Re: Generalized dead times
« Last post by Probeman on September 23, 2022, 01:25:29 PM »
We have non-extendable dead time on WDS on both Jeol and Cameca instruments. Why? 1) because we have PHA peak shifts - again extension of dead time is to prevent that, and as we see the shifts it is clear that there is no extension; 2) If I increase the current it the raw count rate increases, at high current it increase very little, but still it is the increase and no count rate decrease is observable even at >1µA beam at large crystal at most intense lines. It is clearly non paralyzable. 3) EDS for extendable dead time needs many different shapping amplifiers, where one fast shapping amplifier works constantly in parallel to the main high resolution (slower) amplifier. At least on Cameca WDS there is only and only one shapping amplifier integrated with Charge sensitive preamplifier in a single package, which is connected directly to the GPC - because of that there is no way to implement (and hide away in any possible means) EDS-like extendable dead time circuit.

So you agree that WDS dead time is non-extending? I agree this would seem to be true by definition, since all WDS systems count only for exactly as long as the specified count time.  But then why does Brian make this claim:

What I mean is that it appears that loss of X-ray counts in the JEOL pulse processing circuitry is dominated by pulse pileup and not dead time.  Pulse pileup is described mathematically in a manner equivalent to an extending dead time.

How can pulse pileup in a (JEOL) WDS system equate to an extending dead time model when the count time is fixed? Is the (JEOL) pulse processing electronics "saving" pulses to be counted later?  But then you go on to say:

Have pulse pile ups have anything with extendable vs not extendable?... Can pulse pile up do anything to non-extendable circuit? No not at all, as it by design does not care. It is designed with profound superstition that it is fast enough (80es, there were still no large diffracting crystals) and will not come to such situation. Also integral counting method does not care about pulse pile ups.

I agree with this, but then why does Brian say the JEOL WDS system is extending?  How could it be different from the Cameca?  Because of the "enforced" dead time of the Cameca electronics?  I am somewhat confused by these seemingly conflicting statements.

I would very much like to see you and Brian to discuss this question!

Well, there is some still hard to answer questions, i.e. is Cameca integral mode real integral mode or same "pseudo-integral" as Jeol, and other questions which You are stimulating my head to come at. I came to a plan to check that out with injecting the deterministically generated pulse train with signal generator (unplugging the signal cable from detector and plugging it to such generator). Such equipment is expensive $$$$ and out of my budget, but I found out that with some resistor ladder improvised DAC I could do that with Raspbery pico board (4$) and few electronic components (fast opamp to drive the signal $$). I will open separate thread to show how to construct such a device, program it and use it for such a purpose. This board is able to output signals at its clock speed of 133Mhz, but saw someone overclocking it to 250Mhz, anyway that is more than enough to emulate nearly exact pulse shapes emitted and fed to WDS counting electronics from Shapping amplifier near detector. I think this experiment will prove or disprove some of my claims such as:
* GPC's has no dead time (in case it is true, we should see the exactly same rate of missing pulses with increased pulse rate from such generator).
* GPC's pulses are precise - WDS counting electronics introduce PHA spread (feeding the artificially precise pulses with exact same pulse height PHA scan should produce very narrow peak if that claim is wrong). 

These experiments should be performed on both the Cameca and JEOL electronics so we can gain a better understanding of these "black boxes" that we depend on so much!
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Probe for EPMA / Re: Aperture 200
« Last post by John Donovan on September 21, 2022, 02:57:20 PM »
Hi Theo,
I guess I would try checking this checkbox in the Acquisition options dialog (from the Acquire! window):



That should prevent PFE from setting any beam conditions.
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Probe for EPMA / Aperture 200
« Last post by theo_nt on September 21, 2022, 01:54:06 PM »
Hi John,

I would like to use the aperture 200 in our SXFive FE, which is not using beam regulation but always the probewin turn it to 150 aperture and try to regulate the beam there.  Could you please tell me where to set the aperture 200?
Is there an option to set the beam manually like in Cameca software?

Theo
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I want to look at these PHA settings more closely because I think that some of what we are seeing, when performing these constant k-ratio measurements, is due to PHA peak shifting at high beam currents (count rates).

These effects will be different on Cameca and JEOL instruments obviously, so please feel free to share your own PHA scans at low and high count rates so we can try and learn more. This is of course complicated by the fact that on Cameca instruments, we tend to leave the bias fixed at a specific voltage (~1320v for low pressure flow detectors and ~1850v for high pressure flow detectors) and then simply adjust the PHA gain setting to position the PHA peak (normally around 2 to 2.5 v in the Cameca 0 to 5 v PHA range), but for the constant k-ratio method we want to instead position the peak to slightly *above* the center of the PHA range (at low beam currents) to avoid peak shifting from pulse height depression (at higher beam currents), so centered roughly around 3 volts or so.
 
Here for example is Mn Ka on Spc2, LPET, a low pressure flow detector at 30 nA:
 


Note that the peak is roughly centered around 3 volts. Now using the same bias voltage of 1320v here is the same peak at 200 nA:



Please note that the gain is *exactly* the same for both the 30nA and the 200 nA scans!   This is really good news because it means that we don't need to adjust the PHA settings as we go to higher count rates.

But the PHA peak at 200 nA has certainly broadened and shifted down slightly to 2.5 volts or so (which is why we set it a little to the right of the center of the PHA range to begin with!), probably due to pulse height depression.  Note that even though it has broadened out, because we are in integral mode, we don't have to worry about cutting off the higher side of the PHA peak.  The important thing is to keep the peak (including the escape peak!), above the baseline cutoff.

How about a high pressure flow detector? This is a PHA scan on Spc3 LLIF which is a high pressure flow detector, first at 30 nA:



and again at 200 nA using the same (1850v)  bias voltage:



Again, the gain setting is the same, and very little change in the PHA peak (though it is again, slightly shifted down and broadened). Now admittedly we are getting a somewhat less count rate on the LLIF crystal than the LPET, so I do want to try this again on Spc3 LPET, but still very promising.

Again the take away point: check your PHA distributions at both the lowest and highest count rates to be sure you are not cutting off any emission counts when performing the constant k-ratio method.

On JEOL instruments that is an entirely different story because usually the gain is fixed and the bias voltage is adjusted. Question is: can we keep the JEOL PHA distributions above the baseline as we get to higher count rates using a single pair of bias and gain values?  Anette's initial data suggests, no we can't:



I should mention that this PHA shift effect (more pronounced on the higher concentration Si metal primary standard), would tend to produce a constant k-ratio trend as we see in this post, because the primary standard is in the denominator (and as the primary intensity decreases, the k-ratio tends to increase):

https://probesoftware.com/smf/index.php?topic=1489.msg11230#msg11230

Can we see some more JEOL PHA data at low and high count rates for both P-10 and Xenon detectors?
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JEOL / Re: JEOL stage shift issue
« Last post by sem-geologist on September 19, 2022, 07:41:05 AM »
It is good You could fix your problem with shifting stage for Cameca. To add more, there are such metal pieces which holds the shuttle in place, they tend in long time to loosen up (bend back), thus unintended additional shuttle shifts due to stage movement can be also corrected by bending slightly those plates to hold the shuttle much more tightly.

I want also to point out that stage position reproducibility if checked on electronic image can be sometimes misleading. The "shift" can be introduced by shifting (unintended bending) beam (i.e. old contaminated aperture, where charging will bend the beam after setting new current) while stage would work absolutely perfectly. Thus stage reproducibility should be checked on optical image.
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JEOL / Re: JEOL stage shift issue
« Last post by Radek_MM on September 19, 2022, 07:00:46 AM »
Hi,

Maybe I can add some stage shifting issues from my experience here at the geological survey of Finland (mineralogical lab). I had issues on both instruments, our CAMECA SX100 and our new JEOL iHP200F:

1.CAMECA
After programming many spots and returning to the first one it was shiftet some tens of microns in x and y direction, but in the lower part of the holder in the opposite x direction. Long story short, after a few investigations I figured out the stage was "rotating" when moved. This is due to the worn out shuttle on which the sample holder is mounted. You can see the worn out groves where the "fork" of the rod is holding the shuttle when inserting into the sample chamber.

Solution: I replaced the shuttle with a less worn out one and reduced a bit the speed of the stage. No shift after that.

2. JEOL
The new iHP200F has a large shuttle, on which the sample holder is mounted. We use the split holder from Boerder and have our standards permanently inside the sample chamber. When moving in x direction, I got a shift in y direction always towards the gate. The longer the x distance traveled, the bigger the shift in y direction up to several 10s of microns. With the JEOL engineer we took a look at it and, long story short, two metal springs on the side of the stage (with the wheels at the end) are too soft for the massive shuttle, so the faster it moves, the more the whole shuttle "wobbles" off the stage towards the gate.

Solution: (Temporary) We stiffened the metal springs by glueing a small metal pin between the spring and the stage, thus making it stiffer. Long term solution would be to use either a thicker metal plate or a more stiffer material for this part. The JEOL engineer is in discussion with Japan about what to do. Since we were the "first" ones to report that, they are waiting to confirm from another instrument if this happens on any instrument or if it is only in our instrument the case.

In my experience if there is some shift in stage movement it is a mechanical issue and not a software issue (since, like you say John, software is often still the same as before the problem occurs). Maybe mapping the shift (like we did in our CAMECA, testing how the shift appeares throughout the whole movement range) might help to realize what the problem is.

Greetings from the cold North (Finland)!

Radek

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EPMA Standard Materials / Re: Consensus K-Ratio Measurements
« Last post by Probeman on September 17, 2022, 08:18:10 AM »
I'm sure this has already occurred to Will Nachlas and Aurelien Moy, but I'll mention it anyway just to get it off my mind.

When performing the consensus k-ratio measurements on the mounts being distributed by Will Nachlas (e.g., the MgO-Al2O3-MgAl2O4 mounts), I suggest that we measure our k-ratios at several electron beam energies. At the very least we should perform these k-ratio measurements at 10, 15 and 20 keV as this additional information will be helpful to build our consensus k-ratio database with Nicholas Ritchie.

Those wanting additional information can find more at this early topic started by Nicholas Ritchie in 2019:

https://probesoftware.com/smf/index.php?topic=1239.0

Also here is the "Open Letter to the Microanalysis Community" started by Probeman on the importance of global standards:

https://probesoftware.com/smf/index.php?topic=1415.0

And also this post from the "constant k-ratio" topic, which stresses the importance of performing k-ratio measurements at multiple beam currents (count rates):

https://probesoftware.com/smf/index.php?topic=1466.msg11166#msg11166

This is to ensure that our:

1. Dead time constants are well calibrated

2. Our picoammeter is well calibrated

3. Our spectrometers (EDS and WDS) produce k-ratios that are consistent with each other. 

See also starting here for more details on using the constant k-ratio method to calibrate your instrument:

https://probesoftware.com/smf/index.php?topic=1466.msg11100#msg11100

Finally a quick reminder that the current version of Probe for EPMA now contains an easy to use menu to export your consensus k-ratio measurements to an external file, for import into the consensus k-ratio database that Nicholas Ritchie is building:

https://probesoftware.com/smf/index.php?topic=40.msg10835#msg10835
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