Recent Posts

Pages: [1] 2 3 ... 10
1
Discussion of General EPMA Issues / Re: Sulfur Peak Shifts
« Last post by Probeman on June 15, 2019, 01:06:15 pm »
Here's an possibly interesting method for determining sulfur concentrations *and* the approximate oxidation states *at the same time* on a microprobe.

As many of you know, depending on the oxidation state of sulfur, the emission peak on a WDS spectrometer varies enough to make it necessary to accurately position the spectrometer on the actual emission peak position.  Basically there is roughly a 10% change in intensity between the pyrite and anhydrite sulfur peak positions. 

Determining the degree of peak shift in a basaltic glass when the sulfur concentrations are around 1000 PPM is difficult, partly because a high enough precision wavescan requires considerable time, causing sample damage, and also possible oxidation of the sulfur in the glass, which causes further peak shifting. Specifically we've found it necessary to acquire sulfur wavescans on our basaltic glasses for around an hour each, and even then we've found it necessary to have PFE increment the stage position a few microns every minute or so to avoid further oxidizing the sulfur.

The basic idea being that once we determine the actual emission peak position for a given glass sample, we can set the spectrometer to that position and collect our sulfur intensities at the peak position for accurate quantitative analysis, regardless of the sulfur primary standard. 

But earlier this week two graduate students, Dan Rasmussen and Michele Muth, came up with an idea for determining the sulfur peak position by essentially creating a "multi-collector" microprobe for characterizing reduced to oxidized sulfur "species", by tuning each of our 5 PET spectrometers to cover the range of sulfur oxidation peak positions.

So we first tuned all the spectrometers to our pyrite primary standard (-1 valance),  spectrometer offset equals 0, and knowing that the pyrrhotite sulfur peak (-2 valence) is shifted to the right +4 units (in Cameca units), and anhydrite is shifted to the left by 30 units, we adjusted our 5 WDS spectrometers as seen here:

    +4    0    -10    -20    -30

Spectrometer 1 being the spectrometer tuned to the pyrrhotite sulfur peak, spectrometer 2 being the spectrometer tuned to the pyrite peak and spectrometer 5 tuned to the anhydrite sulfur peak position, with spectrometers 3 and 4 tuned to intermediate peaks positions between pyrite and anhydrite.

The idea being that the spectrometer that produces the highest sulfur concentration will therefore probably be the correct concentration, and the also give us information on what the oxidation state of the sulfur is, depending on which spectrometer it is.  Furthermore, instead of counting an hour or so for a high precision wavescan, we only need to count for a few hundred second to get excellent sensitivity for our ~1000 PPM sulfur measurements!

When we then analyzed our ND70 SIMS glass standard for all 5 spectrometers, which reportedly has a sulfur concentration of 900 PPM, we obtained the following results:

Un   24 ND70, Results in Elemental Weight Percents

SPEC:       Si      Al      Fe      Mg      Ca      Na       K      Ti       P      Mn       O       F
TYPE:     SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC

AVER:     .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
SDEV:     .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
 
ELEM:        S       S       S       S       S
BGDS:      LIN     LIN     LIN     LIN     LIN
TIME:   160.00  160.00  160.00  160.00  160.00
BEAM:    49.62   49.62   49.62   49.62   49.62

ELEM:        S       S       S       S       S   SUM 
XRAY:     (ka)    (ka)    (ka)    (ka)    (ka)
   492    .072    .073    .069    .077    .073    .364
   493    .069    .075    .073    .070    .074    .362
   494    .071    .076    .068    .068    .064    .347
   495    .072    .072    .070    .062    .071    .347
   496    .070    .074    .070    .069    .072    .354
   497    .071    .072    .070    .064    .066    .344
   498    .073    .070    .069    .065    .074    .352
   499    .073    .076    .072    .069    .069    .358
   500    .073    .069    .070    .067    .062    .341
   501    .071    .071    .072    .074    .073    .360

AVER:     .071    .073    .070    .068    .070    .353
SDEV:     .001    .002    .002    .004    .004    .008
SERR:     .000    .001    .001    .001    .001
%RSD:     2.00    3.28    2.40    6.43    6.12
STDS:      730     730     730     730     730

STKF:    .5044   .5044   .5044   .5044   .5044
STCT:   152.32  451.70  499.97  127.50  166.44

UNKF:    .0007   .0007   .0007   .0007   .0007
UNCT:      .22     .65     .70     .17     .23
UNBG:      .10     .18     .23     .08     .11

ZCOR:   1.0000  1.0000  1.0000  1.0000  1.0000
KRAW:    .0014   .0014   .0014   .0014   .0014
PKBG:     3.23    4.58    4.08    3.24    3.09

Remember spectrometers 1, 3, 4, and 5 were detuned from the pyrite peak position to accomodate the range of sulfur oxidation states from pyrrhotite to anhydrite.

Anyway, none of the spectrometers gave us a concentration close to 900 PPM, but of course we analyzed sulfur on all 5 spectrometers so 99%+ of the matrix is missing (that's why the ZCOR is 1.0000 because the software thinks this is a pure sulfur sample, with a total of .353 weight percent!

So let's specify a nominal basaltic glass composition, so the matrix correction can perform its physics magic, and now we obtain the following results:

Un   24 ND70, Results in Elemental Weight Percents

SPEC:       Si      Al      Fe      Mg      Ca      Na       K      Ti       P      Mn       O       F
TYPE:     SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC    SPEC

AVER:   23.750   7.441   9.203   4.046   7.947   1.944    .158   1.109    .087    .170  43.964    .045
SDEV:     .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000    .000
 
ELEM:        S       S       S       S       S
BGDS:      LIN     LIN     LIN     LIN     LIN
TIME:   160.00  160.00  160.00  160.00  160.00
BEAM:    49.62   49.62   49.62   49.62   49.62

ELEM:        S       S       S       S       S   SUM 
XRAY:     (ka)    (ka)    (ka)    (ka)    (ka)
   492    .089    .090    .085    .095    .091 100.314
   493    .085    .093    .091    .087    .091 100.311
   494    .088    .093    .083    .084    .079 100.294
   495    .088    .089    .087    .077    .088 100.294
   496    .086    .091    .087    .085    .088 100.302
   497    .088    .089    .087    .079    .082 100.290
   498    .091    .086    .085    .080    .092 100.300
   499    .090    .094    .089    .085    .085 100.307
   500    .090    .086    .086    .082    .077 100.286
   501    .088    .087    .089    .091    .090 100.310

AVER:     .088    .090    .087    .084    .086 100.301
SDEV:     .002    .003    .002    .005    .005    .010
SERR:     .001    .001    .001    .002    .002
%RSD:     2.01    3.28    2.40    6.43    6.12
STDS:      730     730     730     730     730

STKF:    .5044   .5044   .5044   .5044   .5044
STCT:   152.32  451.70  499.97  127.50  166.44

UNKF:    .0007   .0007   .0007   .0007   .0007
UNCT:      .22     .65     .70     .17     .23
UNBG:      .10     .18     .23     .08     .11

ZCOR:   1.2340  1.2340  1.2340  1.2340  1.2340
KRAW:    .0014   .0014   .0014   .0014   .0014
PKBG:     3.23    4.58    4.08    3.24    3.09

Notice two things, first our ZCOR values for sulfur Ka are now 1.2340 (as opposed to 1.0000), and spectrometer 2, which was tuned to the pyrite peak position (spectrometer offset equals 0), now gives us 900 PPM *and* this is the highest concentration measured, so we might assume that this is the correct spectrometer position for this sample's oxidation state.

Does this mean that SIMS standard glass ND70 is quite reduced with a valence similar to pyrite?  I do not know (has anyone out there done EXAFS or XANES work on this glass standard?), but I will say these results are intriguing and maybe there is some value is setting up one's microprobe as a sulfur "multi-collector" using all 5 spectrometers.    8)
2
Discussion of General EPMA Issues / Re: Cameca .Tiff file outputs
« Last post by Probeman on June 15, 2019, 10:21:25 am »
Looking at consecutive BSE Tiff's of the same material, the grey levels are varying.  Is this a scaling thing in the software?

Hi Jon,
You're asking about the TIFF files from PeakSight?  I have no idea, but I do know that we have to set the BSE mode from "Differential" to "Ground", and then adjust the brightness until the image looks good, otherwise the BSE images show streaks when the BSE signal changes from pits and cracks.

Also on my system we have in the past seen gradients from left to right in the BSE brightness at lower magnifications:

https://probesoftware.com/smf/index.php?topic=583.msg3318#msg3318

This can be fixed by adjusting some electronics.
3
Discussion of General EPMA Issues / Re: Cameca .Tiff file outputs
« Last post by jon_wade on June 15, 2019, 08:27:09 am »
cheers John - I can see myself getting Hexedit out at some point  :P

Looking at consecutive BSE Tiff's of the same material, the grey levels are varying.  Is this a scaling thing in the software?

Honestly, I can promise you that should we have a windfall we'll definitely be investing PfEPMA, but cash, for a variety of reasons, appears short right now.

I'd be interested to know from others, but I get the distinct smell in the UK that geoscience demand for EPMA and analysis in general is declining.... :(

4
CalcImage / Re: First time running quant maps
« Last post by Anette von der Handt on June 14, 2019, 02:29:09 pm »
I throw another question into the mix: How is the sample polish? I notice that your Si abundances are quite variable and they should have the best counting statistics.

As a sidenote, while longer dwell times are of course preferable, especially for meaningful minor element abundances, I get decent maps with less scatter in the totals from even shorter dwell times than you used.

Otherwise, if polish was good I would also look at the pha pulse height depression issues. I ran some garnet maps last night (at 500 nA, yes garnets are indeed quite sturdy) and then accidentally analysed a few garnet points with the mapping conditions (using 10 different sample set-ups and sleep deprivation do not always mix well). So the totals of the spots all came out much lower and it was mostly Si and Al that were on the TAPL that were the problem. So either calibrate at higher currents too or make sure that the individual PHA settings are adequate for calibration and mapping.
5
Discussion of General EPMA Issues / Re: Cameca .Tiff file outputs
« Last post by John Donovan on June 14, 2019, 01:03:42 pm »
I know this isn't the place, and I know John's (very valid) answer, but that may have to wait until we win the lottery...

Listen up mate, you talking about our software?  "Win the lottery"?  You're at Oxford University, right?  I think you meant to say, "hold a bake sale".  Either that or lotteries in the UK are pretty disappointing!   ;)

Anyone have experience of exporting images from peak sight 6?  I have a *lot* collected in a mosaic, but each one is being exported with a different intensity, suggesting that, somewhere, they are being auto ranged.
All I really want is raw counts so I can stuff them into python and, if necessary, fix the ranging, but I cannot work out if they are ranged, and if so how, or even how to get the unadulterated raw data out of PS6. 
CSV data looks like 32 bit tiff which appear to be raw counts, but its really not clear how or what is going on in the software.

Anyone got any magic insights?  (granted, its a lot of data... but each .imDAT file is 3+Gb.  Nope, no idea what is in that 3 Gb.....pixies?  unicorns?  analysts tears? ;) )

Don't know anything about the ImDAT file format, but from my failing memory the .ImpDat image file format has a 1 (or 2) kilobyte header and then just long integers (X by Y).  It's a binary file but it would be easy to write some code to process these files if all you need are the intensity values.

And yes, we have asked Cameca repeatedly for the format of the .ImpDat header and they simply refuse to provide it, saying: just use the ASCII export file.  Unfortunately the ASCII export format leaves some things ambiguous, not to mention that they modify it on occasion. So the binary format would be much better to parse, especially if one wants the raw intensities. But maybe someone out there will specify information on the .ImpDat header format as part of their next Cameca microprobe purchase...?
6
Discussion of General EPMA Issues / Cameca .Tiff file outputs
« Last post by jon_wade on June 14, 2019, 10:22:40 am »
Dear collected wisdom

I know this isn't the place, and I know John's (very valid) answer, but that may have to wait until we win the lottery...

Anyone have experience of exporting images from peak sight 6?  I have a *lot* collected in a mosaic, but each one is being exported with a different intensity, suggesting that, somewhere, they are being auto ranged.
All I really want is raw counts so I can stuff them into python and, if necessary, fix the ranging, but I cannot work out if they are ranged, and if so how, or even how to get the unadulterated raw data out of PS6. 
CSV data looks like 32 bit tiff which appear to be raw counts, but its really not clear how or what is going on in the software.

Anyone got any magic insights?  (granted, its a lot of data... but each .imDAT file is 3+Gb.  Nope, no idea what is in that 3 Gb.....pixies?  unicorns?  analysts tears? ;) )

7
Probe for EPMA / Re: Tips and Tricks for PFE quant
« Last post by John Donovan on June 14, 2019, 09:19:05 am »
This is more of a tip than a trick, but I mention it because we recently improved the Report button output to better handle the presence of elements quantified using the EDS WDS integration feature in Probe for EPMA. The WDS and EDS integration in Probe for EPMA can utilize SDD EDS systems from Thermo (NSS and Pathfinder), Bruker (Esprit) and most recently JEOL (OEM) EDS detectors.

The Report button is located in the Analyze! window as seen here and can be applied to any unknown or standard sample in your run:



This feature can be utilized to export both a text description and a tab delimited spreadsheet format of the current analytical conditions and parameters. The text output consists of (almost!) English sentences as seen here that can be edited for including in your own reports and manuscripts:

Probe for EPMA Xtreme Edition for Electron Probe Micro Analysis
Database File: C:\UserData\Eastman\06-2019\Fe, V, C, O_06-03-2019.MDB
Database File Type: PROBE
DataFile Version Number: 12.6.2
Program Version Number: 12.6.3
Database File User Name: Chris Eastman
Database File Description: C and O by WDS, V, Fe, etc. by EDS

Database Created: 6/3/2019 11:01:40 AM
Last Updated: 6/3/2019 11:01:40 AM
Last Modified: 6/13/2019 1:12:23 PM
Current Date and Time: 6/13/2019 1:13:24 PM
Nominal Beam: 54.2881 (nA)
Faraday/Absorbed Averages: 1

Correction Method and Mass Absorption Coefficient File:
ZAF or Phi-Rho-Z Calculations
LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV

Current ZAF or Phi-Rho-Z Selection:
Armstrong/Love Scott (default)

Correction Selections:
Phi(pz) Absorption of Armstrong/Packwood-Brown 1981 MAS
Stopping Power of Philibert and Tixier
Backscatter Coefficient of Love-Scott
Backscatter of Love-Scott
Mean Ionization of Berger-Seltzer
Phi(pz) Equation of Love-Scott
Reed/JTA w/ M-Line Correction and JTA Intensity Mod.
Fluorescence by Beta Lines NOT Included

Un    2 Fe, V, C, O trav1
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 30.0  Beam Size =    0
(Magnification (analytical) =  40000),        Beam Mode = Analog  Spot
(Magnification (default) =     2245, Magnification (imaging) =   2857)
Image Shift (X,Y):                                         .00,    .00

Compositional analyses were acquired on an electron microprobe (Cameca SX100/SXFive (TCP/IP Socket)) equipped with 5 tunable wavelength dispersive spectrometers.

EDS spectra were acquired and processed using a Thermo NSS or PF EDS system.

Operating conditions were 40 degrees takeoff angle, and a beam energy of 15 keV.
The beam current was 30 nA, and the beam diameter was 0 microns.

Elements were acquired using analyzing crystals EDS for Fe ka, Nb la, V ka, PC1 for O ka, and PC2 for C ka.

The standards were Carbon (graphite) for C ka, Vanadium metal for V ka, Iron metal for Fe ka, Niobium metal for Nb la, and Al2O3 (elemental) (#13) for O ka.

Iron metal
From Johnson-Matthey, Vacuum remelted, Batch BM1664
Optical emission: Al < 1ppm, Ca < 1 ppm,
Cr 2 ppm, Co 20 ppm, Cu 3 ppm, Ni 3 ppm
Si 60 ppm, Sn 10 ppm, Ag < 1 ppm
Oxygen 310 ppm, Nitrogen 10 ppm

Vanadium metal
From Aesar, #143594, Lot #19778
99.95%, 1.0 mm wire

Carbon (graphite)
1. single crystal (synthetic) from Union Carbide
Grade 2YA, serial #8403, contains ~2.4% oxygen (from H2O?)


Al2O3 (elemental) (#13)
Specimen from Baikowski Int'l, North Carolina
'crackle' from seed crystal, 99.99%
Si ~330 PPM by EPMA (JJD), 05-30-2012

Niobium metal
Aesar, 99.99%, 0.25mm sheet
Lot #10258
Possible 0.19 wt% Ta (?)

The counting time was 30 seconds for C ka, O ka, and 45 seconds for Nb la, V ka, Fe ka.

The intensity data was corrected for Time Dependent Intensity (TDI) loss (or gain) using a self calibrated correction for C ka, O ka.

The off peak counting time was 10 seconds for C ka, O ka.

Off Peak correction method was Exponential for C ka, O ka.

Unknown and standard intensities were corrected for deadtime.

Interference corrections were applied to C for interference by Nb, and to O for interference by V, Nb,

See J.J. Donovan, D.A. Snyder and M.L. Rivers, An Improved Interference Correction for Trace Element Analysis in Microbeam Analysis, 2: 23-28, 1993

Results are the average of 10 points and detection limits ranged from .037 weight percent for C ka to .177 weight percent for O ka.

Analytical sensitivity (at the 99% confidence level) ranged from 2.222 percent relative for C ka to 10.142 percent relative for O ka.

The quantitative blank correction was utilized.
The exponential or polynomial background fit was utilized.

See John J. Donovan, Heather A. Lowers and Brian G. Rusk, Improved electron probe microanalysis of trace elements in quartz, American Mineralogist, 96, 274­282, 2011

The matrix correction method was ZAF or Phi-Rho-Z Calculations and the mass absorption coefficients dataset was LINEMU   Henke (LBL, 1985) < 10KeV / CITZMU > 10KeV.

The ZAF or Phi-Rho-Z algorithm utilized was Armstrong/Love Scott (default).

Note the integration of EDS and WDS elements including the ability to apply spectral interference corrections between elements by WDS and EDS.

And here is the tab delimited report format suitable for import to Excel as seen here:



Just FYI.  Available for download now.

Edit by John: In case anyone is wondering why we decided to run O and C by WDS and Fe, V and Nb by EDS, it's a long story, but basically the sample is so magnetic (and re-magnetizes in the instrument), that the Bragg defocus between the standards and unknowns was killing us. So we ran Fe, V and Nb by EDS to avoid the Bragg defocus issue, and ran O and C by WDS because the EDS just can't handle these elements at trace levels. Also because the WDS peaks for O and C are so broad that the Bragg defocus is much less of an issue. The remaining problem now is trying to figure out where the darn beam is/was. Tough problem.
8
CalcImage / Re: First time running quant maps
« Last post by Probeman on June 13, 2019, 09:43:34 pm »
Karsten makes a good point. 

To reduce deadtime and PHA shift issues maybe try standardizing and acquiring the x-ray maps at the same beam current, at least to begin with.  Say 50 or even 100 nA since garnets are pretty sturdy. And just for fun acquire a few point analyses on the garnet to check the standardization.

And also use at least a few hundred msec for the pixel dwell time. I bet you'll get much better quant x-ray maps if you do that.
9
CalcImage / Re: First time running quant maps
« Last post by Karsten Goemann on June 13, 2019, 04:01:03 pm »
Also, at 200nA, what sort of count rates have you got for the major elements? You'll probably have dead time correction issues (and maybe PHA pulse height depression issues) if the count rates are excessive.
10
CalcImage / Re: First time running quant maps
« Last post by John Donovan on June 13, 2019, 03:58:12 pm »
Hi Katherine,
This was a stage scan?  One can only do quant mapping using stage scans, unless the beam scanned area is less than 20 um or so.

It's difficult to tell from the info you posted, but what does the totals map look like? Can you export the map set to Surfer so we can see the color scale?

The main problem I see is that you are using *way* too short a pixel dwell time. Instead of 50 msec you should be using 500 msec, at least.  Try doing a 50 msec point analysis and you will see something like "garbage" also.  :)
john
Pages: [1] 2 3 ... 10