Separate lines in a sample

[Heather Lowers]

Is there an option to separate lines in a sample into individual samples?  Naming convention could be SampleName_LineNumber-LineNumber.  On several occasions, users have set linear traverses across a grain, paint chip, etc. or added single points on a zoned mineral to a single sample.  After the fact, we have collected LA-ICP-MS or other data and we would like to specify concentrations for each individual line in a sample.  Or alternatively, for a number of lines in a traverse we'd like to break them out to apply different calculation options. 

Apologies if my search skills did not find a similar thread already discussed.

[John Donovan]

Is there an option to separate lines in a sample into individual samples?  Naming convention could be SampleName_LineNumber-LineNumber.  On several occasions, users have set linear traverses across a grain, paint chip, etc. or added single points on a zoned mineral to a single sample.  After the fact, we have collected LA-ICP-MS or other data and we would like to specify concentrations for each individual line in a sample.  Or alternatively, for a number of lines in a traverse we'd like to break them out to apply different calculation options. 

Apologies if my search skills did not find a similar thread already discussed.

Well, it's a cool idea but a bit of work to implement.

As you well know but I'll spell it out for others, the reason for specifying elements "missing" elements, that is those not analyzed by EPMA such as H2O, OH, etc., is to provide a more accurate matrix correction for those elements analyzed by EPMA.  And of course it provides a more accurate analytical total even if the matrix effects are negligible. This is the topic described here:

https://probesoftware.com/smf/index.php?topic=92.0

And it's sometimes surprising how much a few extra percent of water or oxygen can make in the other analyzed major elements. E.g, missing oxygen from ferric iron as described here:

https://probesoftware.com/smf/index.php?topic=92.msg8593#msg8593

But sometimes it's surprising how little of a difference it makes, for example instead of analyzing 16 or so REEs in monazite, if all one is interested in is a chem-age and one only needs U, Th, Pb (and Y for the interference correction), one can simply specify a CePO4 matrix and the matrix effects on the U, Th and Pb are close to negligible. As opposed to actually having to properly analyze all the other elements. See the first post in the "Specifying Unanalyzed Elements topic" and also this:

https://probesoftware.com/smf/index.php?topic=1029.0

The main reason that the U, Th and Pb concentrations don't change much due to the matrix effects is of course because if they are trace elements then matrix effects have little to no effect at small concentrations as described in this post here (that is, background corrections and interferences dominate the errors for trace elements, while standards, matrix effects and dead time corrections tends to dominate major element errors):

https://probesoftware.com/smf/index.php?topic=610.msg11752#msg11752

But getting back to your request, I mention all this because if the total amount of elements from your LA-ICPMS are less than a percent of so, they may make little to no difference in the concentrations of the other elements.  But that needs to be evaluated on a case by case basis.

So before we implement a new button as you suggest, perhaps you can respond a little about the concentrations you will be specifying from LA-ICPMS...

I assume that you would be wanting to utilize this feature you requested a long time ago:

https://probesoftware.com/smf/index.php?topic=92.msg11837#msg11837

[Heather Lowers]

I tried to use that feature I requested oh so long ago and as you know it applied the same specified values to each line in a sample, thus my current request

Apatite analyses from a carbonatite as an example. We analyzed Ca, Ba, Sr, Na, Ce, Mn, P, S, F, and Cl knowing that LA-ICP-MS would capture the remaining elements thought to be less than 1 wt.% total.  What we found was these oddball apatites appear to also have Si and Mg at appreciable amounts, up to 1 wt. % each. In the example below, I'd like to add Si and Mg to line 7616 based on the laser data but not to line 7617.  Two outputs with and without Si and Mg added. Hardly any effect on the element concentrations listed.  However, we'd also like to add all the other elements to analyses to help calculate OH from difference and it's embarrassing to publish a 94% total! 

Un   71 TOR-02 IND 024
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 10.0  Beam Size =   10
(Magnification (analytical) =    600),        Beam Mode = Analog  Spot
(Magnification (default) =      600, Magnification (imaging) =    270)
Aperture Number: 2
Image Shift (X,Y):                                         .00,    .00

Formula Based on Sum of Cations = .000   Oxygen Calc. by Stoichiometry
Number of Data Lines:   2             Number of 'Good' Data Lines:   2
First/Last Date-Time: 03/07/2023 05:45:11 PM to 03/07/2023 05:49:31 PM
WARNING- Using Time Dependent Intensity (TDI) Element Correction
WARNING- Forcing negative k-ratios to zero
WARNING- Forcing negative interference intensities to zero

Average Total Oxygen:       36.291     Average Total Weight%:   96.867
Average Calculated Oxygen:  36.291     Average Atomic Number:   14.815
Average Excess Oxygen:        .000     Average Atomic Weight:   24.351
Oxygen Equiv. from Halogen:  1.586  Halogen Corrected Oxygen:   36.291
Average ZAF Iteration:        4.00     Average Quant Iterate:     3.00

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Oxygen Equivalent from Halogens (F/Cl/Br/I) was Subtracted in the Matrix Correction

Un   71 TOR-02 IND 024, Results in Elemental Weight Percents
 
ELEM:       Ca      Ba       F      Na      Cl       S      Ce      Mn       P      Sr      Si      Mg       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    SPEC    CALC
BGDS:      LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN
TIME:    30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00     ---     ---     ---
BEAM:    10.03   10.03   10.03   10.03   10.03   10.03   10.03   10.03   10.03   10.03     ---     ---     ---

ELEM:       Ca      Ba       F      Na      Cl       S      Ce      Mn       P      Sr      Si      Mg       O   SUM 
  7616      34    n.d.     3.7    0.22     0.1    0.13     1.5    n.d.    16.8     2.4    .000    .000  34.845      94
  7617    38.7    n.d.     3.8    0.23    0.02    0.19     0.3    n.d.    18.1    0.62    .000    .000  37.738    99.7

AVER:     36.5    n.d.     3.8    0.23    0.03    0.16    0.91    n.d.    17.5     1.5    .000    .000  36.291    96.9
SDEV:    3.140    .059    .056    .007    .021    .039    .870    .010    .879   1.269    .000    .000   2.045   3.958
SERR:    2.220    .042    .040    .005    .015    .027    .615    .007    .622    .897    .000    .000   1.446
%RSD:    8.610 141.399   1.505   3.145  67.914  23.984  96.068 101.461   5.033  83.751    .000    .000   5.636
STDS:     7802    7803     419    7815    7820    7803     457    7845    7802    7879     ---     ---     ---


Un   71 TOR-02 IND 024
TakeOff = 40.0  KiloVolt = 15.0  Beam Current = 10.0  Beam Size =   10
(Magnification (analytical) =    600),        Beam Mode = Analog  Spot
(Magnification (default) =      600, Magnification (imaging) =    270)
Aperture Number: 2
Image Shift (X,Y):                                         .00,    .00

Formula Based on Sum of Cations = .000   Oxygen Calc. by Stoichiometry
Number of Data Lines:   2             Number of 'Good' Data Lines:   2
First/Last Date-Time: 03/07/2023 05:45:11 PM to 03/07/2023 05:49:31 PM
WARNING- Using Time Dependent Intensity (TDI) Element Correction
WARNING- Forcing negative k-ratios to zero
WARNING- Forcing negative interference intensities to zero

Average Total Oxygen:       38.041     Average Total Weight%:  100.331
Average Calculated Oxygen:  38.041     Average Atomic Number:   14.680
Average Excess Oxygen:        .000     Average Atomic Weight:   24.181
Oxygen Equiv. from Halogen:  1.576  Halogen Corrected Oxygen:   38.041
Average ZAF Iteration:        4.00     Average Quant Iterate:     3.00

Oxygen Calculated by Cation Stoichiometry and Included in the Matrix Correction
Oxygen Equivalent from Halogens (F/Cl/Br/I) was Subtracted in the Matrix Correction

Un   71 TOR-02 IND 024, Results in Elemental Weight Percents
 
ELEM:       Ca      Ba       F      Na      Cl       S      Ce      Mn       P      Sr      Si      Mg       O
TYPE:     ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    ANAL    SPEC    SPEC    CALC
BGDS:      LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN     LIN
TIME:    30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00   30.00     ---     ---     ---
BEAM:    10.03   10.03   10.03   10.03   10.03   10.03   10.03   10.03   10.03   10.03     ---     ---     ---

ELEM:       Ca      Ba       F      Na      Cl       S      Ce      Mn       P      Sr      Si      Mg       O   SUM 
  7616      34    n.d.     3.7    0.22     0.1    0.13     1.5    n.d.      17     2.4   1.075    .452  36.585      98
  7617    38.7    n.d.     3.8    0.23    0.02    0.19     0.3    n.d.    18.2    0.62   1.075    .452  39.496   103.1

AVER:     36.5    n.d.     3.7    0.23    0.03    0.16    0.91    n.d.    17.6     1.5   1.075    .452  38.041   100.3
SDEV:    3.140    .059    .055    .007    .021    .039    .870    .010    .889   1.271    .000    .000   2.059   3.977
SERR:    2.221    .042    .039    .005    .015    .027    .615    .007    .629    .899    .000    .000   1.456
%RSD:    8.597 141.399   1.476   3.176  67.904  24.002  96.079 101.451   5.046  83.746    .000    .000   5.411
STDS:     7802    7803     419    7815    7820    7803     457    7845    7802    7879     ---     ---     ---

[John Donovan]

I tried to use that feature I requested oh so long ago and as you know it applied the same specified values to each line in a sample, thus my current request

I totally understand. Just making sure we are on the same page.  Another approach that you can do right now, is to simply disable/enable selected lines and apply whatever specified concentrations you want as necessary.

I know that's a bit tedious, so to confirm, the feature you'd really like to have is to be able to extract selected lines within a single sample and create a new sample for them?  Then you'd of course apply the specified concentrations that are appropriate...  I'm only asking because you also mentioned an idea for splitting up a single sample into separate samples each with one data point (I assume so you could then use the specify concentrations from text input file feature), so just to be sure what it is that you'd prefer since those are very different things.

Also, when posting analytical results, please use the Tt button for text so the columns line up nicely when displaying analytical output.

[Heather Lowers]

I like the splitting up a single sample into separate samples each with one data point so I can then use the specify concentrations from text input file feature.  Please confirm, but then if I wanted to group some of these new individual samples into a new sample, I can use the existing features for that.  Total flexibility!

Thanks for pointing out the Tt button.  I wondering how your outputs lined up so well.

[John Donovan]

I like the splitting up a single sample into separate samples each with one data point so I can then use the specify concentrations from text input file feature.  Please confirm, but then if I wanted to group some of these new individual samples into a new sample, I can use the existing features for that.  Total flexibility!

Thanks for pointing out the Tt button.  I wondering how your outputs lined up so well.

OK, so here's the implementation that should do what you want by splitting up multiple point samples into single point samples. Let's start with a sample with 4 data points as seen here:



Next click the "Separate Samples into Lines" button as seen here:



Probe for EPMA will then separate each of the 4 points (data lines) into separate samples for you each with a single data point.  Let me know if this works for you and if there are any other changes you need.

[John Donovan]

Now that we have a function that can save arbitrary data points from a sample, we decided to go ahead and implement the other idea from Heather. That is, to allow the user to save selected lines from a sample to a new sample.

We start with a sample with multiple data points as shown here:



Next we selected the lines in the sample to save to a new sample (note that the selected lines must be contiguous, sorry!) and now we simply click the new button shown here:



And now we have a new sample with only the previously selected data points...



Note that the latest version of Probe for EPMA now prompts the user for the name of the new sample in case you want to modify the sample name. Of course one can always use the Name/Description button in the Analyze! window to do the same thing.

[Heather Lowers]

Thanks for implementing this.  Now I have the opposite problem   Is it possible to "Combine Data Lines From Selected Samples" and permanently write a new sample to the current probe database?  For example, a user has 1000 samples, some with multiple lines, collected from 8 sulfide separate grain mounts.  100 of the samples are chalcopyrite, 100 pyrite, 100 chalcocite, 100 bornite, etc. and scattered throughout the run.  It would be most useful to combine those 100 chalcopyrite samples into a single chalcopyrite sample.  This would allow one (me!) to change standards, adjust backgrounds, etc. for all chalcopyrite and not accidentally overlook one in the sample list. 

[John Donovan]

Thanks for implementing this.  Now I have the opposite problem   Is it possible to "Combine Data Lines From Selected Samples" and permanently write a new sample to the current probe database?  For example, a user has 1000 samples, some with multiple lines, collected from 8 sulfide separate grain mounts.  100 of the samples are chalcopyrite, 100 pyrite, 100 chalcocite, 100 bornite, etc. and scattered throughout the run.  It would be most useful to combine those 100 chalcopyrite samples into a single chalcopyrite sample.  This would allow one (me!) to change standards, adjust backgrounds, etc. for all chalcopyrite and not accidentally overlook one in the sample list.

I get it, it makes sense.

So we have pretty much run out of space to add more buttons in the Analyze! window, so we decided to modify the Combine the Selected Samples into a New Sample button behavior:



Previously this button only worked for samples each with different elements and/or conditions. For example, when combining samples with different elements, each acquired using different keV, nA or even with TDI curves.

Now the button will ask if you want to combine samples with different elements (must have the same number of data points) or do you want to combine samples with the same elements, but with different data points:



This latest version of PFE (v. 13.4.9) is a beta version of PFE which means you'll have to download it from one of our beta download sites. Please contact me by email for how to obtain this new version.  There's lots of new features in there, so give it a try!