Wish List for PFE Features

[Probeman]

Ah ok no problems, it keeps me ambidextrous anyway. I usually have one hand on the joystick the other on the mouse clicking single point at the same time. With regards to using the Digitize Image feature, I do also use that and use the PictureSnap window quite a lot to display and save point locations, but find that I have to go and review the points anyway as I seem to have quite an offset from what I think I am clicking on from the image and where it actually is on the sample. This is making sure there is no beam shift enabled as well. Is there some X/Y offset in an ini file somewhere I am missing?

Hi Ben,
Sounds like you need to perform a beam scan calibration.  See this topic here on the best method for this:

http://probesoftware.com/smf/index.php?topic=396.0

When calibrating a picture to the stage via 2/3 point calibrations in the PictureSnap window, it would be really good if you could digitally zoom in on the image you are calibrating to make sure the pixel/feature you are clicking on is correct. Mainly an issue when I have whole thin section scans (even at high res) I feel the need to zoom in on the picture to make sure I am clicking on what I think I am.

I understand.
john

[John Donovan]

1) The ability for alternating on/off data to be used to correct data as per TDI (long term wish)

Hi Ben,
I had a small idea.  Since this is essentially a simple percent change in intensity (as displayed in the display dialog), we can utilize those values in the Elements/Cations dialog as a Specified APF.

For example, say your alternating on/off peak intensity showed a 2.5% decrease in intensity in the display dialog. That means that we'd need to increase the measured intensity by 2.5% (times 0.5 relative to the integrated intensity), and we can do that by changing the Specified APF from 1.000 to 1.0125.

This manually entered percent change in intensity would of course be applied to all lines in the sample, so that is not ideal, but it might be better than nothing.  That's just for the moment.  When I get a chance I might implement this in PFE so it automatically computes the percent change for both the on and off-peak intensities and applies them "on the fly" for each line separately in the sample.

I think this would work, what do you think?
john

[John Donovan]

1) The ability for alternating on/off data to be used to correct data as per TDI (long term wish)

Hi Ben,
I think I have a nice solution for this request.

I figured out a way to utilize the existing TDI code for the alternating on/off intensity acquisition for correction of time dependent intensity changes as seen here (note the magnitude of the x axis):



You can assign these alternating on/off intensity corrections using the existing TDI corrections in the Standard Assignments dialog. This graph depicts a 3.1 % decrease in Cl ka intensity over the elapsed time.

Download the latest PFE update now to get this new capability.  It will even work with existing MDB files!
john

[BenjaminWade]

Hi John
Awesome! You are a legend. Just one problem, I can't seem to figure out where to turn it on? Do you mean go under the normal Standard Assignments window and assign "Use TDI Self Calibration.." even though its alternating peak? If so I get the error message "No Time Dependent Intensity (TDI) self-calibration or Alternating On/Off Peak acquisition data for sample row 37, datarow 1, channel 1"? This error comes up for all my samples.

I know I have acquired alternating though as I can plot it under the "Display TDI and Alternating Peak Data" window via the "Run" menu?

Cheers

[John Donovan]

Awesome! You are a legend. Just one problem, I can't seem to figure out where to turn it on? Do you mean go under the normal Standard Assignments window and assign "Use TDI Self Calibration.." even though its alternating peak? If so I get the error message "No Time Dependent Intensity (TDI) self-calibration or Alternating On/Off Peak acquisition data for sample row 37, datarow 1, channel 1"? This error comes up for all my samples.

I know I have acquired alternating though as I can plot it under the "Display TDI and Alternating Peak Data" window via the "Run" menu?

Interesting.

Can you email me the MDB file?
john

----

Edit by John: Ok, I see it's an alternating on/off acquisition, but it's also a multi-point bgd acquisition!

So when it's a multi-point bgd acquisition, the alternating on-off intensities are stored in a different table in the database!   So I'll have to add code to access that table in this situation.

[BenjaminWade]

Edit by John: Ok, I see it's an alternating on/off acquisition, but it's also a multi-point bgd acquisition!

So when it's a multi-point bgd acquisition, the alternating on-off intensities are stored in a different table in the database!   So I'll have to add code to access that table in this situation.

Ah sorry, yes its MPB, which you can't do with TDI hence the error.

[John Donovan]

Edit by John: Ok, I see it's an alternating on/off acquisition, but it's also a multi-point bgd acquisition!

So when it's a multi-point bgd acquisition, the alternating on-off intensities are stored in a different table in the database!   So I'll have to add code to access that table in this situation.

Ah sorry, yes its MPB, which you can't do with TDI hence the error.

Hi Ben,
That's not correct.  You can acquire TDI with multi-point bgds!  I just double checked and yes, one can do both TDI and MPB at the same time.   

But I will get the TDI correction working with MPB alternating on/off acquisitions anyway.  It won't be more than a few hours work and I agree that it could be useful.
john

[BenjaminWade]

Hi John
Ok, my mistake again. I would have swore I tried that in the past and it wouldn't let me. I must have been getting confused with something else.

Many thanks for implementing the on/off. We have a very small Cameca demonstration workshop here in a couple of weeks where Cameca want to show the system to some potential customers here in Aus. I am showing the Ti in quartz data amongst other talks (Karsten giving his shared backgrounds talk, one of the PhD students here showing her quant maps of Au/Pt nuggets using CalcImage). Might be slightly embarassing for Cameca that 3 out of the 4 people talking will be using Probe Software rather than PeakSight for data acquisition...

Cheers

[Dan MacDonald]

Good afternoon, John:

I have two items for a wishlist, and I'm probably not the first to suggest this.  After having trained with Gareth, I found myself wishing that the "Cancel" button at the bottom of the main window was a red colour, so that it would stand out more for beginners like me (or an "Abort run/process".

Also, do you have access to the JEOL triggers that would allow for an electronic autofocus of the electron beam for remote usage?  Perhaps a virtual autofocus button?  Thanks very much for your consideration.

Best regards

Dan MacDonald
Probe Tech
Dalhousie University

[John Donovan]

I have two items for a wishlist, and I'm probably not the first to suggest this.  After having trained with Gareth, I found myself wishing that the "Cancel" button at the bottom of the main window was a red colour, so that it would stand out more for beginners like me (or an "Abort run/process".

Sounds like you solved the problem as you now know where it is!   

Also, do you have access to the JEOL triggers that would allow for an electronic autofocus of the electron beam for remote usage?  Perhaps a virtual autofocus button?  Thanks very much for your consideration.

There's an autofocus button for the stage focus in the Move window, but I don't know of an JEOL auto-focus function for the electron beam.  This is an 8200, correct? 

On my Cameca I usually just look at the electron image on my Axis video server and adjust the electron focus in the Cameca software.  You mentioned getting an Axis video server up and running- did you do that?

I guess you can't remote into your UNIX box?  Is that the issue?
john

[John Donovan]

Awesome! You are a legend. Just one problem, I can't seem to figure out where to turn it on? Do you mean go under the normal Standard Assignments window and assign "Use TDI Self Calibration.." even though its alternating peak? If so I get the error message "No Time Dependent Intensity (TDI) self-calibration or Alternating On/Off Peak acquisition data for sample row 37, datarow 1, channel 1"? This error comes up for all my samples.

I know I have acquired alternating though as I can plot it under the "Display TDI and Alternating Peak Data" window via the "Run" menu?

Hi Ben,
OK, I got it all working.  Here is your last quartz sample:



Wow, I'd say you need a correction all right!   Note that the plot is pretty busy with all 45 data points, so if you use the Plot Nth Point TDI and select every 4th point you get this:



Go ahead and update PFE and all should be well.
john

[John Donovan]

Many thanks for implementing the on/off. We have a very small Cameca demonstration workshop here in a couple of weeks where Cameca want to show the system to some potential customers here in Aus. I am showing the Ti in quartz data amongst other talks (Karsten giving his shared backgrounds talk, one of the PhD students here showing her quant maps of Au/Pt nuggets using CalcImage). Might be slightly embarassing for Cameca that 3 out of the 4 people talking will be using Probe Software rather than PeakSight for data acquisition...

Sounds like a lot of fun.  I wish I could be there!

Hey, if you and/or any other attendees are willing to share your presentations as PPT or pdf files, please feel free to post them to the forum, maybe in the Events/Workshops topic here:

http://probesoftware.com/smf/index.php?topic=99.0

I know that I would be very interested in what was presented.
john

[BenjaminWade]

Hi John
Sweet! Many thanks for that implementation. As you mention, there is certainly a degradation over time, most noticeably at the start of the measurement. I will play around with the log-log fit and see how it affects the data.

Just one thing a bit weird happening, of which I assume I am not understanding the processing. I have attached a series of images to hopefully explain what I am seeing.

The first image (No TDI.jpeg) is the data for Un19 without aggregation and without TDI on. If I turn on the TDI fit for sp1 (TDI sp1.jpeg) the concentrations on sp1 go crazy and the other spectrometers are normal. Looking at the TDI graph the intensity change is nowhere near enough to add an order of magnitude concentration, even with the log-log fit.

If I turn the TDI on for all spectrometers (TDI all sp.jpeg) they all show crazy concentrations. I assumed it was some strange matrix affect so disabled quant for all but sp1 (TDI sp1 disable quant.jpeg) but sp1 still shows crazy high concentration.

BUT if I aggregate spectrometers with all quanted (TDI all sp aggregate.jpeg) I get normal concentrations with a sensible TDI correction from the uncorrected data. E.g. row 133 goes from 0.01594 to 0.01655 with the TDI turned on, an increase of ~6ppm.

I can use the aggregated data fine, but was wondering if there was any way to see TDI corrected data on the individual spectrometers without aggregation? Hopefully that makes sense.

With regards to the workshop, I will definitely speak to people to see if they are OK with putting the talks online here.

Cheers

EDIT
Ok I noticed that its only with the log-log fit that the numbers go crazy, linear and quadratic they are sensible. However it still doesnt explain why the numbers go normal when you aggregate. For example for Un19, row133, sp1, the y intercept goes from ~3.26 cps/nA with linear fit, to ~3.37 cps/nA with log-log fit. The concentrations though go from 0.0161wt%(linear) to 0.0990wt% (log-log) despite the cps/nA only changing by 0.11 cps/nA?

[John Donovan]

Just one thing a bit weird happening, of which I assume I am not understanding the processing. I have attached a series of images to hopefully explain what I am seeing.

Yes.  I need to look at this tomorrow.  The question being:  how should the TDI correction be treated when duplicate elements are aggregated? 

This might be worth a paper...  interested?
john

[John Donovan]

Ok I noticed that its only with the log-log fit that the numbers go crazy, linear and quadratic they are sensible. However it still doesnt explain why the numbers go normal when you aggregate. For example for Un19, row133, sp1, the y intercept goes from ~3.26 cps/nA with linear fit, to ~3.37 cps/nA with log-log fit. The concentrations though go from 0.0161wt%(linear) to 0.0990wt% (log-log) despite the cps/nA only changing by 0.11 cps/nA?

Hi Ben,
OK. I figured out what was going wrong with your TDI plots when the alternating on/off intensities were aggregated (or not). That is fixed.

The reason it was a problem was because I've been thinking about how to implement an idea that Julien Allaz wrote to me a few months ago, but I hadn't been able to think of an elegant way to do it- until today!   (give John a "pat on the back")

The idea Julien had over the summer was that just as we "aggregate" the on-peak and off-peak intensities for better precision/sensitivity, we could also do the same for our (self) TDI correction for beam sensitive samples (and now also for alternating on/of-peak intensities).  The problem was, I couldn't think of a clever way to code it, but today I did and here is an example...

Here is one of Ben Wade's quartz samples measuring for Ti on all 5 spectrometers and using alternating on/off intensities to track the sample damage over time.  As with normal TDI, this allows us to also correct quantitatively for this change in intensity over time. So here are the data points using normal (unaggregated) intensities and fit to a log-log method:

\

A very busy plot but note the scatter in some of the data. Now the same TDI data but this time plotted with the aggregate mode turned on so all TDI intensities from all 5 spectrometers are combined prior to the actual TDI correction:



Obviously the (log) intensities are higher because we increased the geometric efficiency of our instrument by a factor of (roughly) 5 (for a single element!). But also note that the data scatter is reduced due to this improvement in precision.