Wish List for PFE Features

[Ben Buse]

Hi,

I wondered if in "Analysis Calculation Options" the check box "use beam drift correction" could be changed to "use beam current drift correction" - in both probe for epma and calcimage.

I was running calcimage - and I wasn't sure whether it mean correct for spatial drift and had to click on the help button!

What do other people think?

Thanks

Ben

[John Donovan]

Hi,

I wondered if in "Analysis Calculation Options" the check box "use beam drift correction" could be changed to "use beam current drift correction" - in both probe for epma and calcimage.

I was running calcimage - and I wasn't sure whether it mean correct for spatial drift and had to click on the help button!

What do other people think?

Thanks

Ben

Hi Ben,
It's certainly easy enough to edit the checkbox caption.

The only beam (spatial) drift correction that PFE does is from the Automate! window during acquisition when using beam deflection acquisitions (for very high spatial resolution).  This is the Stage Reproducibility Correction feature.

I call it a Stage Reproducibility Correction, but because it's based on the beam scan image one digitized analysis positions on, it doesn't matter if it was the stage or beam that drifted.
john

[John Donovan]

Now that we have error bars for TDI and Multi-point, can we have them for the MAN fits too ? I always wonder if I am overly critical when fitting and excluding standards.

Thanks!

Hi Anette,
Finally got around to implementing errors bars for the MAN fit dialog in PFE (as usual please use the Help menu to update):



This plot is interesting because it shows that all the MAN standards have zero Na within variance, except for the K-411 glass (#162), which I've determined using off peaks is around a couple hundred PPM... so technically, it should be removed from the fit.

Sorry this feature took so long.  I've been busy!   

Hope M&M is going well.  Have you presented the TDI Scanning poster yet?
john

[Ben Buse]

Hi Anette,
Finally got around to implementing errors bars for the MAN fit dialog in PFE (as usual please use the Help menu to update):



This plot is interesting because it shows that all the MAN standards have zero Na within variance, except for the K-411 glass (#162), which I've determined using off peaks is around a couple hundred PPM... so technically, it should be removed from the fit.

Sorry this feature took so long.  I've been busy!   

Hope M&M is going well.  Have you presented the TDI Scanning poster yet?
john

Hi John,

The MAN errors are very nice.

At the moment these are count stats (approximately square root of counts) right? I wonder if it is better to use count stat error or the standard deviation. If people collect multiple points per standard for the MAN backgrounds then the standard deviation of the points is more representative - or maybe a choice?

Ben

[Probeman]

Hi John,

The MAN errors are very nice.

At the moment these are count stats (approximately square root of counts) right? I wonder if it is better to use count stat error or the standard deviation. If people collect multiple points per standard for the MAN backgrounds then the standard deviation of the points is more representative - or maybe a choice?

Ben

Hi Ben,
Yes, they are the square root of the raw intensities, so a 1 sigma variance.

Yes, the standard error would be more appropriate since these are usually the average of several points, but well, no one seems to utilize standard errors even when they should!

I once asked a statistics person why don't people use the standard error rather than the standard deviation for the variance of the average and he said: "I don't know, maybe because it's a more conservative number?"

I normally acquire at least 3 data points on each standard (including MAN standards), but others may not, so the variance is a safe bet to display.
john

[Ben Buse]

Hi John,

What would be nice when you have spare time! is on export wavescan to either

have options like export unknowns - so you can select which columns you want.

or a export option that just exports mm position (SPC) and intensity (cps/1nA)

Thanks

Ben

[John Donovan]

Hi Ben,
Try the Output | Save Wavescan Output | Save Wavescan Samples (Output based on spectro/element) menu.

This only outputs the spectro position and intensities.
john

[Paul Carpenter]

John,
My wish request is as follows, regarding management of the reflected light during automated runs:

Use the "Use Confirm During Acquisitions" flag to set reflected light on/off behavior during automated run. If this is checked, then turn on reflected light so user can check xyz position as run proceeds. If not checked, do not change reflected light on/off state; if light is off, leave it off.

The other request is to add a checkbox to have the reflected light turned off at the end of an automation run. This coupled with turning the filament down (Jeol 8x00, value of 90) would put the instrument in a standby state so that users do not have to somehow turn these two items down either by physically going to the lab or using VNC/Teamview etc. to connect remotely.

The motivation for this is that Jeol 8x00 systems use an Olympus microscope bulb which is no longer manufactured, they have become expensive and difficult to locate. LED substitutes are not available and the power supply is computer controlled on the Jeol.

Cheers,

Paul

[John Donovan]

John,
My wish request is as follows, regarding management of the reflected light during automated runs:

Use the "Use Confirm During Acquisitions" flag to set reflected light on/off behavior during automated run. If this is checked, then turn on reflected light so user can check xyz position as run proceeds. If not checked, do not change reflected light on/off state; if light is off, leave it off.

The other request is to add a checkbox to have the reflected light turned off at the end of an automation run. This coupled with turning the filament down (Jeol 8x00, value of 90) would put the instrument in a standby state so that users do not have to somehow turn these two items down either by physically going to the lab or using VNC/Teamview etc. to connect remotely.

The motivation for this is that Jeol 8x00 systems use an Olympus microscope bulb which is no longer manufactured, they have become expensive and difficult to locate. LED substitutes are not available and the power supply is computer controlled on the Jeol.

Cheers,

Paul

Hi Paul,
I think I've implemented your request the way you describe.

1. The light is not turned back on after an automated acquisition, if the Use Confirm During Acquisition checkbox is *not* checked in the Automate! window.

2. The light is turned off after the automation is completed if it is on.

Please download v. 11.9.9. and try it out.
john

[BenjaminWade]

Hi John
I have another wish, which I don't think would be simple or quick to integrate...

It would be great if we could have more control over the fit data through our MPB points. An example below is a F measurement on my albite standard, with my albite wavescan overlain behind. When all 4 points are included either side you can see that the Lo side isn't fit quite right to the measured MBP. There is a potential outlier on the Hi side, so when I exclude that (second attached image), the Lo side fits better but obviously the turning point of the quadratic is now drawn down so I am probably overestimating my F peak measurement.

Granted you could argue that all those points should probably be kept in anyway, but I still think it would be great if we could have more options (up to cubic polynomials, exponential functions?, changing coefficents, turning points etc) so we could further refine the MBP fits when you are dealing with low peak intensities.

I have attached a screenshot of some software we use to process laser ablation data to illustrate the type of thing I am talking about. Its showing an exponential function and the ability to change parameters manually to fit your data. It has other things that wouldn't really be of use in the screenshot, but I was more thinking of just some slider bars to change coefficients, dropdown to change fit types etc.

Anyway definitely a far future dream, but I think it would be a good addition...

Cheers

[Karsten Goemann]

I really like the feature with images of the standards popping up when digitizing. (That is, if they have been saved in the default position files folder with the standard number at the beginning of the file name.)

Makes it very easy to tell straightaway if I'm on the right standard or not.

Would it be possible to
(a) make it display the images in the correct aspect ratio by default? My images are all 4:3 and it always starts out with square window, although it can be resized manually.
(b) make it remember the window position, similar to the other PFE windows (and maybe size)?

Many thanks!

[John Donovan]

I really like the feature with images of the standards popping up when digitizing. (That is, if they have been saved in the default position files folder with the standard number at the beginning of the file name.)

Makes it very easy to tell straightaway if I'm on the right standard or not.

Would it be possible to
(a) make it display the images in the correct aspect ratio by default? My images are all 4:3 and it always starts out with square window, although it can be resized manually.
(b) make it remember the window position, similar to the other PFE windows (and maybe size)?

Many thanks!

Hi Karsten,
I had forgotten about this feature.  Though it turns out that it's not easy to have both options implemented as you describe above.  But now you can simply resize the standard image and PFE will remember the window position and size from then on.

You can update PFE when you are ready.

Thanks for the suggestion.
john

[Anette von der Handt]

Hi,

not so much a request for PFE but for Drift. Would it be possible to add detector baseline, gain and bias to the output variables?

[John Donovan]

Hi,

not so much a request for PFE but for Drift. Would it be possible to add detector baseline, gain and bias to the output variables?

Hi Anette,
I didn't add the PHA parameters to the Drift app to begin with, mostly because I think of them more as settings as opposed to measurements, but I can see how (user) changes in the gain or bias settings over time might be interesting.

So the latest version of Drift.exe has a new checkbox as seen here:



Ready to download.
john

[Karsten Goemann]

Excellent suggestion there with the PHA parameters in Drift.

Would it be possible to sort the standards in the interference standards drop-down menus in a similar way to the primary standards, i.e. by standard number, or alternatively alphabetically? We tend to have quite a few standards in the runs so it can take a while to find them in there at the moment.