A colleague of ours recently contacted us with questions about the beam deflection feature in Probe for EPMA for quantitative analysis of very small features.

It occurs to me that I should probably explain better the differences in behavior between the beam deflection feature available from the Imaging button in the Acquire! window and the beam deflection feature available from the Automate! and Digitize! windows as described in the previous post in this topic.

1. Beam deflection from the Imaging button in the Acquire! window.

When the Imaging button is clicked in the Acquire! window, the Imaging and Stage Move or Beam Deflection window opens as seen here:

https://smf.probesoftware.com/index.php?topic=70.msg6833#msg6833

From this window one can acquire digital images and save them to the current run, but then one can also click the Beam Deflection or Stage Move buttons to select the beam deflection or stage move mode, and then click the image to move the beam or stage at the pixel clicked on.

When beam deflection is utilized, the beam will be deflected to that pixel and the beam position in the Acquire! window will also indicate the pixel position.  One can then acquire sample data manually from the Acquire! window using this beam deflection position.

When Stage Move is selected, the stage will move to the pixel clicked on, though the pixel to stage accuracy depends on the stage to beam scan calibration accuracy:

https://smf.probesoftware.com/index.php?topic=831.msg13077#msg13077

Of course, one must be careful to not attempt to deflect the beam by more than the Bragg defocus, which is usually around +/- 10 or 15 um from the beam center position.

2. Beam deflection from the Automate! window.

When the Digitize Positions button in the Automate! window is clicked, the Digitize Sample Positions window is opened, then when the Digitize Image button is clicked, the Digitize Sample Positions on Image window is opened.

https://smf.probesoftware.com/index.php?topic=70.msg13372#msg13372

This window is similar to the Imaging and Stage Move or Beam Deflection window opened from the Acquire! window, but is only utilized to digitize sample positions on an acquired image for subsequent point automation. That is, clicking on the image in the Digitize Sample Positions on Image does not actually move the stage or deflect the beam, it merely records the stage positions of the pixels clicked in the Automate! position sample list.

Then once the positions are recorded, these stage coordinates can be acquired using the automation procedures. The default in the Automate! window is to move the stage to each position to maintain Bragg defocus for WDS elements.  But if the Use Beam Deflection for Position checkbox is clicked, the automation will move the stage to the image center and then use beam deflection to perform the acquisition on that pixel.

The advantage of this automated beam deflection acquisition is that the beam will move to exactly the pixel clicked on, regardless of the accuracy of the stage to beam scan calibration. Therefore, very useful for fine scan features. Again, one must be careful to not attempt to deflect the beam by more than the Bragg defocus which is usually around +/- 10 or 15 um.

In the Acquire! beam deflection method it is highly recommended, and in the Automate! beam deflection method it is required to save the image to your current run, for documentation and/or automated beam deflection acquisition.

Quote from: KerstinGruender on October 15, 2025, 10:54:42 PM

Quote from: John Donovan on October 15, 2025, 04:55:32 PMFrom the Automate! window you can create the feldspar/olivine/whatever positions samples (based on a particular sample setup), and append new digitized points to them as you digitize points, and then run the position samples in any order you see fit

Any order you see fit, meaning I can set or change the order of acquisition? Don't think I've come across a how-to for that. Youtube also only goes as far as digitizing a series of unknown samples, unless I've missed it?

There are several videos on using the Automate! window, so be sure to watch these additional videos. Actually you should probably watch all of them! 

You can change the order of acquisition for unknown and wavescan samples using the spin button here:



Remember, to see a brief description of every control in Probe for EPMA, just hover the mouse over the control and the pop up help will show...

If you want to get fancy you can export the position samples to a POS text file, then edit them using a text editor such as NotePad, then import them back into the Automate! window.

Remember, to add points to an existing position sample, be sure to double-click the position sample in the Automate! list to see the currently digitized points for that position sample, then use the Digitize! window to add (or delete) more points to that position sample.

Quote from: John Donovan on October 15, 2025, 04:55:32 PMAll measurements are normalized to cps per nA so you can use different beam currents for different samples and even different beam currents for different elements within a sample

Ahhh, so that is where my thinking was going wrong! So it does work with just one calibration and I will only do the standards once. And also fine to realibrate in between. It will be a 'godmother of all samples', but I can see that working now. Thank you!

Yes, the crystal flipping is an issue I'm aware of. It's been working ok on our instrument for what we've used it. Only doing it for two particular routines, while avoiding flipping most of the time where possible.

Quote from: John Donovan on October 15, 2025, 04:55:32 PMFrom the Automate! window you can create the feldspar/olivine/whatever positions samples (based on a particular sample setup), and append new digitized points to them as you digitize points, and then run the position samples in any order you see fit

Any order you see fit, meaning I can set or change the order of acquisition? Don't think I've come across a how-to for that. Youtube also only goes as far as digitizing a series of unknown samples, unless I've missed it?

Another customer/colleague testimonial:

"Adelaide Microscopy has been utilising Probe for EPMA since the installation of our Cameca SXFive in 2013. Its easy and user friendly implementation of many advanced analytical features, of which our instrument manufacturers software does not contain, made it an attractive purchase and now impossible to go back.

The list of features in Probe for EPMA is extensive ranging from simple to complex applications, however even the more simple routine features such as the Mean Atomic Number (MAN) correction for major element analyses is invaluable, cutting analytical times almost in half for many analyses. The Time Dependant Intensity (TDI) corrections for volatile elements in minerals such as apatite, glasses, and hydrated minerals is extremely important and cannot be done without now.

In addition, it cannot be understated how valuable support is from Probe Software. In these times of fast paced research, analytical ideas and techniques can evolve rapidly. In many situations this can require fast feedback from instrument or software developers, and is typically not the type of response one gets from large companies and manufacturers, where inquiries and suggestions for software changes can go unheard or can take many months to implement.

Over the years there has not been a single time where Probe Software have not responded to inquiries rapidly, and in many cases fixed bugs and developed and implemented software features at the recommendation of its users. The involvement of the Probe for EPMA developers in the scientific community and their willingness to implement features in Probe for EPMA when appropriate is just as important as the software itself, and is another reason why Adelaide Microscopy would highly endorse its use to any probe laboratory."

Benjamin Wade
University of Adelaide

Quote from: KerstinGruender on October 15, 2025, 03:11:28 PMthank you, that's what I've done my setup for feldspar and pyroxene (all elements calibrated first and then break into separate setups). But what about the different currents across the different phases - the beam current has to be the same for calibration? So I can't calibrate all elements with one current and then split it off into something that would use a different current on unknowns? (e.g., glass at 8/10 using combined conditions, fsp/pyroxene at 12, olivine/spinel at 20nA). And all needing a calibration on the Cr2O3 standard.

Sure you can. 

All measurements are normalized to cps per nA so you can use different beam currents for different samples and even different beam currents for different elements within a sample, using the combined conditions option that Ben mentioned:

https://smf.probesoftware.com/index.php?topic=5.0

Quote from: KerstinGruender on October 15, 2025, 03:11:28 PMDo I do different calibrations, within different setups (e.g. glass calibration, save as setup), then apply that specific one to unknowns? Different calibration for px-fsp etc., save as setup and apply? How do I know it is using the correct standard calibration, and won't it be overwritten if there is just one entry in the 'standard' list of samples? If I add another standard it adds it as a second 'set' but the name itself is 'locked' to what's in the standard database?

No your previous standardizations won't be overwritten by subsequent standard acquisitions.

Unlike the Cameca and JEOL software, Probe for EPMA time tags each acquisition. Standard intensities are utilized based on the time of the unknown acquisition. This is how the standard intensity drift correction works (if a standard is acquired both before and after an unknown point (or pixel). And the standard intensity drift correction is automatically applied:

https://smf.probesoftware.com/index.php?topic=168.0

Quote from: KerstinGruender on October 15, 2025, 03:11:28 PMThis also doesn't solve the issue of not wanting to change the current/flipping crystals during analysis of unknown samples around all the time if they are listed in sequence (entered by user as they go), but then have assigned different sample setups (and conditions) for analysis. Can I specify somewhere to acquire 'all samples with the assigned setup A' first, all samples with assigned setup B second, and so on? There will be largely individual unknown sample entries, not one unknown sample with many lines, as needing to keep track of naming of points to track location/sample/etc, if that makes sense. I think it could work if I could individualize/edit the names of lines part of an unknown sample and have all the points as 'lines' within one sample. Then I could have some sort of sequence of unknown samples if all pyroxenes are contained in one unknown, all olivine in another, and so on.

Crystal flipping is an issue that you need to decide for yourself.  Sometimes it doesn't have much effect (e.g., trace elements), sometimes it can (major elements), depending on the reproducibility of the intensities during crystal flipping:

https://smf.probesoftware.com/index.php?topic=210.0

https://probesoftware.com/download/Presentation%20of%20John%20Donovan_China_EPMA_2023.mp4

From the Automate! window you can create the feldspar/olivine/whatever positions samples (based on a particular sample setup), and append new digitized points to them as you digitize points, and then run the position samples in any order you see fit:

https://www.youtube.com/watch?v=7qhu-QvdkcI&t=1s

Hi Ben & John,
thank you, that's what I've done my setup for feldspar and pyroxene (all elements calibrated first and then break into separate setups). But what about the different currents across the different phases - the beam current has to be the same for calibration? So I can't calibrate all elements with one current and then split it off into something that would use a different current on unknowns? (e.g., glass at 8/10 using combined conditions, fsp/pyroxene at 12, olivine/spinel at 20nA). And all needing a calibration on the Cr2O3 standard.
Do I do different calibrations, within different setups (e.g. glass calibration, save as setup), then apply that specific one to unknowns? Different calibration for px-fsp etc., save as setup and apply? How do I know it is using the correct standard calibration, and won't it be overwritten if there is just one entry in the 'standard' list of samples? If I add another standard it adds it as a second 'set' but the name itself is 'locked' to what's in the standard database?

This also doesn't solve the issue of not wanting to change the current/flipping crystals during analysis of unknown samples around all the time if they are listed in sequence (entered by user as they go), but then have assigned different sample setups (and conditions) for analysis. Can I specify somewhere to acquire 'all samples with the assigned setup A' first, all samples with assigned setup B second, and so on? There will be largely individual unknown sample entries, not one unknown sample with many lines, as needing to keep track of naming of points to track location/sample/etc, if that makes sense. I think it could work if I could individualize/edit the names of lines part of an unknown sample and have all the points as 'lines' within one sample. Then I could have some sort of sequence of unknown samples if all pyroxenes are contained in one unknown, all olivine in another, and so on.

Cheers,
Kerstin

Quote from: KerstinGruender on October 14, 2025, 03:23:22 PMIn regards to mosaic stitching, I have been able to stitch the grd files with Surfer following the instructions in your linked forum post, but this then only gave me options of false colour/relief image using the information in the grd files? Not stitching the actual bmp grayscale BSE images that were acquired and are inside the same mosaic folder. Have not worked out yet whether Surfer can do this or what else to use. I didn't do enough overlap to do it in ImageJ/Fiji, but that may work otherwise.

You can mosaic your GRD files in Surfer, and then export as BMP or JPEG or whatever. You might want to check out some of the Surfer webinars from Golden Software:

https://www.goldensoftware.com/support/webinars/

If you acquire PrbImg/TIF files in Probe Image, they can be mosaiced together using the Advanced | Concatenate menu:

https://smf.probesoftware.com/index.php?topic=132.msg542#msg542

I think Ben is correct. You can probably do everything you want to do using sample setups in a single MDB file, by creating a "mother of all samples" sample. Then tuning up all the elements, then breaking that sample into your mineral specific samples with the count times, calculation options, etc. that you want for each specific mineral. Then save those mineral specific sample setup from the Analyze! window using the Add To Sample Setups button. Then assign those sample setups to the positions in the Automate! window using the Sample Setups button.

This is explained starting on page 200 of the User's Reference Manual PDF available from the PFE Help menu (but who reads manuals these days!).



Either way, it is worth mentioning a few more helpful items, for example, what exactly is the difference between sample setups and file setups in the Acquire! and Automate! windows?

Samples setups contains any and all parameters that are specific to samples: elements, count times, background positions and/or types, interference assignments, calculation options, etc.  They can be saved and utilized as described by Ben and I above.

File setups are a specific sample setup from another MDB file. They contain everything that a sample setup contains, but they also load global parameters that are specific to that MDB file into the current MDB file.

For example, the options specified in the Special Options dialog in the Acquire! window for TDI (volatile) acquisitions. For example, one could have two different MDB files, one using TDI (volatile) acquisitions and another MDB not using TDI acquisitions. By switching between those two MDB files using the File Setups assignments from the Automate! window one can decide whether or not to utilize TDI acquisitions for each automated position sample.

Ok if I use line

np.frombuffer(i.items[0].signal.data.bytes, dtype=np.float32)
based on your code

I decode the bytes and I get the intensity column for the wds spectra in values rather than bytes and plot them! Success!

i.items[0] being the intensity values for the first spectrometer scan e.g. LPET on 1 on that sample,
i.items[1] the next crystal scan e.g. LTAP on 2, etc...

And xvalues determined as
xvalues = list(range(i.items[0].signal.wds_start_pos,i.items[0].signal.wds_start_pos+(1000*int(i.items[0].signal.step_size)),int(i.items[0].signal.step_size)))

Thanks for your reply

So I took your linked file, copied element into it, and changed
from .cameca_ks.cameca import Cameca, KaitaiStream
to
from cameca import Cameca, KaitaiStream
Renamed as cameca_read3

Then ran

import cameca_read3
>>> cameca_read3.WdsScanSignal(i.items[0].signal.data.bytes)


with result

Process ended with exit code 3221225725.
The key is how to decode the bytes...
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