Probe for EPMA Tips and Tricks

[John Donovan]

Here's something that some of you might not be aware of:

In the File Information dialog, one can "customize" three of the text field labels as shown here:



For instance the "Account #" label could be changed to "Customer PO" or whatever you want.

To customize these labels simply edit the Probewin.ini file for the following keywords in the [general] section using any text editor:

CustomLabel1="Department"        ; user defined user log label field
CustomLabel2="Account #"        ; user defined user log label field
CustomLabel3="Project"            ; user defined user log label field

[Scott B.]

Ever selected 173 samples in Analyze! and hit "Raw Data" or "Analyze" and PFE takes off doing its thing, but then you realize you messed something up and need it to stop? In my experience the "Cancel" button in the lower corner doesn't actually cancel in this situation, and one is left waiting for it to finish.

My "tip/trick" is that you can go up and click "Pause Between Samples", and when it finishes whatever sample it's currently working on, it will pause and the "Next" button will light up. At this point, the "Cancel" button will now stop PFE in its tracks.

[John Donovan]

Ever selected 173 samples in Analyze! and hit "Raw Data" or "Analyze" and PFE takes off doing its thing, but then you realize you messed something up and need it to stop? In my experience the "Cancel" button in the lower corner doesn't actually cancel in this situation, and one is left waiting for it to finish.

Note that the Cancel button in the Analyze! window *will* stop the data and/or analysis output, but one might have to click it a few times to "catch it" at a proper place in the processing so the cancel message gets recognized...

[John Donovan]

As Anette von der Handt demonstrated in her recent PictureSnap/PictureSnapApp Probe Software webinar video:

https://www.youtube.com/watch?v=Q6tzYdyOJmE&ab_channel=ProbeSoftwareInc

One can export stage positions from Probe for EPMA point analyses and import/display them in a PictureSnapApp project for locating your analyses on an image of your sample:



Anette later requested that we give some export options for the type of annotation label that is exported and we responded by adding these additional menu options when using the right click menu in the Analyze! window of Probe for EPMA:

[John Donovan]

Tips for re-processing JEOL or Cameca EPMA data on an off-line computer... that is, a computer that is not actually connected to your EPMA instrument.

As many of you know, all of our Probe Software applications support both JEOL and Cameca EPMA instruments. And we also allow users to download and install our Probe for EPMA/CalcImage software on their own computers (office, home, etc.), for re-processing of point analyses and quantitative x-ray maps off-line (not connected to the EPMA instrument):

https://www.probesoftware.com/resources/

However, as I'm sure you all are also aware, JEOL and Cameca EPMA instruments utilize different stage coordinates and more importantly, different stage orientations:

https://smf.probesoftware.com/index.php?topic=101.msg8444#msg8444

Basically the Cameca stage is Cartesian (max X/Y is upper right), while the JEOL stage is anti-Cartesian (max X/Y is lower left). It would have been too easy otherwise! 

Now most EPMA instruments around the world are of the JEOL variety, so when our Probe Software applications are downloaded and installed for the first time, the default instrument configuration is JEOL (we had to choose one of them!). This works just fine if you are re-processing data from a JEOL instrument, and to be clear one can also re-process Cameca data in a JEOL configuration, as long as one clicks "No" when Probe for EPMA first asks if you want to connect to the instrument when starting up.

But if you are re-processing data or maps from say, a Cameca instrument on a computer with a JEOL configuration, the caveat is that images and maps in Probe for EPMA or CalcImage will be flipped in both X and Y and of course the stage coordinates will be different (mm vs. microns). And the same is true when reprocessing JEOL data in a Cameca configuration (though I assume that this only happens for me!).

Note though, that in these "mixed" configuration situations, although the the images/maps are inverted in X/Y, all analysis points and other data are correctly displayed on the images and maps, so you are "OK to go"!

But if it concerns anyone that their images are flipped because they, for instance, opened a Probe for EPMA database acquired on a Cameca instrument, in a Probe for EPMA off-line computer installation (e.g., in your office or at home), that is in a JEOL configuration (because that's the default installation!), there is a quick and easy solution to change the image/map orientations to be as seen in the actual instrument.

The easiest thing to do is to simply open Probe for EPMA on your off-line computer, and when it asks if you want to interface to the instrument, click "Yes". This puts your off-line computer into EPMA "simulation mode". But, now you have a choice of EPMA simulation modes:



If you want to re-process data acquired on a JEOL EPMA instrument, just click the Use JEOL Simulation Mode menu, and it will convert the computer to default JEOL configuration (DO NOT DO THIS ON YOUR COMPUTER THAT IS ACTUALLY RUNNING YOUR EPMA INSTRUMENT, BECAUSE IT WILL OVERWRITE YOUR INSTRUMENT CONFIGURATION FILES!). Likewise, if you want to re-process data acquired on a Cameca EPMA instrument, click the Use Cameca Simulation Mode menu and it will convert your off-line computer to a default Cameca configuration. 

The software will then close, and you can re-start it and this time click "No" when asked if you want to interface to the instrument. Open your probe run database and your images and maps will also now be correctly oriented!

There's another trick that is even more useful and this allows one to simulate their exact instrument configuration on an off-line computer. This trick is especially useful for teaching, when you would like your students to learn to run the software without taking up valuable time on the actual instrument:

https://smf.probesoftware.com/index.php?topic=837.0

What you do is obtain a Probe for EPMA database, which you created on your ON-line computer connected to the instrument, and copy/transfer it to your OFF-line computer.

Then, open Probe for EPMA on your off-line computer, click "No" when asked whether you want to interface to the instrument, and then open the probe database from your on-line computer. Then click on this menu:



and select the Export All button as shown here:



This will then overwrite your off-line computer configuration, with the actual configuration from your EPMA instrument.  And it will detect that this is an off-line computer and put the off-line configuration into simulation mode if you click "Yes" when asked.

This way, you not only get into the same JEOL vs. Cameca configuration for off-line processing of data and maps, but you also get the exact actual instrument configuration for teaching EPMA in simulation mode (you click "Yes" when asked if you want to interface to the simulated instrument on the off-line computer(s).

To obtain the same standard compositions used on your ON-LINE computer (connected to the instrument), go to the C:\ProgramData]\Probe Software\Probe for EPMA folder and copy the STANDARD.MDB file. Then copy that file over to the OFF-LINE computer after installing Probe for EPMA on the OFF-LINE computer to the same folder.

Sorry for such a long post, but it can be a little confusing, so if anyone has any questions, I'm happy to answer them.

[Joe Boesenberg]

Hi John

A few questions for you about PfE.

First, for the standards database file, does it contain X,Y, and Z positional information that can quickly be accessed to drive the stage to the standard. I often just want to go to benitoite (as one example) to set up the beam and the optics, but I am not using that standard in the analytical routine. At present, you have to load or start a database file, load the standard, then go to another option, such as Automate, to double click and move to the standard position. Is there a shorter means of doing this? Seems like this should be easy, but I don't do programming......

Two, Scott B. did me the huge favor of importing my Cameca .mdb standard file into PfE. However, because of the way the .mdb file was created over the 22 years of the probe (the first ten years of which I wasn't at Brown yet), the standards I use the most are scattered throughout the 300+ standards listed. Is there a way of editting the database file so that the standards could be organized back to the different blocks they are mounted in (and they would appear organized rather than somewhat randomly numbered)?

Three, in looking around PfE I came across the Move window. It has periodic tables (much like Cameca and JEOL for selecting element lines, as well as doing peaking and PHAs). If I do any measurements through this window, do those run parameters (peaks, PHAs, etc.) get saved to the database I am working on? They appear to be independent of the database file based on a couple tests I did, but I may be ding something wrong.

Thanks.
Joe 

[John Donovan]

First, for the standards database file, does it contain X,Y, and Z positional information that can quickly be accessed to drive the stage to the standard. I often just want to go to benitoite (as one example) to set up the beam and the optics, but I am not using that standard in the analytical routine. At present, you have to load or start a database file, load the standard, then go to another option, such as Automate, to double click and move to the standard position. Is there a shorter means of doing this? Seems like this should be easy, but I don't do programming......

Great questions.

The standard composition database (Standard.mdb) does not contain any stage positions per se. This is because one might have the same standard in multiple standard mounts.

Your best bet is to make sure all your standard mounts are digitized as .POS files. These are position files (ASCII text) that can be imported in and exported out of the POSITION.MDB position database from the Automate! window. Here is a nice tutorial by Karsten Goemann on using .POS files in Probe for EPMA:

https://smf.probesoftware.com/index.php?topic=405.0

Be sure to inscribe fiducial marks on them to calibrate your digitized positions so if you remove them or replace them in the instrument you can easily re-calibrate them to correct for mount rotation.  See here for more details:

https://smf.probesoftware.com/index.php?topic=46.msg9615#msg9615

Also these video tutorials by Mike Matthews on digitizing standard positions:

https://www.youtube.com/watch?v=SOTncio2sVY&ab_channel=ProbeSoftwareInc

and on using the Automate! window to digitize of standard (and unknown and wavescan) points:

https://www.youtube.com/watch?v=7qhu-QvdkcI&t=186s&ab_channel=ProbeSoftwareInc

and on confirming standard (and unknown and wavescan) points:

https://www.youtube.com/watch?v=m4icM84Mkw8&t=28s&ab_channel=ProbeSoftwareInc

Note that one can also simply use the StageMap window to quickly drive to an approximate stage position:

https://smf.probesoftware.com/index.php?topic=417.0

Two, Scott B. did me the huge favor of importing my Cameca .mdb standard file into PfE. However, because of the way the .mdb file was created over the 22 years of the probe (the first ten years of which I wasn't at Brown yet), the standards I use the most are scattered throughout the 300+ standards listed. Is there a way of editting the database file so that the standards could be organized back to the different blocks they are mounted in (and they would appear organized rather than somewhat randomly numbered)?

Your best bet here (rather than re-number your standards) is to utilize the standard material type and standard mount name(s) feature in the Standard application. Here is an explanation of the standard material type field which can be accessed from the Standard application under the Standard | Modify menu:

https://smf.probesoftware.com/index.php?topic=40.msg10422#msg10422

One can also specify each of the standard mount name(s) in which that standard composition occurs. If more than one mount simply separate with a comma.  These names are simply a convention so decide on a name for each of your standard mounts and be consistent.



Once you've specified a material type for each standard and which standard mounts they are in, you can go into Probe for EPMA and from several places (Acquire! window, Standard menu, Digitize window), open the Add/Remove Standards window and select the standards materials you want to see and/or the standard mounts you want to see the standards listed for.

Three, in looking around PfE I came across the Move window. It has periodic tables (much like Cameca and JEOL for selecting element lines, as well as doing peaking and PHAs). If I do any measurements through this window, do those run parameters (peaks, PHAs, etc.) get saved to the database I am working on? They appear to be independent of the database file based on a couple tests I did, but I may be ding something wrong.

The Move window is a simple utility that doesn't actually save anything to your Probe for EPMA probe database, with one exception. Which is mainly what I use it for!

That is, if I want to add some more elements to a new or existing run I open the Move window, click the periodic table to specify the spectrometer, crystal, element and x-ray line, then clock the Go Spectros button to move to each of the spectrometers to the appropriate line positions.

Then I go into the Elements/Cations window from Acquire! and click the element buttons that have been saved from the Move window to add them to the current sample:



It's easy!

[Probeman]

Here's a useful feature for certain analytical or testing situations when running different wavescan samples. That is, the "Use Last Unknown as Wavescan Setup" checkbox in the Acquisition Options dialog from the Acquire! window:



First of all this option is set by default in the [software] section of your Probewin.ini file as shown here:

UseLastUnknownAsWavescanSetup=0        ; 0 = use last wavescan as default wavescan setup, 1 = use last unknown as default wavescan setup

Some notes on this option:
If there are no wavescan samples in the run, then when the first wavescan sample is created it will be based on the last unknown (or standard) sample elements. Unless you select a specific sample setup from the New Sample/Setup dialog. But once a wavescan sample exists, then the next new wavescan sample that is created will depend on what this setting in the Acquisition Options dialog is set to. 

But once you have a wavscan sample in the run, and you want to create a new wavscan sample, if this option is not checked, it will base the new wavescan on the previous wavescan, but if this option is checked, it will create a new wavescan sample based on the last unknown sample elements.

For example, let's say that you are working with more than one sample setup with different analytical elements (e.g, silicates, sulfides, oxides, etc.), and you wanted to check your off-peak backgrounds for each different sample setup once they were peaked up and had their PHAs adjusted. So after each each sample setup is peaked and PHA'd, you make sure the Use Last Unknown as Wavescan Setup is checked, and when you create a new wavescan, the new wavescan will be based on the last unknown setup, whatever it is.  Then create the next new sample setup, and peak and tune that up, then again create a new wavescan based on the last unknown.

But let's say you wanted to run a bunch of different wavscans, each with slightly different scan parameters, well then you'd probably want to uncheck the Use Last Unknown as Wavescan Setup option, so each new wavescan is based on the last wavescan sample setup.

Just FYI.

[John Donovan]

UseLastUnknownAsWavescanSetup=0        ; 0 = use last wavescan as default wavescan setup, 1 = use last unknown as default wavescan setup

Interestingly, what count time controls are enabled/disabled in the PFE Count Times dialog also depends on this flag. It's best to use the code to explain:

Code Select Expand

' Check for wavescan sample
If GetTimTmpSample(1).Type% = 3 Then
FormSETTIM.TextOnTime.Enabled = False
FormSETTIM.TextHiTime.Enabled = False
FormSETTIM.TextLoTime.Enabled = False
FormSETTIM.TextPeakTime.Enabled = False
FormSETTIM.TextUnknownMax.Enabled = False
FormSETTIM.TextUnknownFactor.Enabled = False
FormSETTIM.CommandStatistics.Enabled = False

' Check for standard
ElseIf GetTimTmpSample(1).Type% = 1 Then
FormSETTIM.TextWaveTime.Enabled = False
FormSETTIM.TextQuickTime.Enabled = False
FormSETTIM.TextUnknownMax.Enabled = False
FormSETTIM.TextUnknownFactor.Enabled = False

' Check for unknown
Else
If Not UseLastUnknownAsWavescanSetupFlag Then
FormSETTIM.TextWaveTime.Enabled = False
FormSETTIM.TextQuickTime.Enabled = False
End If
End If


[Probeman]

Here's a Windows feature that can be very helpful in situations where one needs to run several copies of an application at the same time.

For example, let's say you are running Probe for EPMA to acquire new data from your instrument, but you want to look at some data from a previous run. When you start another instance of Probe for EPMA the software will warn you that another copy of Probe for EPMA  is already running and therefore not offer to connect you to the instrument:



But you can continue and open the run in off-line re-processing mode and examine your previously acquired data. The problem is that if you start opening a bunch of windows in both copies of Probe for EPMA it can get confusing as to which window belongs to which instance.

Part of the reason for this is that all Probe Software applications will remember the current window position and/or size for the next time they are opened. Therefore, when a second instance of PFE is opened, the new windows will open on top of each other and although they can be moved to a different position, it can get a bit confusing.

The trick is to use the New Desktop feature in Windows 10 and 11:

https://support.microsoft.com/en-us/windows/configure-multiple-desktops-in-windows-36f52e38-5b4a-557b-2ff9-e1a60c976434

So, if you want to open additional copies of Probe for EPMA, simply click the overlapping rectangle icon next to the Windows search icon as seen here:



then click the blank new + New Desktop and you will get a clean blank copy of your current desktop. Then run Probe for EPMA (or any other application for that matter!), and open your previously acquired data!

Now I was worried that Probe for EPMA might not recognize that Probe for EPMA is already running and allow you to connect both copies to the instrument, but no, PFE recognizes the already running version in the new desktop just as if it were running in the original desktop:



If you want to add a third instance of Probe for EPMA (or any other application), simply click the + New Desktop icon again.

You know what would be a really cool use of this feature?  Where you want to reprocess multiple CalcImage projects at the same time, but don't want all the windows overlapping on each other:



I'd known about this feature previously, but hadn't taken advantage of it before. But now I will!

 

[John Donovan]

Previously one could only export image annotations by either using the Copy To Clipboard button in the Run | Image Analog Signal Images menu dialog, or using the Save Image To BMP and GRD Files menu from the Output menu:



But in the latest version of PFE we've added a Save To BMP (annotated) button to the Run | Display Analog Signal Images menu dialog:



Thanks to Panseok Yang for the suggestion! With this new button you can export individual annotated images as seen here:



But the Output | Save Images To BMP Files menu does save all images as raw (unannotated) BMP, annotated BMP and GRD files with the stage calibration data as ACQ files for import into PictureSnap or PictureSnapApp.

[Ben Buse]

Hi

I'm often asked about how to use auto increment, any tips or recommendations. I observe the following behavour:

A label 'unknown sample_1' becomes 'unknown sample__001', because it removes what ever after '_' and replaces it with '_001' etc.

whilst 'unknown sample' becomes 'unknown sample_001' so it's best to avoid using '_' in the naming.

To reset to 1? I found if counter is 1, you uncheck and re-check 'auto increment'

[John Donovan]

Gareth Seward asked for a new button in the PHA dialog that will update the PHA settings for all elements in a sample from the current PHA settings on the instrument:



The code will only update the element PHA parameters for an element, if the spectrometer number and Bragg crystal match.

Download/update the latest Probe for EPMA from your Help menu.

[John Donovan]

Someone recently asked: How can I edit the position sample description in the Automate! window before the samples are run?

Here's how:

[John Donovan]

Here's a tip for working with multiple sample setups and switching back and forth between them using the Add To Sample Setups button from the Analyze! window using, and then loading a saved sample setup from the New Sample/Setup button dialog in the Acquire! window.

In short, the Add To Sample Setups button in the Analyze! window merely creates a "pointer" to the selected samples (one or more) which can then be recalled to create new samples later on from the New Sample/Setup button from the Acquire! window.

Here is the Add To Sample Setups button in the Analyze! window:



Clicking this button will save the selected sample(s) to the sample setups list.

Then whenever you want to recall one of these samples to use, simply go to the New Sample/Setup button in the Acquire! window and click the Load Sample Setup button as seen here:



Then select the sample setup you want to load and click OK:



Optionally re-name the new sample and click OK, and that selected sample setup will now become the current sample for future acquisitions.

Note that one can also view/edit the list of sample setups from the Elements/Cations dialog in the Analyze! window as seen here: