Hi,
I was hoping that someone can explain beam deflection mode during acquisition to me. I am imagining that I can take a BSE image at a relatively high mag, and then use beam deflection to analyze specific points within that field of view? Is this correct?
Is there a sequence of steps that will ensure this works correctly?
Thanks.
-Dan
Hi Dan,
Sorry no one was able to get back to you until now.
The answer is yes, absolutely. It's actually pretty sweet.
First, make a new position sample from the Digitize! window and click the Digitize Image button:
(https://smf.probesoftware.com/oldpics/i43.tinypic.com/296f2hu.jpg)
Then set the scan speed and acquire an analog signal (SE, BSE, etc) image of the area of interest and save it to the database (images are the only data that are not automatically saved to the PFE database!). Now using the mouse just click on the pixels you want to acquire data from. The software will automatically record the stage positions to the position database (see the Automate! window).
(https://smf.probesoftware.com/oldpics/i43.tinypic.com/2yke0zo.jpg)
Both random selected points and traverses can be digitized.
(https://smf.probesoftware.com/oldpics/i42.tinypic.com/1zez38i.jpg)
You can also digitize grids based on polygon areas as seen here:
(https://smf.probesoftware.com/oldpics/i43.tinypic.com/152gxsg.jpg)
Now, from the Automate! window simply select the position samples, and acquire using normal stage moves or, for high resolution features, one can instead select the Use Beam Deflection option in the Automate! window.
Attached is a screenshot of this digitizing technique used to acquire a traverse on minerals in Martian meteorite EETA00079. The acquired traverse points shown can be displayed right on the BSE image or not, along with analysis line labels, etc.
Thanks for the detailed reply John. Do I have to explicitly click the 'beam deflection' button, or will the software be smart enough to realize that it doesn't need to move the stage when I click on points at high magnification?
-Dan
Hi Dan,
No, the software can't read your mind (if that's what you mean!) ;)
You need to select the samples you want to run, then select the Use Beam Deflection For Position option and finally select which types of samples (stds, unks, wavs) you want to apply the beam deflection to.
(https://smf.probesoftware.com/oldpics/i44.tinypic.com/2805aip.jpg)
I should explain better!
There are two methods to using digital beam deflection in PFE for point acquisition.
1. Manual beam deflection. In this mode the user acquires an image in the Imaging window from the Acquire! window and then selects the Beam Deflection button as seen here and clicks a spot on the image to move the beam spot to that position as seen here:
(https://smf.probesoftware.com/oldpics/i59.tinypic.com/ek1102.jpg)
This method assumes that the stage position is in the center of the acquired image. When the point is manually acquired from the Acquire! window, the current beam deflection position is shown on the progress display as seen here:
(https://smf.probesoftware.com/oldpics/i57.tinypic.com/30suhwn.jpg)
Note that the stage position recorded for this analysis position is based on the beam calibration.
2. One may also run manually digitized points using automated beam deflection. In this method, the user generally utilizes the Digitize Image feature in the Digitize! window to specify analysis points using the mouse. The stage positions recorded are again, based on the beam scan calibration as seen in the post above:
http://smf.probesoftware.com/index.php?topic=70.msg263#msg263
When the position samples containing digitized positions are acquired, the program automatically moves the stage to the digitized stage positions, but if the user clicked the Use Beam Deflection For Position checkbox, then the program will instead move to the image center of each position sample and then utilize beam deflection for the point acquisitions as seen here:
(https://smf.probesoftware.com/oldpics/i57.tinypic.com/118q0lh.jpg)
Hi John,
I've been looking at using beam deflection to do quantified line scans across crystals 1um in size. Beam deflection is ideal because I want to position the line scan accurately. So I'm using digitize-digitize image-draw traverse on image-then from automate use beam deflection.
But there are two issues the stage does a backlash before starting the analysis which defeats the point of what I'm trying to do - can I stop this - I've suppress ROM based backlash but this is the spectrometers rather than the stage I guess.
Secondly would it be possible to disable Faraday cup measurement for this adds a large amount of time to the analysis. With it just measuring the cup at the beginning and end of the traverse.
Also because it sets the beam current before analysis - this also shifts the image.
I guess the easiest way would be to do it as a 1-d map in probe image and run it through ProbeImage. But you'd need to be able to do a 1-d beam map. Also surfer can't open 1-d grid files as it does contouring on them.
Thanks
Ben
Quote from: Ben Buse on August 03, 2016, 01:46:01 AM
I've been looking at using beam deflection to do quantified line scans across crystals 1um in size. Beam deflection is ideal because I want to position the line scan accurately. So I'm using digitize-digitize image-draw traverse on image-then from automate use beam deflection.
But there are two issues the stage does a backlash before starting the analysis which defeats the point of what I'm trying to do - can I stop this - I've suppress rom based backlash but this is the spectrometers rather than the stage I guess.
Hi Ben,
I have information on turning on/off the spectrometer backlash modes from JEOL, but nothing for the stage backlash, though with some experimentation it might be implemented. Would you be willing to run some tests for us? In the meantime the easiest thing might be to just turn off the automatic stage backlash using the JEOL PC software before your PFE run and then turn it back on again afterwards.
Quote from: Ben Buse on August 03, 2016, 01:46:01 AM
Secondly would it be possible to disable Faraday cup measurement for this adds a large amount of time to the analysis. With it just measuring the cup at the beginning and end of the traverse. Also because it sets the beam current before analysis - this also shifts the image.
You can turn off beam current measurements and skip setting column conditions from the Acquisition Options dialog from Acquire! There is no option for just measuring the beginning and end points for beam current.
(https://smf.probesoftware.com/gallery/1_03_08_16_8_39_54.png)
Quote from: Ben Buse on August 03, 2016, 01:46:01 AM
I guess the easiest way would be to do it as a 1-d map in probe image and run it through ProbeImage. But you'd need to be able to do a 1-d beam map. Also surfer can't open 1-d grid files as it does contouring on them.
I would do it as a 1-d scan in Probe Image for sure. I know Philippe Pinard did lots of very tiny carbide grains using Probe Image and CalcImage. There's no need to use Surfer, though it should be able to handle a 1-d array...
There another possibility which I've tested on the Cameca Sx100, but I'm not sure if anyone has tested on a JEOL instrument, and that is the new stage reproducibility command in Probe for EPMA in the Automate! window as described here:
http://smf.probesoftware.com/index.php?topic=653.0
If I were you I would first test it on a fluorescent material to check if it works as advertised. On the Cameca one cannot test it by tweaking the stage a little because of an oddity with the Cameca instrument- the system tracks the beam if the stage is moved manually! But it worked fine for normal stage reproducibility issues on the Cameca.
john
Hi John,
Thanks that looks very promising. I need to give it a try. I hadn't noticed you could turn of beam measurement. I'd prefer to do it through PFE rather than putting it into calcimage.
One thing though is if you use 'do not set conditions during acquisition'. How do you set up the beam beforehand. For in doing a beam deflection traverse it needs to move the beam. Maybe I need to try stage reproduciblitiy instead.
Thanks
Ben
Quote from: Ben Buse on August 04, 2016, 01:40:10 AM
One thing though is if you use 'do not set conditions during acquisition'. How do you set up the beam beforehand. For in doing a beam deflection traverse it needs to move the beam. Maybe I need to try stage reproduciblitiy instead.
It will deflect the beam in the appropriate mode, just not set the keV, beam current, beam size...
john
Hi John,
The other thing I realised is that it should not need jog turning off as the stage is not moved. Like when you run an acquisition from the Acquire! window. But I guess when using automate its always assuming the stage is moving. Would it be difficult and of interest to anyone else - if when beam deflection selected it checked if the stage was at the analysis coordinates before calling stage move?
Thanks
Ben
Quote from: Ben Buse on August 08, 2016, 03:20:02 AM
The other thing I realised is that it should not need jog turning off as the stage is not moved. Like when you run an acquisition from the Acquire! window. But I guess when using automate its always assuming the stage is moving. Would it be difficult and of interest to anyone else - if when beam deflection selected it checked if the stage was at the analysis coordinates before calling stage move?
Hi Ben,
Interestingly I used to check to see if the current stage position was already close to the target position when I supported a number of old instrument interfaces using direct control of stepper and servo motors. I never added such a test for the Cameca interface because the stage position is defined in integer microns and so if you move to a Cameca stage position, that is where you are, and so if you send a command to move to the same stage position, the instrument will simply ignore the command!
I realize that the JEOL is different because it returns fractional millimeters, but I guess I assumed there was something similar in the JEOL firmware (was there on the 8900/8200/8500?), that checked to see if the current stage position is "close enough". However, I can see that it might initiate a stage jog even if it is close enough to the actual target position.
I also guess that you can turn off the firmware stage jog from the JEOL software? Also since you mentioned acquisition from the Acquire! window, did you know that you can use the Imaging window in Probe for EPMA to manually deflect the beam position and acquire manual data from the Acquire! window on that deflected beam position? Try it on a fluorescent sample and see for yourself. Note that the deflected beam position is displayed in the Acquire window with a little circle and cross... this same beam deflection display is also utilized for automated beam deflection from the Automate! window.
Finally there is also a parameter in the MOTORS.DAT file called "backlash tolerance" which is used to decide if a software (not hardware) backlash is necessary based on the current and target position (and motion direction). So this parameter could also be utilized for deciding if a stage move is necessary at all...
The "MotBacklashTolerances" are defined in fractional units where 0.002 is 0.2%. For the software backlash feature the code compares the motion distance, to the backlash tolerance fraction of the total stage axis range, to avoid issues where the position is close to 0,0 (as can be the case for Cameca instruments!).
For example if "pos" is the stage position to move to, and "RealTimeMotorPositions" is the current stage position:
If Abs(pos! - RealTimeMotorPositions!(motor%)) < Abs(MotHiLimits!(motor%) - MotLoLimits!(motor%)) * MotBacklashTolerances!(motor%) Then So I could implement a check like this for a normal stage move, but we need to think about this carefully. Do we want this behavior for all stage moves, or just stage moves from the Automate! window? For example, someone might be depending on the current behavior to be sure that a stage jog is *always* performed before each acquisition, even if it's in the same position. Or we could only perform this stage move check if we are using beam deflection from the Automate! window...
What do you (and everyone else) think about this?
john
Hi John,
I just looked further into it
On the jeol its rounded to 4 decimal places e.g. 2.7085 mm and if you change it by 0.0001 it jogs (i.e. 100 nm).
By testing it in PFE using Move window - it seems to be all to do with rounding on the Y - which is expressed to 5 decimal places. So sometimes PFE and PI will jog it and sometimes it won't. Although to all purposes the stage is areadly in the correct position it is just the rounding which triggers jog. This is important for 10 um FOV beam map or beam line scan where the stage is already in the correct position.
I think therefore your suggestion of checking whether the stage is already in the correct possible before instructing the stage to move is a good idea
Thanks
Ben
Quote from: Ben Buse on September 15, 2016, 02:41:41 AM
I think therefore your suggestion of checking whether the stage is already in the correct possible before instructing the stage to move is a good idea
You think therefore I am! ;)
Seriously, it might be better to add some new keywords to the Probewin.ini file such as:
MoveStageToleranceX
MoveStageToleranceY
MoveStageToleranceZ
So what units should these above keywords be in? Fractional units? Microns? Nanometers?
Also please consider the following questions from my last post:
QuoteSo I could implement a check like this for a normal stage move, but we need to think about this carefully. Do we want this behavior for all stage moves, or just stage moves from the Automate! window? For example, someone might be depending on the current behavior to be sure that a stage jog is *always* performed before each acquisition, even if it's in the same position. Or we could only perform this stage move check if we are using beam deflection from the Automate! window...
And welcome back to school (I assume)!
john
Quote from: Ben Buse on September 15, 2016, 02:41:41 AM
I think therefore your suggestion of checking whether the stage is already in the correct possible before instructing the stage to move is a good idea
Hi Ben,
The latest version of PFE (11.6.4) has new keywords in the Probewin.ini that you can use to define if a stage move should be initiated or not. See the [hardware] section:
MoveStageToleranceX="0.1"
MoveStageToleranceY="0.1"
MoveStageToleranceZ="0.1"
The default is 0.1 um difference before a move is attempted. You can edit these to whatever you require for your automation purposes.
john
That's great, can't wait to give it a go!
Ben
Hi John,
It seems to work really well. I've tried it at 1 micron and I can do beam deflection without jog called.
Would it be possible to include this in probeimage?
Also I've tried doing a linescan again - not measuring beam current - but it still takes the cup in and out for each point, which for 100 points 1 second each adds a lot of time - anychance of disabling it? - I've just found 'blank beam after move and acquistion' - but unckecing this does not seem to do it
Thanks
Ben
Quote from: Ben Buse on September 19, 2016, 05:33:22 AM
It seems to work really well. I've tried it at 1 micron and I can do beam deflection without jog called.
Would it be possible to include this in probeimage?
Hi Ben,
Yes. I will speak to Brian.
Quote from: Ben Buse on September 19, 2016, 05:33:22 AM
Also I've tried doing a linescan again - not measuring beam current - but it still takes the cup in and out for each point, which for 100 points 1 second each adds a lot of time - anychance of disabling it? - I've just found 'blank beam after move and acquistion' - but unckecing this does not seem to do it
OK, so this is a question on PFE? I will check the behavior.
Note that the beam blank and read faraday are two separate operations.
john
Quote from: Ben Buse on September 19, 2016, 05:33:22 AM
Also I've tried doing a linescan again - not measuring beam current - but it still takes the cup in and out for each point, which for 100 points 1 second each adds a lot of time - anychance of disabling it? - I've just found 'blank beam after move and acquistion' - but unckecing this does not seem to do it
Hi Ben,
I found the place where it was inserting the faraday cup when it didn't need to. That is now fixed in the latest version.
Just make sure the "Do not set beam conditions" checkbox is checked.
john
Normally when you deflect the beam in the Acquire! | Imaging window, the beam stays deflected until you acquire another image or the Imaging window is closed.
The reason being that you can utilize the imaging window to select small phases using the acquired image for manual point acquisition in the Acquire! window even if the phase isn't visible in the optical monitor. Of course you want to be sure you aren't deflecting the beam more than 20 microns or so to avoid Bragg defocusing (unless of course you are only acquiring EDS spectra in Probe for EPMA). In this mode one can see the beam deflection spot in the Acquire! window acquisition displayed as a small yellow circle.
In addition, the actual stage position of the deflected beam is recorded in the acquisition parameters and can also be displayed in the acquired image (assuming you saved it to the PFE database).
Recently Julien Allaz asked if we could add a button to re-center the beam without closing the Imaging window and rather than add yet another button I added a beam re-center call to the toggle beam/stage button as seen here:
(https://smf.probesoftware.com/gallery/1_01_03_18_6_33_50.png)
Hopefully this will work for everyone. Available in PFE 12.2.0.
Version 12.2.0 contains optimized code for Beam Deflection acquisition both manually from the Acquire! window and automated from the Automate! window.
Beam deflection acquisition is useful for analyzing small phases that are not easily visible in the light optics display, where precise positioning of the beam spot is essential. But of course one needs to be careful to not deflect the beam outside the Bragg defocus limit which is usually about 20 - 30 um.
As a reminder, manual beam deflection acquisition is performed using the Acquire! window. Basically one acquires an image in the Imaging window, then using the mouse they click on the image. The beam is deflected to that pixel. Note that one can observe the beam position in the Acquire! window display as seen here:
(https://smf.probesoftware.com/gallery/1_05_03_18_8_01_12.png)
The stage coordinates of the deflected beam are displayed. Then one simply acquires manual acquisition points from the Acquire! window for the current beam deflected position, and the beam deflected stage coordinates are recorded. If you saved the image to your probe run database from the Imaging window, one can also display the beam deflected positions on the saved image just as one does for stage movement acquisition.
For automated beam deflection acquisition (say a very small step size traverse across a small inclusion), one uses the Digitize Image option from the Automate! window. First one creates a new std, unk or wavescan position sample using the Digitize (button) window, then one clicks the Digitize Image button and acquires an image of the appropriate sample area, and using the mouse, one clicks on the image to digitize selected beam spots.
For automated acquisition of these beam deflected positions, one then simply checks the Use Beam Deflection for Position checkbox in the Automate window, and the software will move the stage to the center of the position sample image and then deflect the beam as digitized. For subsequent position samples, the software will then again move the stage to the center of each position sample, and again deflect the beam based on the image extents of each digitized image position sample.
(https://smf.probesoftware.com/gallery/1_05_03_18_8_10_29.png)
We don't usually post about bug fixes, but this one is worth explaining a bit.
For those who don't know, Probe for EPMA has a beam deflection feature in which one can specify an amount of beam deflection from a centered beam position in order to perform fine scale (micron to sub micron) WDS and EDS point analyses. However, if one is acquiring WDS intensities one should limit the maximum beam deflection from the center to around 20 um or so, to avoid Bragg defocus effects.
But such beam deflection analyses can be very useful when attempting to acquire high spatial resolution data, where the stage movement to each point might be too coarse or unreproducible.
There are two ways such beam deflection acquisitions can be acquired: first using the Imaging window in the Acquire! window where one can acquire points by manually deflecting the beam on a newly acquired image, as seen here:
https://smf.probesoftware.com/index.php?topic=70.msg6833#msg6833
or one can use the Digitize Image option for digitizing points on an acquired image from the Automate! window as seen here:
(https://smf.probesoftware.com/gallery/1_10_04_25_2_03_17.png)
The basic steps are:
1. Create a new positions sample and open the Digitize Image window.
2. Acquire an image using BSE, SE or CL.
3. Save the image to your probe database.
4. Select the Single Point(s) (or Traverse or Grid Points) option.
5. Digitize the single points(s) (or traverse or grid) on the image by clicking the image with the mouse.
Then, to run the points using beam deflection, simply check the Use Beam Deflection checkbox option (and position sample types), to acquire the point data using beam deflection in an automated fashion as shown here:
https://smf.probesoftware.com/index.php?topic=70.msg6849#msg6849
For each position sample, Probe for EPMA will automatically drive to the center of the saved image for that position sample, then deflect the beam for each digitized positions, and then acquire the data.
Once the data is acquired you can see the beam deflection analysis positions by selecting the sample in the Run | Display, Export and Annotate Analog Signal Images menu dialog as seen here:
(https://smf.probesoftware.com/gallery/1_10_04_25_2_03_33.png)
To display the points for a specific sample, double-click the image list and select the specific sample.
Thanks to Ben Buse for spotting the issue (the software wasn't always recognizing the correct image magnification) and testing the fix. Update as usual from the Help | Update Probe for EPMA menu or downloading from our Resources web page here:
https://www.probesoftware.com/resources/
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.
While the beam deflection feature can be very useful for high precision point analyses of small features, if utilized for more than one stage location, it does rely on the reproducibility of the stage mechanicals.
But when the beam deflection feature is combined with the stage reproducibility feature as described here:
https://smf.probesoftware.com/index.php?topic=653.0
which relies on adjusting the image shift for the beam deflection, based on comparing the image recorded during the Digitize Image procedure with an image acquired after moving to the specified image center, one should be able to perform high precision and high accuracy point analyses on very small sample features, in multiple image areas.
Yeah, it's a complicated set of features, but it was tested back in the day, so it should work.