In setting up a sample analysis that has combined conditions, I noticed something weird. I typed "new sample" (unknown) and then proceeded to set up a condition wherein oxygen was measured at 20nA and rare earth elements were measured on the same location at 100nA. To do this, I used the "combined condition" window in Acquire! The measurement would begin as I expected with oxygen at 20nA, but then when the column switched to 100nA, the filament saturation changed and the beam alignment changed. Why does this happen and what am I doing wrong?
Karen
Hi Karen,
Make sure that in the Combined Conditions dialog you have the Use Analytical Conditions options selected. Otherwise the program will try and load the specified column condition file for each condition. Does that help?
john
(https://smf.probesoftware.com/oldpics/i43.tinypic.com/2wps7xy.jpg)
and whilst in the 'Combined Conditions' window, don't forget to 'modify channel (element) order' so that like-conditions are grouped together on a given spectrometer (and temporally across the spectrometers - using 'Count Times' window). I always seem to forget this step, then wonder why my acquisition order has been changed.
Note, that when using 'Combined Conditions' the acquisition order cannot be changed in the usual 'Acquisition Options' window.
Gareth
Edit by John: actually yes, you can change the order on a per spectrometer basis in Acquisition Options dialog. What you can't do is force two elements with the same conditions to run at different times. So elements with similar conditions should be "grouped" together using the Combined Conditions "channel order" option. Otherwise the program will try and figure out the acquisition order on its own...
OK, here's a twist on the combined conditions.
Suppose I have a number of standards that I measure and that I don't use the same condition for each. Say I use condition 1 for some and condition 2 for the others. Suppose further that the temperature in my lab is extremely variable so I want to make sure that I use drift correction and use automation to re-measure the standards every 4 hours. Finally, I use condition 3 on my unknown.
I set everything up, measure my standards initially using conditions 1 and 2, then I program in 20 hours of measurements on my unknown using automation. How can I get my unknown spots to measure using condition 3, and my standards to measure every 4 hours for drift correction using condition 1 for some elements and condition 2 for other elements, and do all this with automation?
Karen
Quote from: wrigke on July 09, 2013, 07:11:59 AM
OK, here's a twist on the combined conditions.
Suppose I have a number of standards that I measure and that I don't use the same condition for each. Say I use condition 1 for some and condition 2 for the others. Suppose further that the temperature in my lab is extremely variable so I want to make sure that I use drift correction and use automation to re-measure the standards every 4 hours. Finally, I use condition 3 on my unknown.
I set everything up, measure my standards initially using conditions 1 and 2, then I program in 20 hours of measurements on my unknown using automation. How can I get my unknown spots to measure using condition 3, and my standards to measure every 4 hours for drift correction using condition 1 for some elements and condition 2 for other elements, and do all this with automation?
Hi Karen,
By "conditions" do you mean the operating conditions or the element setup or both?
So maybe I don't understand the question but it seems to me you can simply use the Sample Setups button in the Automate! window and assign a different sample setup to each standard or unknown position. The software will then automatically load that setup for each digitized standard and/or unknown.
Is that what you mean?
Hi Karen,
this is great. :) I can see that you are working in a similar lab as I do, facing the same troubles of temperature, different conditions, etc. In fact it is a quite special situation. And I have bugged John many times and tried to explain these special needs... Thanks for your patience, John! I am having the same temperature issues, and there is no easy solution to that, in my case they reduce the ventialtion at night by 50% that means the T goes up, and then down again in the morning. And it is impossible to convince "them" to leave the ventilation on... That's how it is.
To your question: I figured with the help of John, that those "sample setups" he mentioned above are the key to our problems. This will make it work. We can go through it in more detail when you come to Karlsruhe...
Cheers
Philipp
Hi All
I'm the new guy in town - as such I'm going to be asking pretty basic questions for a while.
Here's my first one:
I want to analyse a block of glasses followed by a block of pyroxenes all in the same "job".
I'll do all my glasses with a gentle beam current and a defocussed beam, then i want to switch conditions as the pyroxenes will take more current and a more focussed beam. I'll keep my element-spectro assignments the same for both batches but i'd like to push the count times up for the pyroxenes.
Can you walk me through setting up and running the analyses from the very beginning (i'm wary of missing an important check box somewhere). I intend to call back a "general purpose" silicate setup from previous work and then edit it. Its changing beam conditions and count times as i switch from glass to pyroxene that i'm unsure of.
Thanks
Richard
Hi Richard,
That is a great question and my answer will please you! ;D
What you want to do is create two "sample setups". This procedure is documented in the Advanced Topics manual accessible from the Help menu in PFE (but who reads manuals!).
The opening text is:
Sample Setups
Normally, PROBE FOR EPMA uses the sample setup from the last unknown (or standard if
there are no unknown samples) to create the next new sample setup. Sample setups on the other
hand are designed to allow the user to easily recall a previous sample setup within a current run.
This allows the user to create and re-use multiple setups comprised of different groups of
elements within a single run. In the example below, sample setups for pyroxene and olivine will
be created, each with a different set of elements and conditions, that may be recalled at anytime
during the current probe run.
The saving of a sample setup actually saves only a pointer to the sample selected. All of this
sample's acquisition and calculation options, elements/cations, standard assignments, etc will be
utilized when a new sample is created based on this sample setup.
A new PROBE FOR EPMA run is opened in the usual manner. Ten elements and appropriate
standards for pyroxenes are loaded from the SETUP.MDB database and the STANDARD.MDB
database, respectively. Each element is then calibrated and standardized. Count times,
acquisition and calculation options are adjusted to optimize the analyses and output
requirements.
(https://smf.probesoftware.com/oldpics/i42.tinypic.com/2i9rocp.jpg)
So basically there are three methods for recalling setups:
File Setups load the selected sample setup and all global flags from a previous probe run
Sample Setups load a sample setup from within the currently open run
Element Setups load a single element setup to the current sample
So you'll first load a file setup from another run, modify as necessary and then click the Save Setups button from the Analyze! window to "save" the selected sample as a Sample setup. This sample setup generally should not contain data so you can continue to modify it further if desired.
Then select the sample setup from the Acquire! New Sample button for manual acquisition or assign a selected sample setup to the position sample list in the Automate! window using the Sample Setups button.
Repeat as necessary for each additional sample setup you want to utilize.
There is also a thread that discusses this here:
http://smf.probesoftware.com/index.php?topic=110.msg404#msg404
Let me know if you have further questions.
I have an interesting one here which many people may have done in the past.
We are currently thinking about using the 1411 glass as a round-robin. I have a piece from before so decided to give it a test drive. My difficulty has always been with the analysis of boron. PfE has fortunately helped with the loss of sodium so there are no worries there. ;D
I was planning to do everything at 20kv but ran into problems with boron detection (as can be expected when you use calzaf). My question is can I combine 5kv boron with 20kv for the rest? And, with the combined conditions it would seem that it does each sample as 5kv then 20kv so if I do the standards at the same time it will be yo-yoing from 5 to 20kv, not good for the FEG! Or am I missing something subtle in the setup? Can I even do this type of analysis or should I just do lower KeV for everything? :-[
Glass 1411
Na2O 10.14
SiO2 58.04
Al2O3 5.68
K2O 2.97
CaO 2.18
TiO2 0.02
Fe2O3 0.05
MgO 0.33
B2O3 10.94
BaO 5
ZnO 3.85
SrO 0.09
Hi Gareth,
what about programming your points, then doing first everything at 20 kV and then the rest at 5 kV, or vice versa as you prefer? And then combine everything into one analysis? We used to do that in our lab quite often, first, analyze the 25 kV elements, then the 20 kV elements, and then the 15 kV ones. Works great. And PfE lets you combine afterwards all your elements into one analysis line.
Cheers
Ph
Quote from: Gareth D Hatton on March 25, 2014, 09:30:39 AM
I was planning to do everything at 20kv but ran into problems with boron detection (as can be expected when you use calzaf). My question is can I combine 5kv boron with 20kv for the rest? And, with the combined conditions it would seem that it does each sample as 5kv then 20kv so if I do the standards at the same time it will be yo-yoing from 5 to 20kv, not good for the FEG! Or am I missing something subtle in the setup? Can I even do this type of analysis or should I just do lower KeV for everything? :-[
You can do as Phillipe suggests above (combine the samples post acquisition), *or* you can simply use the combined conditions feature and assign each element the appropriate voltage for acquisition in a single sample. Just remember to run your standards the same way...
John, I noticed something with the combined conditions: When I choose the combined conditions for different elements, and I set a value for nA and a column string, it would only save the column string. I need to open the element a second time, set the nA, and then it will remember. Is that right like this?
Cheers
Philipp
Quote from: Philipp Poeml on July 03, 2014, 10:08:13 AM
John, I noticed something with the combined conditions: When I choose the combined conditions for different elements, and I set a value for nA and a column string, it would only save the column string. I need to open the element a second time, set the nA, and then it will remember. Is that right like this?
Yes. Because if you are using column setups the current will be set from the column setup, not from the analytical conditions.
I suppose you are entering the beam current for documentation purposes? That is a good idea. I modified the regular analytical conditions dialog to remember the analytical conditions for a given column setup and try to anticipate the user, but I didn't implement that yet under combined conditions.
john
Well... There is a little box in that window that says: "If you are using column string, don't forget to set the according value in the analytical conditions" or similar. I can send a screen shot tomorrow, probe is running right now. So I thought this was necessary to do.
Quote from: Philipp Poeml on July 03, 2014, 10:19:09 AM
Well... There is a little box in that window that says: "If you are using column string, don't forget to set the according value in the analytical conditions" or similar. I can send a screen shot tomorrow, probe is running right now. So I thought this was necessary to do.
Not necessary, but nice for documentation as I said. Note that for keV, this field entry is absolutely necessary when using column conditions (*.PCC files), since the beam energy value gets used in the quant routines.
john
Ok, I understand. Then still, even for the kV, the nA for documentation or necessary: If I open the dialog, and I set a column string AND nA, why wouldn't it remember the two? It is much more convenient that in remembers what you change.
Would it be possible to change this behaviour?
Quote from: Philipp Poeml on July 03, 2014, 12:32:28 PM
Ok, I understand. Then still, even for the kV, the nA for documentation or necessary: If I open the dialog, and I set a column string AND nA, why wouldn't it remember the two? It is much more convenient that in remembers what you change.
Would it be possible to change this behaviour?
I think so, let me look at it.
john
Hi Philipp,
I may not be understanding you properly, but it appears that the software does exactly want you want it to do...
That is, when you click the Apply Conditions To Selected Elements, it saves all conditions and the column condition file as you suggest...
(https://smf.probesoftware.com/oldpics/i61.tinypic.com/153wnte.jpg)
Maybe you forgot to click this button?
Strange. I swear, I programmed today 48 lines and it did not work. What I did: I opened the dialogue, I changed the beam current to 250, then I clicked "browse", I selected my file, I pressed "apply" and it applied the file, but not the nA. I will try again tomorrow. Did you try without setting kV? Otherwise the dialogue looks exactly like mine.
Another question: Is the image shift saved in the pcc file? Or do I have to set it in the same dialogue, or both?
And the red text warns about "beam current" as well, that's why I tried to set it.
Thanks for looking into this!
Quote from: Philipp Poeml on July 03, 2014, 01:27:21 PM
Strange. I swear, I programmed today 48 lines and it did not work. What I did: I opened the dialogue, I changed the beam current to 250, then I clicked "browse", I selected my file, I pressed "apply" and it applied the file, but not the nA. I will try again tomorrow. Did you try without setting kV? Otherwise the dialogue looks exactly like mine.
Another question: Is the image shift saved in the pcc file? Or do I have to set it in the same dialogue, or both?
And the red text warns about "beam current" as well, that's why I tried to set it.
Ok, I see the confusion. Yes, just selecting the column condition file does not load the beam current automatically. You have to enter the keV, beam current, beam size yourself manually, but, it will save everything you specified.
The confusion was caused by me mentioning that I have some code which *tries* to load these analytical parameters from the column condition file, but it was originally designed to handle a situation (Cameca SX50), where the column condition file is in the instrument memory and can't be read and parsed easily. It gets more complicated, but that is the general issue.
Yes, image shift is saved to the column condition files, that is one of the main uses for this feature. I also think you can specify different image shifts for different keVs in the Automate! Conditions button for use with the Digitized Conditions automation basis.
Hi John, I think I did not express myself correctly. I should be more clear in what I am saying. Sorry. I try again:
What I did: I opened the dialogue, I typed in the beam current 250 into the Beam Current field , then I clicked "browse", I selected my file, I pressed "apply" and it remembered the file , but the beam current was given in the channel list as 20 nA. I opened the channel again, and the beam current in the field was written 20 nA, so not remembered. I typed in 250 into the Beam Current Field, selected "apply" and now I saw in the channel list (and also when reopening the channel) that it had saved 250. So I had to edit the channel twice to get both settings saved. Does that make more sense?
Do I understand correctly: On the right is a dialogue about "Select beam mode and..." where I can set the image shift. In your example this is set to 0 and 0. Is this overridden then by loading the column string?
Is it correct that the SX50 is not supported any more by the V10 of PfE? Maybe then it would be better to change the wording "column string" into "column conditions file" or something? Or is it still valid for the Jeol?
Quote from: Philipp Poeml on July 03, 2014, 02:00:12 PM
Hi John, I think I did not express myself correctly. I should be more clear in what I am saying. Sorry. I try again:
What I did: I opened the dialogue, I typed in the beam current 250 into the Beam Current field , then I clicked "browse", I selected my file, I pressed "apply" and it remembered the file , but the beam current was given in the channel list as 20 nA. I opened the channel again, and the beam current in the field was written 20 nA, so not remembered. I typed in 250 into the Beam Current Field, selected "apply" and now I saw in the channel list (and also when reopening the channel) that it had saved 250. So I had to edit the channel twice to get both settings saved. Does that make more sense?
Do I understand correctly: On the right is a dialogue about "Select beam mode and..." where I can set the image shift. In your example this is set to 0 and 0. Is this overridden then by loading the column string?
Is it correct that the SX50 is not supported any more by the V10 of PfE? Maybe then it would be better to change the wording "column string" into "column conditions file" or something? Or is it still valid for the Jeol?
I would click the column condition file first, then edit the analytical condition fields if necessary. Then click Apply.... why? Because the browse/selection of the column condition file might update the analytical condition fields, if they have been specified before and therefore they might need to be updated manually. Remember, in combined conditions mode each element can have a separate set of conditions.
Yes, the image shifts are overwritten by the column condition file and are there for "documentation" purposes just like the beam current, etc. when running in column condition mode.
Yes, the SX50 is no longer supported in v 10 of the software, and yes, I will be moving more in that direction to clean up remnants from older instruments ASAP.
Ok, so, it works, if I choose the file first, and then type the 250 nA.
When I type 250 nA first, then choose a file, it sets the field back to 20 nA.
So the order of doing things matter.
Thanks for looking into this!
Hi,
I think what would be useful for combined conditions - is within the combined conditions to have a button to read and apply column conditions.
When you finish an analysis - say it does 20nA and then 100nA. It is an 100nA an the end, you want to use the SEM to find the next point - it be good to be apply to go into combined conditions and apply 20nA (i.e. the first condition) back onto the column.
What do you think?
Thanks
Ben
Quote from: Ben Buse on October 11, 2016, 09:49:39 AM
I think what would be useful for combined conditions - is within the combined conditions to have a button to read and apply column conditions.
When you finish an analysis - say it does 20nA and then 100nA. It is an 100nA an the end, you want to use the SEM to find the next point - it be good to be apply to go into combined conditions and apply 20nA (i.e. the first condition) back onto the column.
What do you think?
Isn't PFE re-setting the first condition again after it finishes the combined condition acquisition? It should, unless you have something turned off in Acquisition Options...
Right so I guess its because I had "return to on peaks after acquisition" unchecked (oops!)
On a related note - I'm not sure its necessary - But is it possible to 'use column condition string' to have a different focus for the two beam conditions - ensuring both are in focus & also to shift beam to correct for 1-2um shift from 20 to 100 nA?
Thanks again
Ben
Quote from: Ben Buse on October 11, 2016, 04:18:15 PM
Right so I guess its because I had "return to on peaks after acquisition" unchecked (oops!)
Hi Ben,
Don't worry about it. I had to think about myself.
Quote from: Ben Buse on October 11, 2016, 04:18:15 PM
On a related note - I'm not sure its necessary - But is it possible to 'use column condition string' to have a different focus for the two beam conditions - ensuring both are in focus & also to shift beam to correct for 1-2um shift from 20 to 100 nA?
So, this is the issue. JEOL (in their infinite wisdom) has forced me to go through their EIKS interface for the 8230/8530 column control rather than direct calls to the instrument. This means that I am limited to what they expose in their EIKS interface. Currently these are the column parameters that JEOL needs to add to their EIKS interface:
ObjectiveLens
AstigmationX
AstigmationY
ScanRotation
For beam focus this is the objective lens setting.
So we (as a community- and I'm thinking specially of those buying a new instrument where one has some leverage), either have to get JEOL to add these functions to the EIKS interface or we need figure out how to make a direct call to the instrument as we have with a number of other parameters.
However, I do have many other column parameters including getting and setting the image shift. So if you run at very high magnification in scan mode and utilize the image shift parameters that are contained in the probe column condition files (.PCC), yes, you can adjust the beam position for different keVs or beam currents.
john
Hi John,
That's very interesting.
So I guess we currently have limited control on focusing by changing the beam size i.e. if at 10nA its 1um beam size, it might be possible to recover some of the defocusing at 100nA by setting the beam size to 0um.
Regarding PCC files how would I go about creating them - can I get them from the Jeol software, or are there examples of what they should look like - I guessing there text files essentially.
Thanks
Ben
Quote from: Ben Buse on October 12, 2016, 02:50:30 AM
So I guess we currently have limited control on focusing by changing the beam size i.e. if at 10nA its 1um beam size, it might be possible to recover some of the defocusing at 100nA by setting the beam size to 0um.
Hi Ben,
If the beam size control on the JEOL is anything like the Cameca, it's just an offset from the last time the beam was manually focused, so not sure if that will help.
Quote from: Ben Buse on October 12, 2016, 02:50:30 AM
Regarding PCC files how would I go about creating them - can I get them from the Jeol software, or are there examples of what they should look like - I guessing there text files essentially.
They can be saved and loaded from the Window menu in PFE. And they can be selected from the Analytical Conditions button in Acquire! or the Conditions button in Automate!
john
Quote from: Ben Buse on October 12, 2016, 02:50:30 AM
Regarding PCC files how would I go about creating them - can I get them from the Jeol software, or are there examples of what they should look like - I guessing there text files essentially.
Hi Ben,
Just FYI, now that we have the firmware call to set the beam current on the 8230/8530, I will add that call to the PCC load condition code.
Right now the code saves/loads the condenser lens values, but I don't think that will turn on the beam current regulation. Adding the firmware call for set beam current should fix that.
john
Hi John,
Thanks - I will have a play with it when I get a chance - see what it can do. What I've done in the past when I require high spatial accuracy is run the two conditions separately and then combine them in the Analyze! window. - which also works well, but for most things combined conditions is very handy!
Quote from: John Donovan on October 12, 2016, 09:23:13 AM
Hi Ben,
If the beam size control on the JEOL is anything like the Cameca, it's just an offset from the last time the beam was manually focused, so not sure if that will help.
Yes that's right which means you can "focus" it in one direction only - which makes it limiting!
Thanks
Ben
Quote from: Ben Buse on October 13, 2016, 11:19:30 AM
Thanks - I will have a play with it when I get a chance - see what it can do. What I've done in the past when I require high spatial accuracy is run the two conditions separately and then combine them in the Analyze! window. - which also works well, but for most things combined conditions is very handy!
Hi Ben,
I understand. As I said I will try to add the set regulated beam current functions to the 8230/8530 save/load probe column condition code (now that I have it), but if you're interested in working with us to figure out how to get/set the objective lens for beam focus, let me know.
john
Quote from: John Donovan on October 12, 2016, 01:49:44 PM
Quote from: Ben Buse on October 12, 2016, 02:50:30 AM
Regarding PCC files how would I go about creating them - can I get them from the Jeol software, or are there examples of what they should look like - I guessing there text files essentially.
Hi Ben,
Just FYI, now that we have the firmware call to set the beam current on the 8230/8530, I will add that call to the PCC load condition code.
Right now the code saves/loads the condenser lens values, but I don't think that will turn on the beam current regulation. Adding the firmware call for set beam current should fix that.
john
Hi Ben,
I added code for setting the regulated beam current to the 8x30 set column conditions from a PCC file. Ready to download now.
john
Hi John,
Thats good I hope to try PCC the end of the week. Do you there's any chance of getting objective lens control for focus - it be good if we could that working
Ben
Quote from: Ben Buse on October 17, 2016, 05:37:23 AM
Thats good I hope to try PCC the end of the week. Do you there's any chance of getting objective lens control for focus - it be good if we could that working
Hi Ben,
I will ping JEOL and see if they can provide that for us in the EIKS API.
john
Hi an update on using PCC combined conditions for Jeol 8530F. Thanks to John's hard work this now works really well.
Here's a brief outline on what I do and the nature of the problem
I run major elements at say 20nA and trace elements at 200nA. When switching from 20nA to 200nA the beam goes out of focus and becomes stigmatic. It also shifts position. Now using PCC this can be corrected for - allowing high spatial resolution dual conditions. It corrects for beam shift using image shift - and needs the beam to be in scanning mode - but this can be at 300,000 mag.
Part one - setup PCC files
(1) Set up column for major elements - 20kV, 20nA,x300000mag, good focus and stigma.
(2) Using Window menu in main window - select "Save PCC"
(2) Find a feature and put it in the middle of the field of view
(3) Set up column for minor elements - 20kV, 200nA, good focus and stigma.
(4) Check the shift from the feature. - how much shift in x and y
(5) In Analytical conditions (read conditions if necessary) and choice beam scan mode - enter required x and y shift.
(6) Press ok to apply to column - check if the amount of shift is correct to return the feature to the middle of the field of view. If not repeat step (5)
(7) Set mag to 300,000 and Using Window menu in main window - select "Save PCC"
(8) Load each PCC file - Window menu "Load PCC.." check focus, image shift is correct - otherwise correct and resave PCC files.
Part Two - set up combined conditions
In Combined Conditions window (from Analzye window). For each element select the required PCC file. Then your ready to go!
In combined conditions you can have some elements using PCC file and some elements using anaytical conditions - giving flexiblity.
The PCC files are good in that they load very quickly onto the column - no need to iterate beam current - giving rapid beam condition changes
Ben
Quote from: Ben Buse on January 11, 2017, 03:31:30 AM
Hi an update on using PCC combined conditions for Jeol 8530F. Thanks to John's hard work this now works really well.
Thank-you Ben for helping to test the new PCC files for the 8530. I also want to thanks Glenn Poirer who helped with the 8230 testing.
I have to say, I don't take advantage of this feature (PCC probe column condition files in a combined condition) as much as I should, but it works just as well on Cameca instruments. Quite essential for combined condition analyses of tiny inclusions.
john
Hi all,
Ben and John, I was just looking at your work around for the focus and shift issue with combined conditions. I tried it with our JEOL 8530F and couldn't get it to work. Specifically, I couldn't get my PCCs to save.
First, when you say the main window, I assume you are talking about the opening window for PfEPMA. Is this correct? When I go Window -- Analytical Conditions -- it won't let me save here. I can 'save' in the combined conditions setup. But when I go to load, the saved conditions are not in the directory.
Ben, could you post more specific instructions on how to do this?
In the mean time, I'm gonna run the analyses majors then minors.
Thanks for the help!
Dawn
Quote from: dawncruth on February 18, 2017, 12:15:00 AM
Ben and John, I was just looking at your work around for the focus and shift issue with combined conditions. I tried it with our JEOL 8530F and couldn't get it to work. Specifically, I couldn't get my PCCs to save.
Hi Dawn,
The only issue I can think of is that you should update PFE to the latest version using the Help menu. Then you should be able to do exactly as Ben described.
Also, after updating PFE, check your Probewin.ini file and find the keyword "ColumnConditionPresent" and make sure it says:
ColumnConditionPresent=1
john
Hi Dawn,
Sorry I've only just seen your post - did you sort it. For saving PCC - it should be as shown on screenshot below
Ben
(https://smf.probesoftware.com/gallery/453_22_02_17_1_17_45.png)