Author Topic: Questions about Probe for EPMA and Probe Image (GUI design and function)  (Read 4114 times)

John Donovan

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I have a few more questions about PfE (if this is right post to ask about it). While I looked over all those screenshots and this last one, I get impression that all options and setups are put into same windows as acquisition. I guess PfE is not using the same convention as cameca: setup->acquisition->interpretation/results. Putting all the setup options at the same window as the acquisition list looks a bit overcomplicated (Particularly that lots of our customers concentrates not on analytical difficulties, but on what to analyse, leaving complexity to operator, which we solve in the setup phase). Is my impression right?

Since you asked...    :D  you have a point about GUI complexity. I agree there is a delicate balance between too little information presented (forcing the user to drill down), and too much information (preventing the user from seeing a specific item they are looking for).  This is a topic of ongoing discussion, but our efforts try to find the balance based on our own experience and user feedback. That is why our slogan is "software designed by users for users!    :)

In our Probe for EPMA software we divide up the operations into a log window for the "stream of output", and 4 main windows for (manual) Acquire, Analyze, Automate and Plot. Each window is an attempt to balance between too little and too much, with "drill down" for more information. This topic has some powerpoint presentations by some of our users that are very out of date but might be informative:

http://probesoftware.com/smf/index.php?topic=592.msg3361#msg3361

Our main design effort is to present the "sample" as the focus of study, as opposed to the "instrument".  Both the JEOL and Cameca software (to my eye at least) have a very "instrument centric" perspective. As an analyst, my focus is on the *sample*, not the instrument so much.

That said, our efforts are on making the user experience as easy as possible.  Our guiding principle has always been "make it easy to do the right thing, because if it's easy to do the right thing, maybe people will do the right thing"!   One example being scanning for backgrounds. In our software if you are analyzing for 18 elements, and need to check the backgrounds, you simply start a new wavescan sample and click the start wavscan acquisition and the software automatically goes to all 18 element ROIs and acquires scans around the peaks for setting the background positions by simply clicking on the plotted wavescans.  Of course if you want to only perform scans on selected element ROIs, you can do that as well...

One more point, since you care about lab efficiency, you'll want to get users off your instrument and onto another computer for data reprocessing as soon as possible to make room for the next user, and our software license allows for *unlimited* copying of the software to as many computers as you like. Every user of your lab gets a complete copy of the software for re-processing.  In addition, the software has an extremely realistic "simulation" mode for both EDS and WDS "demo" operation (based on Penepma Monte Carlo) that many labs use to train their students using the software on their laptops.  I've had many labs report to us (and I've seen this myself) that once the students are trained in the classroom on the software, when they are placed in front of the instrument, and the beam turned on, they don't need any further help from the lab manager! More info on this here:

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

What about mapping? If you use same cameca firmware for map acquisitions does not PfE suffer from the same limitation: in particular the video card memory size (I guess 64MB) which makes it not possible to run High definition mappings (e.g. 2048*2048 pixels) when selecting 5 WDS spectrometers, two analog signals (e.g. BSE, CL). Does PfE suffer from this?

As far as Probe Image is concerned yes, we are limited to the same firmware limits (as is the case for most instruments) as PeakSight.  But we try to make things easy with regards to quantitative mapping because quant is what we are focused on.  That is why we made the acquisition of background maps is so easy for just one example. Our CalcImage app also makes map quantification really easy:

http://probesoftware.com/smf/index.php?board=4.0

Be aware also that although the PI acquisition setup window looks complicated, normally one just messes with the items at the top of that GUI, as all the element specific parameters are read in with one button click (the "ELM All" button or the "Inst All" button).

This is only little connected with above, Cameca's PeakSigh also hold limit for WDS scans which is 2048 points (I guess it is impossed by binary format where wdsDat covers partly with imgDat), does PfE have such hard limitation for WDS scan?

There is no limit to WDS scans in PFE if using the step/count method.  Well a single run is limited to 99,999 points, but that could be increased if necessary.  I've done runs with many thousands of points over a weekend and they are quite impressive when plotted up.

As for the lab closest to you I'm not exactly sure whom that might be, but take a look at our customer list here and let me know if you need their contact info:

http://www.probesoftware.com/Customer.html

I hope that wasn't too much of a sales pitch!    :-\
« Last Edit: March 26, 2018, 12:14:46 PM by John Donovan »
John J. Donovan, Pres. 
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John Donovan

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Questions about Probe for EPMA and Probe Image (GUI design and function)
« Reply #1 on: March 26, 2018, 11:58:14 AM »
Can you do multi area dataset?

I think I forgot to answer this specific question...

If by "multi area datasets" you mean acquire multiple point analyses and/or multiple maps on multiple areas, yes, of course. But maybe you mean something else?
« Last Edit: March 26, 2018, 12:00:17 PM by John Donovan »
John J. Donovan, Pres. 
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John,
Thank you for your answers.

One more thing bothers me: what about optical camera, I saw some discussion about mossaicing... But in the first place camera needs to be accessed somehow: SxFiveFE have firewire camera, and only single AVT driver can control/view camera at once. Does PfE deal with this problem on software level, or some additional hardware (Firewire DV splitter) needs to be invested in? or does PfE works only with older type of optical cameras?

John Donovan

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One more thing bothers me: what about optical camera, I saw some discussion about mossaicing... But in the first place camera needs to be accessed somehow: SxFiveFE have firewire camera, and only single AVT driver can control/view camera at once. Does PfE deal with this problem on software level, or some additional hardware (Firewire DV splitter) needs to be invested in? or does PfE works only with older type of optical cameras?

Hi Petras,
The mosaic feature in our software (Stage utility app) is designed to acquire analog electron signals (SE, BSE, CL, Abs), not the video image from the video camera. On the Cameca that signal goes to the frame grabber in the Cameca PC.

I should also explain that our software is not a replacement of the Cameca software. It runs alongside at the same time as the Cameca software and provides many additional features and methods for acquisition and analysis that Cameca and JEOL do not. Here is a pic of the computer setup in our lab:



So we have one computer running PeakSight with the monitors on the bottom, and another computer running Probe for EPMA (and also Thermo NSS/Pathfinder) on the upper monitors.  We connect to the instrument just like PeakSight using a single CAT5 cable.  The Cameca computer loads the firmware when PeakSight starts and then we can start our software and make a network connection also from our computer.  In my UofO lab in Oregon, we almost only use PeakSight to change samples and align the gun, though we also run our PictureSnapApp on the Cameca computer using one of the lower monitors (just for sample holder navigation) though we could instead just use the PictureSnap feature in Probe for EPMA. 

We then use a USB switch to share a keyboard and mouse between the two computers.  It's a nice setup for SX100 or SXFive instruments though every lab has a somewhat different arrangement of computers and monitors.  Our only request is that people install PFE on a separate computer from the Cameca or JEOL OEM software, as we don't think that is very practical for users and JEOL and Cameca also prefer it.  Once the Cameca software has loaded the firmware to the instrument we could turn off the Cameca computer, but we always leave it on to change samples, monitor the vacuum, etc.

We integrate with JEOL instruments in a similar but slightly different way because every EPMA instrument model is different!  On JEOL 8900/8200/8500 instruments we connect our software to the instrument on a separate computer (PFE won't run under UNIX!), again at the same time alongside the JEOL UNIX box and software, using a single CAT5 cable. We could actually run our Probe Software apps on these older JEOL instruments without the UNIX box, but because some service engineers depend on their UNIX macros for service of the instrument, we suggest that people keep their UNIX box up and running.  Also to monitor the vacuum, EOS, and align the gun, though our GunAlign and Monitor apps also provide similar functions. Here is a topic on JEOL instrument computer/monitor arrangements in case you are interested:

http://probesoftware.com/smf/index.php?topic=1057.msg6957#msg6957

On the new JEOL 8230/8530 instruments we again run on a separate PC computer alongside the JEOL PC-EPMA/SEM computer/software. But because at the time JEOL insisted we utilize their EIKS interface for stage and column control, we make *two* network connections from our computer. One to connect to the JEOL computer for stage/column control via EIKS and a second network connection directly to the instrument for the WDS and mapping calls.   This means that the JEOL software has to stay up and running while our software is also connected to the instrument, but this is no problem and again it allows users to monitor the vacuum, etc., etc. 

We aren't an engineering company per se, but rather a bunch of scientists like yourself that want a better experience for the acquisition, automation and analysis software than what the OEMs provide.  We actually prefer that Cameca and JEOL handle most of the basic instrument specific operations like changing samples or monitoring the vacuum system, as we want to concentrate on the science of EPMA.

Sorry to be so wordy but sometimes I think it's worth detailing these computer/software/instrument connection particulars in order to understand just how our software "fits into the picture".   Let me know if you have any further questions.
john
« Last Edit: April 12, 2020, 07:46:18 PM by John Donovan »
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From my experience auto-z works not always satisfactory (particularly on our SX-100) so having no camera integration sounds a bit troublesome. Also Bruker is installed on the SX-PC... These brings me to the point below.

What is the real technical obstacle/issue which insists to install PfE on the separate machine? (I don't believe in computer magic, for me computer is the strictly deterministic system, so any "probably this or that" does not count). The PC coming with SX-machines (which we have) is a top-notch "workhorse" class workstations (with highly efficient Xenon processor, which is already overkill for single threaded Cameca apps). If only main SX apps executed ("SX control" and "interpretor", without executing the memory-leaky SxSAB or crashy "SX-Results") there is really plenty computing resources available (mainly RAM, and 7 processing threads). I see installing the separate PC as a complete waste of the available resources and unnecessary expenses (single time and runtime). Additional heat sources to the room (from additional PC and monitors) and raised complexity also brings no advantage.
The single additional high quality network interface card (NIC) is the only hardware I see the installation of PfE would rather need (so that PfE would connect with machine through different IP avoiding the clash with same port), and maybe bunch of additional ECC ram (to expand from 8GB to 16GB) which is always nice to have. But I am in doubt that additional NIC is really necessary, as multiple Cameca apps connect through the same port.
Finally, the Cameca can't forbid installing custom software on the same PC as they officially advice keeping windows updates on (and there is really rich continues history of MS blue Tuesdays... fortunately we had not once evaded the mess). That means PeakSigh rather is independent from system configuration (for comparison, windows on ZEISS SEM PC are forbidden to be updated as ZEISS software highly depends on particular driver versions... which me brings to the logical conclusion: the Peaksigh is really independent from sys configurations, as Cameca knows what they are doing, else they would not advice windows updates). So if PeakSigh is system-conf independent there is no obstacle to install other software. Right?

What about scriptability of PfE? Our machine (And I guess some other SXFiveFE machines) have specific (non-standard) standby procedure invoked from interpretor. Can PfE execute some kind of internal scripts (controlling machine internally) or external? (i.e. *.bat files which could invoke interp.exe with following standby script, do some data copy to ftp... and etc).

Btw, I don't think KVM switch is the best solution for dual-PC configuration. There is many nice mouse/keyboard sharing software solutions (some very cheap or even free) working over network connection (particularly when both PC is on the same network), e.g. Synergy, ShareMouse, Mouse without Borders... We use Synergy on our Zeiss SEM machines as Bruker EDS have separate PC – both keyboard and mouse (and clipboard works too!) are shared between monitors/PCs as it would be a single system.



 

John Donovan

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What is the real technical obstacle/issue which insists to install PfE on the separate machine?

Hi Petras,
There is no technical reason for installing PfE on another computer.  One could certainly install PfE on the Cameca PeakSight computer.  As you say, a good computer could certainly handle it.  That said, Cameca originally provided our CAMCOR facility with a Dell Optiplex (consumer grade) computer which was not a sufficiently high end computer for this purpose.  We recently replaced it for a couple of reasons: one it was running Windows XP, and second, the capacitors on the motherboard had been replaced several times after "popping".  The Dell Precision Workstation we replaced it with uses tantalum caps on the motherboard that can better handle running continuously for 10-15 years.

But as I mentioned previously, both JEOL and Cameca prefer we not install our software their computers and since computers are so cheap nowadays, it doesn't seem like a big deal to have another computer.  That's one thing I really like about networked instruments. That one can have multiple computers all connected and talking to the instrument at the same time.  We even have some customers that want to run their EPMA instrument from their laptop computer, especially if they are developing a script, as I describe below.  The only limitation then would be the responsiveness of the instrument firmware...  and I have seen that one can have too many apps running, which can affect the instrument's responsiveness.

The only other reason I can think of for a separate computer is that it's nice to have more monitors to spread out on.  The monitors that Cameca usually provides are pretty small.  Perhaps you saw this post for a new JEOL 8530 install by Anette von der Handt:

http://probesoftware.com/smf/index.php?topic=173.msg6956#msg6956

And in fact in our own CAMCOR lab we run our PictureSnapApp product on the Cameca PeakSight computer because we are only using PeakSight to change samples, monitor the vacuum and align the gun, so the second monitor usually doesn't have anything displayed, so PictureSnapApp just sits there for easy sample navigation.

What about scriptability of PfE? Our machine (And I guess some other SXFiveFE machines) have specific (non-standard) standby procedure invoked from interpretor. Can PfE execute some kind of internal scripts (controlling machine internally) or external? (i.e. *.bat files which could invoke interp.exe with following standby script, do some data copy to ftp... and etc).

PfE itself has a filament standby option that can invoke a user defined custom script, batch file or app, And yes, we have a very extensive scripting capability in our Remote Server app:

http://probesoftware.com/smf/index.php?board=9.0

Many labs use Remote Server to create custom applications. For example, the GE Global lab uses Remote to develop their own custom apps for automated feature recognition.  In fact Ben Vos just posted (this morning) an interesting script he wrote using Remote for controlling the beam current on his SX100 LaB6 gun using the emission current:

http://probesoftware.com/smf/index.php?topic=1052.msg6964#msg6964

Using our Remote Server interface (see the Remote.pdf document for a complete list of instrument functions supported), one can script from Excel, MatLab, LabView, whatever OLE container they prefer. 

You asked about camera/frame grabber support... well if you don't like what Cameca provides, then using our Remote Server interface you could buy a frame grabber for $100 and write an app to mosaic the optical camera signal using Remote.  It is custom applications like this, that our Remote Server interface was developed for.

Btw, I don't think KVM switch is the best solution for dual-PC configuration. There is many nice mouse/keyboard sharing software solutions (some very cheap or even free) working over network connection (particularly when both PC is on the same network), e.g. Synergy, ShareMouse, Mouse without Borders... We use Synergy on our Zeiss SEM machines as Bruker EDS have separate PC – both keyboard and mouse (and clipboard works too!) are shared between monitors/PCs as it would be a single system.

Using a KVM switch or not is totally the users choice (the customer is always right!).  Or one could have separate keyboards and mice.   Personally I've tried a couple of software solutions for sharing the mouse/keyboard in our CAMCOR facility and both of them have had minor problems.  Anette mentions in her "flight deck" post above some "glitches" she's had with "Mouse without Borders". You are certainly free to use your preferred mouse/keyboard sharing solution.

Please let me know if you have further questions.
john
« Last Edit: March 29, 2018, 11:49:17 AM by John Donovan »
John J. Donovan, Pres. 
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