Author Topic: What is the "state of the art" in combined WDS-EDS quant mapping?  (Read 19748 times)

Probeman

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So the basic problem as described by John Fournelle here:

http://probesoftware.com/smf/index.php?topic=397.0

is that we need a method to integrate both the WDS and EDS ROIs (or even better a full EDS spectra, heck also the full CL spectra as well) for each pixel.  The ideal method is to utilize a single scan generator to acquire the WDS stage map while storing a full EDS (and CL spectra) for each pixel.

The method described here:

http://probesoftware.com/smf/index.php?topic=83.0

is a possible work around by acquiring the WDS map using Probe Image (via the JEOL or Cameca mapping scan generator) and then acquiring an EDS spectrum image using the EDS scan generator and correlate the quantified WDS pixels with the EDS spectra from the "nearest neighbor" pixel in the spectrum image.  This can be done right now with Thermo spectrum images, but Bruker has yet to send me any information on reading their spectrum image files.

However, this "hyper-imaging" method correlates the WDS quant image, only with the raw intensities of the EDS spectrum image. The next step, which I hope to implement shortly would be to obtain the EDS spectra for each SI pixel, then the net intensities for the specified EDS elements from the Bruker or Thermo API, and then calculate a k-ratio for each EDS element and combine those with the WDS k-ratios as is currently performed for single point analyses in probe for EPMA using the EDS net intensities from Bruker and Thermo.

Another method would be to utilize a hardware pixel sync signal from the JEOL or Cameca stage scan electronics and correlate this pixel sync to an external EDS and/or CL spectrum acquisition (passive scan method). This is already the case for JEOL instruments with Colin MacRae's ExCLent system from CSIRO using an Ocean Optics CL spectrometer and for Cameca instruments I believe it is possible with some work by Paul Edwards at  Strathclyde University.

The basic problem as it currently stands for both Cameca and JEOL instruments is that they have external mapping inputs, but these inputs only accept TTL pulse level signals, not full spectra signals.

Let's discuss this further and see if we can't come up with a "crowd sourced" solution for both Cameca and JEOL instruments!
« Last Edit: December 23, 2014, 11:39:40 AM by Probeman »
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Probeman

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #1 on: December 23, 2014, 11:55:57 AM »
I should also mention that this issue is complicated by several other mapping/hardware issues:

The JEOL 8900/8200/8500 and Cameca SX100 instruments have WDS TTL outputs for input into Bruker and Thermo mapping inputs. Note that Bruker has 5 mapping inputs as an option. Thermo has one WDS mapping input which can be switched (and/or summed) using this hardware from Probe Software:

http://probesoftware.com/smf/index.php?topic=77.msg289#msg289

But Thermo can also add 4 more WDS mapping inputs as described here:

http://probesoftware.com/smf/index.php?topic=77.msg284#msg284

and here:

http://probesoftware.com/smf/index.php?topic=77.msg289#msg289

However, the current JEOL 8230/8530 instruments have the WDS TTL outputs removed (for possible integration with Bruker and Thermo).  We need to either get these added back in *or* have a full spectrum EDS/CL integration with the WDS stage mapping.

Another alternative is to have Thermo or Bruker implement a stage mapping method for WDS, but currently they both do nothing with the WDS intensities except to display them.
« Last Edit: December 23, 2014, 03:15:54 PM by Probeman »
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John Donovan

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #2 on: December 24, 2014, 11:38:41 AM »
OK, I think I have an excellent solution, unfortunately which will require a little effort from Bruker and Thermo...

With this solution we will be able to acquire stage (and beam) scan maps on our JEOL and Cameca instruments and synchronize the WDS mapping pixels with the EDS spectrum acquisition to allow a full WDS and EDS spectrum image with each EPMA acquired pixel.

How?  Well we already know that both the JEOL and Cameca instruments output a pixel sync signal at the hardware level during stage and beam scans (JEOL provides this for Colin MacRae's ExCLent CL acquisition system and Paul Edwards at Strathclyde University has also figured this out on his SX100, also for CL acquisition).

Now, if Bruker and Thermo added a single TTL input BNC that would direct the EDS spectrum acquisition system to save the ongoing EDS spectrum acquisition as the next pixel in their spectrum image files, each EPMA WDS pixel would be perfectly synchronized with each EDS spectrum image pixel.

This "passive" acquisition EDS spectrum image file could just be saved as a linear number of pixels because at the application level, the software already knows what the X/Y pixel dimensions are and therefore could just read in the EDS spectrum image pixels as a stream.

Problem solved!   8)

Now we just need to get Bruker and Thermo (and JEOL and Cameca for the output sync signals) on board for the input signal hardware flag!

Edit by John: Ok, I've learned that Thermo already has a hardware pixel sync input on their EDS so implementing this should be simple for them.  Does anyone know if Bruker has a hardware sync input already?

Edit by John: Another thought: does Gatan have a hardware level sync input on their CL systems?  They do on their EELS system on TEM instruments...

Edit by John: We now have the pixel, line and frame sync pulse hardware pinouts from Cameca for their SX100 and SXFive instruments.

Edit by John: Thermo is now integrating these signals to their EDS SI hardware sync input.  But we're still waiting to hear back from JEOL on their mapping sync signal pinouts- if your lab would like to have this capability on your JEOL instrument(s), you might want to rattle their cage a bit!
« Last Edit: June 06, 2015, 07:42:59 AM by John Donovan »
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kthompson75

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #3 on: January 06, 2015, 03:37:05 PM »
Yes. John is correct. The ThermoScientific Noran System 7 as it exists today can take the hardware input trigger. Our NSS-PORTAL also takes commands to collect the data and to send the full spectrum in each pixel back through the portal to the computer that is asking for this data. Depending on the dwell time and beam current, that spectrum may have anywhere from a couple of energy events to a couple of thousand energy events. We do this with GATAN EELS system on TEMs for concurrent EDS-EELS and it works quite well.




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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #4 on: June 30, 2015, 09:51:39 AM »
A quick update on our EDS WDS integration efforts which forum members received as an email a couple of weeks ago:

Dear Colleagues,
Probe Software has now implemented a new WDS-EDS integration feature for point analyses in our Probe for EPMA software package, providing new analytical flexibility for on-line and off-line data processing.

The just released feature works with both Thermo and Bruker SDD detectors (and can also be utilized off-line on any computer- with Bruker you will need an off-line license), and is described here on our EPMA forum:

http://probesoftware.com/smf/index.php?topic=482.msg2826#msg2826

We are also excited to report that we have a new EDS-WDS synchronized mapping feature (see link below) in the works, hopefully to be released this fall:

http://probesoftware.com/smf/index.php?topic=400.msg2174#msg2174

Using a Thermo (we hope to implement this with Bruker as well) SDD EDS system (for EDS spectrum imaging), and our Probe Image Software (for EDS/WDS acquisition), and our CalcImage Software (for quantitative map processing), an EDS spectrum map can be acquired (that is, a full EDS spectra for each map pixel) with WDS elements in perfect hardware synchronization.

All intensity signals will then be quickly and easily quantified using normal standards with drift corrected k-ratios and full background, matrix and interference corrections. This works for both beam scan and stage scan mapping!

Think of it this way: in one pass you'll be able to acquire all your major (and minor) elements using EDS and your trace elements using WDS.

Of course if required, you can acquire additional WDS elements in subsequent passes, and these will be automatically integrated into the previous EDS/WDS quant processing and mapping presentation output. As described above for point analyses, you'll also be able to change and/or add EDS elements in post processing for these x-ray maps as well!

Right now we are working with Thermo to implement this system on the Cameca SX100 and SXFive. We also hope to make this available for JEOL users.

Probe Software will be at Microscopy and Microanalysis 2015 in Portland Oregon! We hope to see you there!

Please let us know if you have any questions.
john
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Probeman

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #5 on: July 22, 2015, 01:41:03 PM »
Here's another idea: once we get the WDS and EDS mapping synchronized in Probe Image, and if the user wants/needs to acquire off-peak maps for the WDS elements, maybe we could simply acquire additional "frames" for the EDS spectrum image to improve statistics rather than just sit there during the off-peak WDS map acquisition...

Of course, now with the MAN background correction working so well for WDS mapping, maybe we won't be acquiring WDS off-peak maps anymore?
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Karsten Goemann

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #6 on: July 28, 2015, 10:52:03 PM »
That's a brilliant idea, if the EDS "frames" can be easily combined to a single data cube, also assuming no position shift between the frames.

John Donovan

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #7 on: July 29, 2015, 07:59:50 AM »
That's a brilliant idea, if the EDS "frames" can be easily combined to a single data cube, also assuming no position shift between the frames.

Hi Karsten,
I'm thinking that maybe the acquisition could be paused instead of stopped and then maybe, an additional frame (or two) could be appended during the off-peak acquisition(s).

The subsequent frame(s) would be synchronized to the off-peak pixel dwell time, but that still improves the statistics.
john
« Last Edit: July 29, 2015, 08:16:43 AM by John Donovan »
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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #8 on: September 05, 2015, 08:29:43 AM »
As you may know Probe Software is working with Bruker and Thermo to integrate synchronized WDS mapping and EDS spectrum imaging acquisition on Cameca instruments. One "test bed" for this is John Fournelle's new SXFIVE in Madison with his Thermo NSS system.

We would also like to have a "test bed" for this WDS-EDS mapping integration with either Thermo or Bruker on a JEOL instrument. At least for the 8200/8500 and 8230/8530 instruments (sorry 8900!). We know JEOL can provide a board with the WDS mapping sync signals that can be utilized for this purpose on the 8200/8500. It's the same board that Colin MacRae utilizes for integrating WDS and CL spectrum acquisition mapping with his xCLent system.  Similar sync signals are also available on the JEOL 8230/8530 instruments as well.

If someone with a JEOL 8200/8500 (or 8230/8530) instrument is interested in buying a new Thermo or Bruker EDS, or already has a Thermo or Bruker EDS and would like to work with us on getting this new technology going on their JEOL instrument, please let us know.

This will be fun!
john
« Last Edit: September 05, 2015, 08:51:21 AM by John Donovan »
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Julien

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #9 on: September 05, 2015, 09:28:14 AM »
Hi John,

As you know we will be receiving a new JEOL 8230 by January or March next year, with a Thermo EDS. JEOL will have to perform some minimal hardware modification to (re)create WDS outputs to be linked to the Thermo NSS box. This modification, for those who are interested, is budgeted at $2.5K for the WDS board modification and an additional $10K for a multiplexor box.

I had some discussion with Charlie Nielsen, and I believe, John, you had a positive chat with him at M&M. In his own words regarding a major outcome of this discussion you had with him:

Quote
We have agreed to implement a “get photo” command in the dll’s that will allow PFE to set pixel size, dwell time as well as start, status and get file. This will allow acquire fast images from the JEOL side and synchronize it with the thermo EDS output. As far as I can tell there will be no additional hardware required.

So... Good sign? Anyway, as soon as we have this new instrument, I'll be on board for this testing...

Julien

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #10 on: September 05, 2015, 10:46:45 AM »
Hi John,

As you know we will be receiving a new JEOL 8230 by January or March next year, with a Thermo EDS. JEOL will have to perform some minimal hardware modification to (re)create WDS outputs to be linked to the Thermo NSS box. This modification, for those who are interested, is budgeted at $2.5K for the WDS board modification and an additional $10K for a multiplexor box.

I had some discussion with Charlie Nielsen, and I believe, John, you had a positive chat with him at M&M. In his own words regarding a major outcome of this discussion you had with him:

Quote
We have agreed to implement a “get photo” command in the dll’s that will allow PFE to set pixel size, dwell time as well as start, status and get file. This will allow acquire fast images from the JEOL side and synchronize it with the thermo EDS output. As far as I can tell there will be no additional hardware required.

So... Good sign? Anyway, as soon as we have this new instrument, I'll be on board for this testing...

Julien

Hi Julien,
This is a very good sign. Yes, we had a good meeting with JEOL at M&M and they have been indicating cooperation, but it is good hear to hear confirmation.

Just two minor comments:  first, the fast video imaging is good.  We lost that when JEOL de-integrated the video imaging from the 8230/8530 instruments, but this effort will bring that back.

And second, the WDS mapping and EDS synchronization is using the JEOL mapping scan generator for both stage and beam scanning and the sync pulse outputs that the JEOL board is providing is then sent to the Thermo sync input so the Thermo is essentially running a "passive" EDS SI acquisition synchronized with the WDS mapping.  And once Thermo and Bruker finish the new API calls we will be able to fully quant these synchronized WDS-EDS maps! 

And one will be able to change the EDS map elements at will in off-line processing!

Thanks for your help with all of this Julien!
john
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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #11 on: November 19, 2015, 09:17:07 AM »
John, Julien,

For the purpose of combining both EDS and WDS in PI, I understand that a sync pulse is required to be sent from the EPMA to the EDS hardware to synchronize the EDS data collection with stage/beam movement. I don't understand why one would still need a multiplexer? This would imply that one wants to send the WDS info to the EDS system. Do we need to do this when using PI? I guess this adds extra functionality for someone without PI, but I imagine if using PI, this is not required?

Assuming one wanted to send the WDS signals to the EDS hardware, would the multiplexer be needed on an EDS system with 5 wds inputs?

Gareth


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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #12 on: November 19, 2015, 02:13:07 PM »
John, Julien,

For the purpose of combining both EDS and WDS in PI, I understand that a sync pulse is required to be sent from the EPMA to the EDS hardware to synchronize the EDS data collection with stage/beam movement. I don't understand why one would still need a multiplexer? This would imply that one wants to send the WDS info to the EDS system. Do we need to do this when using PI? I guess this adds extra functionality for someone without PI, but I imagine if using PI, this is not required?

Assuming one wanted to send the WDS signals to the EDS hardware, would the multiplexer be needed on an EDS system with 5 wds inputs?

Gareth

It's a good question.

There are several ways to combine WDS and EDS acquisitions. Let's look at each of them.

1. Integrated WDS and EDS full spectrum point analyses.

With this method, implemented in Probe for EPMA, we can acquire a normal WDS point acquisition and also a full EDS spectrum (and soon a full CL spectrum!) for each data point. PFE can acquire full EDS spectra from Penepma12 (Demo mode), or Thermo NSS or Bruker Esprit using only a software API. 

The WDS and EDS data is acquired on all samples (standards, unknowns and wavescans) and can be quantified for standards and unknowns using full k-ratios where the net intensities for the EDS elements are obtained from the Bruker or Thermo interface (no demo mode net intensity function as yet) in on-line or off-line mode (note Thermo NSS is free for data re-processing, Bruker Esprit is not). Full matrix and interference corrections are applied.

See here for more details:

http://probesoftware.com/smf/index.php?topic=79.0

2. Integrated EDS and WDS with Bruker or Thermo applications.

With this method, the WDS raw PHA counts are sent via a BNC cable (multiplexer hardware) to the Thermo or Bruker hardware and displayed in the Thermo NSS or Bruker Esprit application for x-ray maps only. 

The WDS map data cannot be background corrected or quantified, only displayed in NSS or Esprit.

See here for more details:

http://probesoftware.com/smf/index.php?topic=134.0

http://probesoftware.com/smf/index.php?topic=77.msg284#msg284

3. Integrated WDS and EDS mapping in Probe Image (using ROI mapping inputs)

With this method, we utilize Probe Image to acquire WDS maps and if the Bruker (not available for Thermo) mapping outputs are available we can send those to the Cameca or JEOL mapping inputs and display the EDS ROI data along with the WDS maps in Probe Image.

As is the case with method #2, we cannot quantify the EDS maps.

At the current time, this only works for JEOL instruments and the JEOL EDS, though we will be implementing the EDS element ROIs mapping outputs at some point for Bruker EDS systems, but since the EDS maps cannot be quantified using this method, it is not a top priority.

See here for more details:

http://probesoftware.com/smf/index.php?topic=77.0

4. Integrated WDS mapping and EDS spectrum imaging in Probe Image.

The is the so called "holy grail" of EPMA where we acquire full WDS maps and at the same time, using a pixel sync pulse from the EPMA map scan generator, trigger a full EDS spectrum acquisition for every pixel, all fully synchronized.  This is the subject of this topic.

Thermo and Bruker (and also JEOL) are currently working on implementing this "passive" WDS EDS mapping acquisition method using their hardware sync input and an API which I designed for obtaining the net intensity maps for quantitative post processing of the maps.

Using this method both the WDS and EDS map data can be fully quantified for background, matrix and interference effects using standard intensities from Probe for EPMA, maps from Probe Image and quantified using CalcImage.

I will be posting progress updates here.
« Last Edit: November 19, 2015, 09:39:50 PM by John Donovan »
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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #13 on: November 20, 2015, 09:41:24 PM »
so the bottom line is, for scenario 4, the holy grail (for now):

all that is required from the EPMA vendors is the sync pulse; all that is required from the EDS vendors is the ability to trigger acquisition on the external sync and a large file containing the EDS spectra.

Sounds easy! I'll expect we'll see the holy grail next month  ;)

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Re: What is the "state of the art" in combined WDS-EDS quant mapping?
« Reply #14 on: November 20, 2015, 09:50:04 PM »
so the bottom line is, for scenario 4, the holy grail (for now):

all that is required from the EPMA vendors is the sync pulse; all that is required from the EDS vendors is the ability to trigger acquisition on the external sync and a large file containing the EDS spectra.

Sounds easy! I'll expect we'll see the holy grail next month  ;)

There's also some software (API) "glue" that needs to be developed and applied, by both Thermo/Bruker and Probe Software... I'm already working on my end!
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