Author Topic: Question: Is it possible to output a serial port command (CL Acquisition)?  (Read 24228 times)

Probeman

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For reference a parabolic mirror, for example like the ones Gatan uses in many of their systems is roughly 80-85% efficient.
Ed

Hi Ed,
That is just the mirror geometric efficiency I'm assuming?

I can't wait to make some absolute measurements on my two CL systems!    ;D
john
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Probeman

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Paul Edwards at StrathClyde, who has added a CL spectrometer to his Sx100 in place of the PMT, writes:

Yes, I use the Cameca optics and the PMT port. However, I don't use a fibre at all, but directly focus the light to the entrance slit of a small (0.125 m) spectrograph which is bolted to that port. I use a simple achromatic doublet lens to focus the light. I don't remember the focal length of the lens I use, but it was chosen to match the f-number of the spectrograph (f/3.7, or NA0.135). You will need one which matches the acceptance cone of your fibre, which is probably NA0.22. If I remember right, the rays are diverging by the time they get to the port, as the image plane lies some distance into the optics assembly.

On thing to bear in mind when choosing a fibre is that the diameter will determine the field of view of the CL. In my case, the image formed at the detector is magnified by around ×3, so when I use a 25µm spectrometer slit I have a field of view of around 8µm. Of course this is not a problem when acquiring point spectra or stage maps. I think in your case the the total magnification should be nearer 2×, as your fibre will have a larger acceptance angle than my spectrograph.

I focus the light to an image at the entrance of the spectrograph, whereas you would focus it to an image at the entrance of the fibre. I just called it "directly coupled" as I don't go via a fibre. In either case you are collecting a lot more light than if you were to just stick the end of the fibre into the port. I avoided a fibre because this would have lost some of the light, but I can see how the flexibility (literally) of a fibre-based system would appeal.
« Last Edit: June 29, 2015, 09:31:38 AM by Probeman »
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John Donovan

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It just occurred to me that we'll probably want to export both the dark spectrum and signal spectrum to the EMSA format file, so that would require a 2 column EMSA format (which does seem to be supported in the description I have).

However, I haven't seen any examples of a 2 column EMSA format file.  Can any one send me a 2 column EMSA format file, ideally one with CL intensity data containing both the dark and signal spectra?

Also, one more question: what Ocean Optics spectrometer should people be buying for use on an EPMA?  I have a Ocean Optics USB 4000 which cost something around $3-4K I think.  Here is the info on it:

http://oceanoptics.com/product/usb4000-custom/

Of course I guess it might matter whether one will be connecting directly to the instrument light optics as Paul Edwards does on his Sx100, or whether one wants to connect via fiber...
« Last Edit: July 05, 2015, 12:32:26 PM by John Donovan »
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qEd

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I am unaware of CL spectra collected in MSA format. X.DM3 and X.epmx are more common formats from Gatan and XCLent. Regarding your need for a two column MSA file, examine your Thermo NSS 2.X/3.X spectrum files as they are native MSA (not EMSA BTW).


John Donovan

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I am unaware of CL spectra collected in MSA format. X.DM3 and X.epmx are more common formats from Gatan and XCLent. Regarding your need for a two column MSA file, examine your Thermo NSS 2.X/3.X spectrum files as they are native MSA (not EMSA BTW).

Hi Ed,
Thanks.  I'm just noting that in the EMSA specification the EMSA file format is intended for CL spectra also.

The Thermo EDS spectra files are EMSA (they have a .EMSA file extension!), but yes they have been *extended* by Thermo with additional "custom" parameters as is allowed in the EMSA format specification using a "##" line specifier. Also these Thermo EMSA files are only one column... here is the first few lines from a Thermo EDS file:

#FORMAT      : EMSA/MAS Spectral Data File
#VERSION     : 1.0
#TITLE       : Moacyr(1)
#DATE        : 09-SEP-2013
#TIME        : 14:26:29
#OWNER       :
#NPOINTS     : 2048
#NCOLUMNS    : 1
#XUNITS      : keV
#YUNITS      : Intensity

So I would still like to get my hands on a CL two column format if possible for my own enlightenment.  Can the Gatan or xCLent apps export an EMSA format file that you can send me?   Thanks!
« Last Edit: July 06, 2015, 09:59:19 AM by John Donovan »
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qEd

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I can check what Gatan export options are later in the week. I do not have an XCLent system. You're right the file suffix is outdated! Below is a 5 column Y only example file. Does that help?

From the original spec EMSAMASFF (EMSA MAS file format):

Hi Ed,
Better if you would just attach the file to this post below so the characters aren't "interpreted" by the forum software!
john
« Last Edit: July 06, 2015, 02:26:44 PM by John Donovan »

qEd

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Here you go, I saved a multicolumn .MSA file using Bruker software.

Probeman

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Here you go, I saved a multicolumn .MSA file using Bruker software.

Thanks Ed.

If do you find that Gatan does output an EMSA file (EMSA or MSA apparently it's the same format), please send that CL spectrum data file also.

Thanks again.
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Hi John,
I am  sorry for my long silent.

If you guys would like to beta-test the CL acquisition feature for us, we can provide the PFE CL acquisition feature and driver to you for free- everyone else will have to pay a nominal cost!    :P

I've mentioned this briefly to Jason (the JX1 Master) before his trip, I think he will allow me to beta-test CL feature :p.

Quote
Can you provide us with any information on the collection optics hardware circled in the picture in this post:

http://probesoftware.com/smf/index.php?topic=517.msg2883#msg2883

For example, who makes it, how much is it and how well does it seem to work (the geometric efficiency question)?

The stem  made by JEOL. I think it came as a package with the system. The docs doesn't give much details (attached), just " a specially made relay lens for CL". Since it is was made for CL, it should worked pretty well.

-riko-


John Donovan

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Quote
Can you provide us with any information on the collection optics hardware circled in the picture in this post:

http://probesoftware.com/smf/index.php?topic=517.msg2883#msg2883

For example, who makes it, how much is it and how well does it seem to work (the geometric efficiency question)?

The stem  made by JEOL. I think it came as a package with the system. The docs doesn't give much details (attached), just " a specially made relay lens for CL". Since it is was made for CL, it should worked pretty well.

Ok, cool.  So do you have an Ocean Optics spectrometer that you can connect to it now?
john
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RIKO

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Quote
Ok, cool.  So do you have an Ocean Optics spectrometer that you can connect to it now?
john

Yes, I have Ocean Optics USB4000 configured for UV-VIS (180-850nm) at hand now.
Extra : I may have another one that cover 350nm-1100 nm soon, but may not from ocean optics.

-riko-

John Donovan

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Quote
Ok, cool.  So do you have an Ocean Optics spectrometer that you can connect to it now?
john

Yes, I have Ocean Optics USB4000 configured for UV-VIS (180-850nm) at hand now.
Extra : I may have another one that cover 350nm-1100 nm soon, but may not from ocean optics.

-riko-

Hi Riko,
Ok, very good.

I will get back to you.  Ocean Optics is fixing a problem I found with their driver, so as soon as they send me a fixed driver I will get that out to you.
john
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RIKO

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Re: Question: Is it possible to output a serial port command (CL Acquisition)?
« Reply #27 on: November 01, 2015, 09:32:10 PM »
Hi John,

As mentioned before, we just obtained a 2nd spectrometer. It is Avantes AvaSpec-3648. This time it come with the DLL and should be able to supply it to you. Let me know if you are interested.

Regards,
Riko

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Re: Question: Is it possible to output a serial port command (CL Acquisition)?
« Reply #28 on: November 01, 2015, 09:53:05 PM »
Hi John,

As mentioned before, we just obtained a 2nd spectrometer. It is Avantes AvaSpec-3648. This time it come with the DLL and should be able to supply it to you. Let me know if you are interested.

Regards,
Riko

Hi Riko,
I will have to check that the DLL is a royalty free distribution. 

By the way, I now have the Ocean Optics "omnidriver" DLL and will also be implementing that soon for sure, as it is a royalty free distribution.
john
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Re: Question: Is it possible to output a serial port command (CL Acquisition)?
« Reply #29 on: December 21, 2015, 04:07:00 PM »
Hi Riko,
I have successfully interfaced an Ocean Optics spectrometer to Probe for EPMA.

It automatically acquires a dark spectrum (before the cup comes out), and then acquires a CL spectrum during the WDS/EDS acquisition as shown here:



The extra space at the top of the acquisition time display is because the WDS data is for 30 seconds, but the CL acquisition is specified at 40 secs. See here for more details:

http://probesoftware.com/smf/index.php?topic=42.msg3855#msg3855

The acquired CL spectra can be displayed and/or exported in EMSA format with both the dark spectrum and normal CL intensity data for further processing and reporting.
« Last Edit: December 21, 2015, 04:10:06 PM by John Donovan »
John J. Donovan, Pres. 
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