Oxford Instruments Aztec import?

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HyperspyNewbie

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Jan 21, 2018, 7:16:14 AM1/21/18
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Hi,

I wanted to know if it is possible to import Oxford Instruments Aztec project in HyperSpy? The Aztec project file has .oip and the data files have .dat file extension.

If it's not possible to import directly, any suggestion regarding how can I process the data using HyperSpy will be highly appreciated.

Thomas Aarholt

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Jan 21, 2018, 7:26:43 AM1/21/18
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Yep. In the right hand menu of Aztec, you need to right click, export each map/line spectra as a raw/rpl file. It's called the Ripple format and we support it.

That'll export the dataset into two files - with a rpl and raw extension. You'll need both files sitting in the same folder, and you feed the rpl one to hyperspy.

There's no way to read in the oip or dat files. 

Best, 

Thomas 


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HyperspyNewbie

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Jan 21, 2018, 10:52:38 AM1/21/18
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Hi Thomas,

Thank you for the tip. What other file formats should I export from Aztec? I will only have one chance to export the required file so trying to be future proof.

That'll export the dataset into two files - with a rpl and raw extension. You'll need both files sitting in the same folder, and you feed the rpl one to hyperspy.

Is there a tutorial regarding the processing of the above scenario (e.g. rpl and raw file)?

Thomas Aarholt

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Jan 21, 2018, 12:44:10 PM1/21/18
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Good point. You will also want to export two other things. I forgot that the entire rpl file will be a uncalibrated file (someone correct me if I'm wrong):

1. a single spectra as a .msa format in order to have a file to calibrate the spectrum image.
2. In order to calibrate the navigation space of the eds map, you'll need to export the electron image as a .tif (not the one with overlaid scale bar) from whatever map you're wanting. That can be loaded into hyperspy as well.



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Thomas M. Aarholt

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Pierre Burdet

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Jan 21, 2018, 1:37:39 PM1/21/18
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That’s exact Thomas,

The following notebook can be used as a tutorial

http://nbviewer.jupyter.org/github/hyperspy/hyperspy-demos/blob/master/electron_microscopy/EDS/SEM_EDS_4D_visualisation.ipynb

The single spectra must of course be recorded with the same condition as the map or extracted from the map. If I’m not mistaken you can derived the pixel size from the information given by Aztec on your map


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Thomas Aarholt

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Jan 21, 2018, 3:10:58 PM1/21/18
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Pierre, the pixel size information - is that given in the rpl or some other manner? 

Glad to hear i got it right :) 

Pierre Burdet

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Jan 21, 2018, 3:20:39 PM1/21/18
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The rpl contains just data without any sort of calibration. But when your mapping is open in Aztec, look for the pixel size (or for the frame size and for the number of pixel in x and y) in the displayed information. I don’t work on an Oxford system anymore, I don’t remember exactly.


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HyperspyNewbie

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Feb 6, 2018, 9:15:50 AM2/6/18
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Related older thread, "Oxford Inca project (ipj) files" - https://groups.google.com/forum/#!topic/hyperspy-users/YbM5F7cN950

HyperspyNewbie

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Feb 6, 2018, 10:16:42 AM2/6/18
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Hi Thomas,

I have exported the suggested files. I did go through the tutorial suggested by Pierre Burdet but I am pretty new to EDS analysis. I have only gone through training and did the EDS acquisition in the Aztec software (Oxford Instrument) but do not know what actually the analysis is about.

Would it be possible to give me a step-by-step rundown on what I have to do and why I need to do it?

Thanks.

Thomas Aarholt

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Feb 6, 2018, 11:07:57 AM2/6/18
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Hi Rashed, 

What is your motivation for using hyperspy? Most people use it to do advanced EDS analysis. Unless you know what you're doing in terms of basic EDS analysis (background subtraction, what the different lines mean) or at least have a relatively good background in python, I wouldn't really recommend hyperspy as a starting point. 

If you don't have access to Aztec elsewhere, then I understand the use-case, but then my question is: what do you want to get out of your data? What is the end result you wish to obtain? 

Best regards, 

Thomas 

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HyperspyNewbie

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Feb 6, 2018, 11:22:32 AM2/6/18
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Hi Thomas,

I do not have access to the commercial software and will not have in future as well since microscopy is not my major field. I would like to be knowledgeable in a free/opensource software that can be a good alternative to the commercial software package. For example, I use MTEX for EBSD analysis. Is there any other free or opensource software beside HyperSpy to process EDS data?

The goals of using HyperSpy are (for now) -
1. Obtaining %wt element composition
2. The spectrum with peaks
3. Images of individual element concentration over the sample scan area

As you see these are basic outcomes I'm trying to achieve.

kopriv...@gmail.com

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Oct 8, 2018, 2:46:00 PM10/8/18
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Hi Thomas,

Please see the NIST DTSA-II program in Java, https://cstl.nist.gov/div837/837.02/epq/dtsa2/index.html.
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