Spectris: Graphical spectral data processing

[#1]

UPDATES TO THIS ADD-IN WILL NOW BE AVAILABLE IN THE JMP MARKETPLACE

You can find the new version of Spectris here: Spectris on the JMP Marketplace

Purpose

This add-in provides a needed bridge between the capabilities of the Nonlinear/Fit Curve platforms and Functional Data Explorer.  It is designed to handle common spectroscopic tasks like background subtraction, automatic peak searches, curve refinement, and empirical Area Under the Curve calculations.  These tasks are all done through point and click interface.  The add-in also provides a library of peak shapes common to spectroscopic applications, but not included in JMP.

Walkthrough

Support

Spectris Analyzer

JMP Version: JMP Pro 17

Operating System: Windows or MacOS

Spectris Quick AUC

JMP Version: JMP 17

Operating System: Windows or MacOS

[Kast]

Hi Mike,

This looks like a really useful add-in. Is it not supported by JMP 17? I.e. Is the pro version required?
I just wanted to make sure it wasn't working because of my version not an install issue.

Thank you.

[gail_massari]

@Kast Spectral data analyis requires JMP Pro as @MikeD_Anderson put in the description. 

[MikeD_Anderson]

Hi, @Kast!

The add-in currently expects JMP 17 Pro.  There is also a little bug that I just ran into that makes the tool expect the Y, Response variable to have the name "Counts."  If you run into that issue just rename your response column to be "Counts" and it will work fine on JMP 17 Pro.  I'll be pushing out a bug fix along with some additional enhancements in the coming weeks. 

Best,

M

[hogi]

i just noticed that the addin generates ~ 100 variables in the global Namespace.

[MikeD_Anderson]

@hogi - Yep - those are the parameters for the Spectris Function Library - a side effect of the way the custom function library is set up.  Should be going away once 18 is out (assuming things still look like they do in the EA).

[MikeD_Anderson]

@Kast - just an update since you asked about this I've made the empirical AUC calculation tool in Spectris available in base JMP.

Best,

M

[ehchandlerjr]

@MikeD_Anderson This is amazing. Thanks to y'all for developing it!

Is there a way or plans to make a way to supply your own background? When working with quantifying additives in materials, being able to remove background to find peaks that are otherwise hidden because their proportion is so low is very helpful.

Also, are there plans to include a "group by" input for batch processing where the peak positions are roughly known, but the fitting still needs to happen?

Again, this tool is amazing. Thank you.

[MikeD_Anderson]

@ehchandlerjr  - hi!  Thanks for the kind words!  I've had those two requests a few times now. I'm currently thinking about the best way to implement them.  I hope to be able to support the batching at some point ( the harder problem of of the two). The baseline correction is easier.  

[MathStatChem]

i just noticed that this add-in creates a large number (104) global symbols related to the custom functions that are specified and that this add-in uses.   

 Looking at the code, I think this could be improved by just adding "Name Default to Here(1);" statement at the beginning of the function definition files.  The custom functions are still created, but no global symbols are created.  

[Nazarkovsky]

Could you provide us with an example file like you used during the presentation, please? It would be ok to check some series of spectra like for different substances (e.g., oils). This option must have been elucidated in the presentation, actually.

Thank you for the developed tool!

[MikeD_Anderson]

@Nazarkovsky, Hi!  Thanks for trying out the tool. You can get the Olive Oil data set that I was using for the video in the supplementary materials  for this paper: https://doi.org/10.1007/s00216-010-4366-4 

Best,

M