Description
Spectral Tools is a collaborative effort of @JeremyAshJMP and @Bill_Worley . It provides some convenience functions for analyzing spectral data, or related data (chromatograms, etc.). Most of the functionality can already be performed in JMP, but the intent was to streamline the process. Hopefully this will help lower the barrier to entry for new users, and make routine tasks faster for experienced users. See part 1 and part 2 of our blog describing the spectral analysis workflow.
Usage
Example Data: An example spectral data set from Martens et al. Anal Chem. 2003 Feb1;75(3):394-404.
Import Spectra: When importing spectra, Spectral Tools assumes that each spectra is in a separate file in a single directory.
Import Spectra > Import Delimited Text Files: Spectra can be in delimited text files (.csv or .tsv, for example). Spectral Tools assumes the X variable is on the first column, and the Y variable is on the second.
Import Spectra > Import JCAMP-DX Files: The simplest variation of JCAMP-DX files is also supported. This means JCAMP-DX files without compression and with a XYDATA=(X++(Y..Y)) variable list. I have not tested this out on different variations of the file format. I plan to add to this post some data that I did test with, once I get permission from the owners.
Preprocessing > Standard Normal Variate: Makes a new column with the standard normal variate applied to the spectra. Assumes your data is in the stacked format.
Preprocessing > Savtizky-Golay Smoothing: Launches Graph Builder with a Savitzky-Golay smoother applied to each spectra. Select your smoothing parameter (local width) and then use the button at the top left of the report to make a new column for the smoother. Assumes your data is in the stacked format. Only available in JMP 16 and higher.
Launch Graph Builder: Launches a spectra line plot for one spectra column or two spectra columns for comparison (e.g., before and after pre-processing). Some of the features you might want to use are set up for you. Assumes your data is in the stacked format.
See this blog post for a Savtizky-Golay derivative filter addin and demonstrated usage.
Disclaimer
There is a disclaimer that appears in each launch dialog. Basically it says that this is only a prototype. This has not been rigorously tested, and does not do much in terms of error handling. We do not intend to provide regular maintenance or support, and this is only a first step towards making analyzing spectra more convenient in JMP.
That being said, it would be great if you could try it out and give us feedback in the comments, or by message to @Bill_Worley. We probably won’t have time to implement new features in the add-in, but it would be helpful for development to hear about features you would like to see in the future. The JMP Wish List is also a great place to make requests.