Spectrometer Introduction, Tear-down, and Data Analysis for Plant Phenotyping

Spectrometers decompose light into a rainbow of colors and then measure each color accurately. In this video I tear-down a spectrometer, describe the theory, and use of a spectrometer. A recent leaf clip spectrometer is used to for a plant phenotyping application to predict tree lead species.

Finally, I demo software that I’ve written for storing, organizing, analyzing (using PLS-DA), and reporting spectra. If you need help with a plant phenotyping project, let me know, I may be able to help your project.

The geranium drought experiment is not fully described due to time. There’s additional background information that’s needed for understand water absorption spectra. The device used in the video is not ideal for a drought application and so the results are not clear. Let me know if you would more details.

The spectrometer that is tore-down is from Ocean Optics. The leaf spectrometer is from CID Bioscience. A Microsoft Surface tablet is used to power the spectrometer and collect data.

CID CI-710 Leaf Spectrometer: here
Ocean Optics USB4000: here
PLS-DA paper (“So you think you can PLS-DA,” Ruiz-Perez and Narasimhan): here
Other PLS resources:
Properties of Partial Least Squares (PLS) Regression, and differences between Algorithms: here
A survey of Partial Least Squares (PLS) Methods, with Emphasis on the Two-Block Case: here