Process and Analyze Agilent Cary 620 FTIR Microscope Images

A set of tools to read, process, and summarize Agilent Cary 620 uFTIR Microscope hyperspectral images primarily intended for microplastic analysis.

uFTIR

An R package to read and process Agilent Cary 620 FTIR microscope -hyperspectral- images. As it is, the package performs image classification to look for microplastics in environmental samples.

When I wrote the package I took some ideas from:

1. The implementation of the Spectal Angle Mapper algorithm in RcppArmadillo was copied from RStoolbox. I modified the function to do the two for-loops in C++, instead of only one as in Leutner, B. et al.’s version.
2. I’m using the R raster package to plot. This is not efficient -I need to coerce every object to a RasterLayer-, and it makes the package huge -I need to import the raster methods-. But it is enough for now.
3. The spectral library included as reference comes from Primpke et al (2018).
4. The function read_tile is based on the Octave/Matlab code of Alex Henderson, published here. He solved the Agilent-provides-binary-files problem.