In fcorra/uFTIR: Process and Analyze Agilent Cary 620 FTIR Microscope Images

NOTES

[Spectral Library]

The spectral library included in the package and the data in the ./extdata folder come from:

Primpke, S., Wirth, M., Lorenz, C., Gerdts, G. 2018. Reference database design for the automated analysis of microplastic samples based on Fourier transform infrared (FTIR) spectroscopy. Analytical and Bioanalytical Chemistry 410: 5131-5141.

The article is available here

[References]

I took the reference samples in ./references with the following settings:

Mode: Transmission
High magnification: off
Sample scan: 8
Background scan: 16
Resolution: 8 cm-1
Scan type: Absorbance
Scan range: 3500 - 1300 cm-1
Beam splitter: KBr
Beam attenuator: 100%

The ./references/bg_anodisc_15x.* sample corresponds to an anodisc place above the KBr glass. The background for that sample was the same anodisc above the same KBr glass. In other words, the sample is a background re-reading. It was taken with 15x objectives to reach a IR pixel size of 5.5 x 5.5 um.

The ./references/ps.* sample corresponds to a Polystyrene sheet. It was taken with 4x objectives to reach a IR pixel size of 20.6 x 20.6 um

[Getting the references]

The references are too heavy to be shared through Github. We extracted a vector from each (all you need to make the examples) and include them in the /references folder. The process was:

ps <- tile_read("data-raw/references/ps.bsp")
bg <- tile_read("data-raw/references/bg_anodisc_15x.bsp")

bg <- bg@Spectra[45,45, bg@wavenumbers %in% ps@wavenumbers]
wn <- ps@wavenumbers
ps <- ps@Spectra[24,72,]

dput(bg, file = "data-raw/references/bg_vec")
dput(ps, file = "data-raw/references/ps_vec")
dput(wn, file = "data-raw/references/wn_vec")