ParticleFinder

Description: An API for the FilterView class. This class is designed to take a directory of CSV files exported from Thermo Fisher Scientific's OMNIC spectroscopy software. CSV files of every spectra in an OMNIC chemigram can be exported by selecting the "Split Map" option from the Atlus drop down menu. The exported file type can then be selected as CSV and then OMNIC will export all spectra in the chosen chemigram as CSV files to the selected directory. This program performs a rough analysis on those csv spectra to determine which likely originate from microplastic particles. This program assumes that spectra that display decreased reflectance (increased absorbance) at 2850 wavenumbers, corresponding to the sp3 CH stretching region of the IR spectrum, are likely to be microplastics. Spectra that meet the "decreased reflectance" criterium are determined by subtracting the reflectance intensity at 2850 wavenumbers from the reflectance intensity at 2750 wavenumbers (a proxy for the spectral baseline) for all spectra in the given directory. Spectra that are outliers in the resulting Gaussian distribution of reflectance differences are assumed to be spectra that were obtained from microplastic particles on the filter surface. The functionality of the FilterView class and API is detailed below. For those who are interested, the provided code framework could be expanded upon to accomodate a more sophisticated form of spectral matching. A good place to start would be in the diffList function and the pixelList function, both located in the utilities file. A spectral matching algorithm was not included in this version because spectral quality was not sufficient to perform spectral matching, therefore the more rudimentary approach based on reflectance differences was carried out, as discussed above. Of note, it is acknowledged that both function implementations and program runtimes at the moment have not been optimized. This program can accomodate all spectral ranges and assumes that the chemigram step size matches the aperture x & y dimensions, which should be the same (i.e. a square aperture).