To create Raman maps, we processed spectra into a map using an in-house Matlab script. In the script, we began by background-correcting the spectra in two steps. First, we subtracted a measured background spectrum. Next, we removed any residual background using asymmetric least-squares . We then smoothed the corrected spectra using Savitzky-Golay filtering. Intensities of relevant spectral peaks (943, 1005, and 1443 cm -1 ) provided pixel intensity values which were processed by a 2D linear interpolation of the intensities and their spatial coordinates. Next, we normalized the resulting interpolants between 0 and 1 with respect to their maximum and minimum values. Finally, we plotted the interpolated intensity as a color map on top of a brightfield image of the mapped oocyst.