A tentative assignment of the major peaks is given in Table . Raman spectra of the oocysts show peaks associated with amino acids and fatty acids, which is within expectation for the oocysts. In particular, the reported Raman spectra of oleic acid and the related phospholipid phosphatidylcholine shows strong similarity to the oocyst spectra. The reported peaks for phosphatidylcholine are at 719, 1088, 1270, 1301, 1442 and 1660 cm -1 34 which closely matches the measured peaks of the oocysts. Phosphatidylcholine was previously reported to be the predominant lipid in the oocysts which is consistent with our Raman data. Another study failed to find detectable amounts of phosphatidylcholine in the oocyst walls , which indicates that the phospholipid is within the oocyst, and not the walls. Two more Raman peaks from the oocyst, situated at 872 and 943 cm -1 , are characteristic of several prevalent amino acids such as tryptophan, proline, and valine . They also correspond well to the sharp Raman peaks found from galactosamine . The presence of galactosamine in Cryptosporidium oocysts is further mentioned in a study by Stein et al. where the authors suggest that galactosamine is present on the surface of Cryptosporidium oocysts, aiding the oocyst in binding to host cells . Finally, the strong 1005 cm -1 peak likely corresponds to phenylalanine 40 . When trapping oocysts and measuring a Raman spectrum, we noted that oocysts were orientated differently in the trap and that peak intensities varied within the population. We hypothesised that different orientations of oocysts and peak variations originated from trapping a non-homogeneous large object, as indicated in Figure A. Since oocysts are much larger than the beam waist of the laser used for Raman spectroscopy (∼ 5 m compared to 400 nm beam waist), we only take a spectrum of a small region with a measurement, which can contribute to the variation seen between samples. To resolve this variation, we Raman mapped oocysts with 1 m resolution, sampling 30 pixels. A representative Raman mapping measurement of an oocyst illustrating the intensity distribution of three different Raman bands, is seen in Figure . All five Raman mapped occysts are shown in Figure . The results show heterogeneity in the intensity distribution of the different Raman peaks, which has overlaps with structures that are visible in the brightfield image. We speculate that these structures may be the sporozoites, as these would have a different chemical composition than the rest of the oocyst content. The heterogeneity is likely caused by the different viewing angles at which the sporozoites are observed and their location in the oocyst. Since the sporozoites are only 4 × 0.6 m 41 , there are many possible ways they can fit into the oocyst.