Purpose

We mapped live cells of Chlamydomonas reinhardtii and Chlamydomonas smithii at three excitation wavelengths (473, 532, and 785 nm) using two commercial confocal spontaneous Raman systems. Here, we share the analysis notebook used to load, mask, baseline-correct, and decompose the resulting spectral maps. All three datasets captured carotenoid signal, with the 473 nm dataset resolving the most peaks overall and giving the clearest spatial information, due to resonance enhancement, scattering efficiency, and optimized focus. PCA on both unmasked and masked data recovered localized structures consistent with the chloroplast and the eyespot, while NMF possibly picked up the chloroplast as well.

View the notebook

In the future, we hope to host notebook pubs directly on our publishing platform. Until that’s possible, we’ll create stubs like this with key metadata like the DOI, author roles, citation information, and an external link to the pub itself.