Understanding the light-harvesting properties of algae and higher plants are a fundamental topic in photosynthesis research. Much oceanographic research has focused on characterizing the in vivo chlorophyll-specific absorption coefficient, a*ph (λ) in phytoplankton because it serves as an input variable for bio-optical modeling of photosynthesis using remote sensing instrumentation such as moorings, drifters, and satellites. Values of a*ph (λ) vary spectrally and the magnitude depends on accessory pigments, photo-protective pigments, and pigment packaging effects. Several studies have shown that the contribution of cellular characteristics to a*ph(λ) varies with growth conditions including temperature, light, and nutrients. It has been shown that a*ph (λ) values in Phaeocystis vary predictably at 4°C over light intensities under light limitation. Phaeocystis demonstrated significant pigment package effects that depended on single cell diameter and thylakoid membrane stacking. Using thick sections obtained from fixed and embedded cultures of colonial P. antarctica, we calculated tomographic reconstructions of individual chloroplasts under light-limiting conditions for net photosynthesis in order to gain an understanding of the continuity of thylakoid membranes and understand the spatial relationship between the pyrenoid, the starch containing organelle, and thylakoid membranes.