Vegetation indices can be calculated from multispectral or hyperspectral measurements. A vegetation index is calculated from the spectral reflectance of a plant sample at two or more wavelengths. Such indices serve to characterize developmental or physiological properties of the plants. For instance, greenness indices relate to chlorophyll abundance, pigment-related indices refer to e.g., anthocyanin or carotenoids, or stress-related indices are responsive to biotic and abiotic stress factors. Dozens of indices are reported in the literature, and it is possible to establish customized indices, too.

Color phenotyping delivers information about the plant surface and the colors. In particular, greenness is informative on chlorophyll abundance. Colors can also indicate stress, such as yellowing or browning that relates to wilting. Moreover, many pathogen infections are linked to characteristical colors. In combination with data on morphology of the plants, color data provide an insight in the developmental status. They can be used in genotype-phenotype studies as well as in the assessment of environmental influences or treatments.

Multiview phenotyping serves to determine plant dimensions and structure. Viewing the plants from multiple angles delivers comprehensive information on the structure and morphology of the plant. Data can be used to determine digital biomass. In time series, the method can serve to determine growth and development. The method not only serves to address the impact of environmental factors on plant development, but it is also applied to analyze the genetic control of growth and development.