Methods of determining and characterizing photosynthesis in plant parts of one or more plants includes capturing a plurality of images of the plant parts of the one or more plants with a sensor are provided. Fluorescence of the plant parts of the one or more plants can be measured by storing a sensor image of observed fluorescence. Light absorbed by the plant parts of the one or more plants can be estimated by observing red and/or infrared reflectance of the plant parts. A characteristic of photosynthesis such as linear electron flow in plant parts of the one or more plants can be derived using the measured fluorescence of the plant parts, the reflectance and the light absorbed by the plant parts, and/or the three-dimensional model comprising the plant parts of the one or more plants. Related apparatus and systems are also provided.