This chapter provides the basis for the absorption and internal scattering properties of leaves derived from theoretical spectroscopy of various chemical components. The absorption of electromagnetic radiation by leaf constituents occurs in different regions of the spectrum. Molecular electronic transitions take place in the ultraviolet (UV) and visible spectrum. This occurs when electrons in a molecule are excited from one energy level to a higher energy level. Transitions between two levels can occur upon the absorption of a photon.

A model is a simplified mathematical representation of a phenomenon that simulates its functioning. Science has long used, explicitly or implicitly, approaches that associate models with pure theory and experimentation. These three lines of research are inseparable. We expect a theory to explain the experimental results and predict new results; from an experiment we generally expect it to verify the validity of existing theories and to collect new data. With the exception of a few cases where experimentation is not possible, the confrontation of a model with experimental data is needed to validate it. Sometimes, however, this comparison is misleading.

Great progress has been made over the last two decades in the simulation of photon transport within vegetation canopies using radiosity or ray tracing models. At the leaf scale, similarly, it is possible to track a single photon from cell to cell and to derive the optical properties of the entire blade by following the paths of hundreds, thousands, or even millions of photons (see Section 8.2.5). Ray tracing techniques require a detailed description of leaf geometrical properties, as well as knowledge of the mechanisms involved in the scattering and absorption of light at different levels of organization from organelle to leaf and at different wavelengths.

Applications of leaf spectroscopy have many different end uses. Leaf level information is crucial to quantify the state of physiological processes, for example the energy budget and transpiration. It is used to monitor photosynthetic rates and respiration rates. It provides a basis to scale environmental processes from the molecule to the planet. Leaf spectroscopy is also used in remote sensing studies to calibrate processes and provide ground truth data for interpretation, and in agriculture to indirectly calibrate foliar nutrients like nitrogen concentration.

Changes in leaf internal structure may affect leaf optical properties to varying degrees in different parts of the solar spectrum, but they are most evident in the near infrared (NIR) where absorption by pigments is minimal. The mesophyll anatomy of leaves of terrestrial plants is highly variable. To illustrate the effect of such variability on leaf optical properties, Gausman et al. (1971c) selected 11 species displaying a wide range of internal structures (compact, dorsiventral, isolateral, and succulent) and thicknesses.

This chapter provides a background on measurements of optical properties. First, we review the terminology used to describe electromagnetic radiation, starting from definition of terms used in describing electromagnetic radiation, blackbody radiation, solar spectrum, and radiometric units (radiance, irradiance, etc.).

This chapter aims to describe the basic anatomy of common groups of higher plants. including the tissues of leaves, their main cell types, and the biochemical constituents that characterize their functional properties. It should provide enough detail on the main construction of plant leaves and how major groups of plants are distinguished based on anatomy, morphology, cell type distribution, and biochemistry. The three-dimensional structure and arrangement of the organelles, cells, and tissues in the leaf are critical to understanding the photon transport in leaf tissue and how these traits relate to the physiological processes of photosynthesis, respiration, and transpiration.

Leaf directional-hemispherical or bidirectional reflectance and transmittance spectra can directly feed canopy reflectance models as input parameters, but the measurement of these properties is not an end in itself. A large number of spectral analysis methods have been proposed to detect plant biochemistry, ranging from simple band ratios to inversion of radiative transfer methods of varying complexity. The estimation of leaf biophysical parameters is often developed in parallel with the estimation of canopy characteristics, using the same methods as detailed below.