Transparent monolithic aerogels based on silica, the bioderived polymer chitosan, and coordinated ions have been employed to serve as a three-dimensional scaffold decorated with Au, Pt and Pd ions. The coordination states of metal ions and the initial gel in one or several of the ions are established in the thickness of the monolith that is produced by supercritical CO2 extraction to form the aerogels. Also in this work, it has been found that the Au(III) aerogels can be imaged photolytically in the two planar dimensions. The spatially controlled photolysis produces nanoparticles, (Au)n in the range of from 5 to 85 nm, for example, that constitute two dimensionally imaged arrays whose volumetric concentration also varies in the third dimension. These images microarrays of nanoparticles provide a basis for localization and detection of thiols, disulfides, amino acids and protein molecules. The formation of these arrays, including the dependence of their properties on light intensity, frequency and exposure, and distribution of target molecules and ions in the initial aerogel is presented.