Systems, methods, and apparatus for large scale, high throughput phenotyping of items including plants to derive environment/genetics correlations based on controlled variation of environment. Spatial and temporal resolution is improved by an integrated system that can use space efficiently yet concurrently process a large number of replicates but in varying environments. This is accomplished by using an array of miniature greenhouses, each in communication with one or more generators or regulators of an environmental factor that can be independently supplied and controlled to each miniature greenhouse. The controller also controls acquisition of data from each greenhouse as well as processing of that data into phenomic/genomic correlations.
