One aspect of the invention relates to methods for analysis of phenotypic parameters or a trait in a plant comprising using a digital analyzing device, comparing phenotypic parameters or traits between plants in a population, and selecting plants with a selected parameter or trait. The invention also relates to an apparatus suitable for use in conjunction with a container in which one or more plants is growing and having associated with it a device which comprises a unique identifier.The apparatus may comprise a transporter system for moving the containers, and may comprise a workstation at which an operation, such as imaging, is performed on plants in the containers. The operation may be performed automatically, and/or at a high throughput rate. The unique identifier of each container and the information derived from each plant may be linked to this identifier via a computer, and may be stored in a digital database.