This thesis presents research associated to phenotyping of plants by applying informatics techniques which includes databases, web technologies, image processing and feature measurements of 2D and 3D images. The thesis presents two enabling bioinformatics tools related by a shared set of research objectives and distinct by the nature of their applications. The first project called ClearedLeavesDB, is a common platform for plant biologists to share data and metadata about cleared leaf images. This project resulted in an online interactive database of cleared leaf images. The second project called Digital Imaging of Root Traits (DIRT), is an application to store, manage, share and process root images as well as analyze root image traits with respect to different experiments. This application is deployed on iPlant's cyber-infrastructure and currently supports management of 2D root images and high-throughput processing and structural descriptor/trait estimation from root images. The application enables storage, management and sharing heterogeneous image data and metadata including dynamic environmental and descriptor data. In the final part of the thesis, I describe ongoing challenges in developing new methods to measure global and local descriptors from reconstructed 3D root images.