Plant phenotyping research plays a key role in providing tools to identify productive species and sustainable practices for increasingly resource-limited environments. The growing interests of stakeholders and recent technological advances have fostered the development of research infrastructures to support multidisciplinary and high throughput research. In this paper, we present an integrated research infrastructure for plant phenotyping that includes various instruments providing complementary perspectives from physiological to metabolomics scales. This high throughput plant phenotyping infrastructure provides extensive multi-scale datasets using remote sensing sensors mounted on different platforms. Alongside these sensors, the necessary computational resources to process and analyze complex datasets have been constructed to share pipelines and results over the cloud.