Phenotyping plays a key role in plant breeding, and image-based high throughput phenotyping (HTP) has been widely adopted to expedite a breeding pipeline with advantages of large coverage and image processing for morphological and spectral signature of the plant canopy. To meet the demand of a cost-effective and globally consistent HTP data processing pipeline, customized software was developed to process field data and images to extract plot-level metrics of plant phenotypes. Graphic user interface allows the user to easily perform image processing, data visualization and batch processing. The algorithm includes GIS interface for field and plot boundaries, geometric calibration to align the data with the plots, and spectral calibration to accommodate ambient illumination change. Ground registration and spectral analysis in plant-level resolution are delivered and validated with ground and aerial truthing.