JIC (John Innes Centre) and TGAC (The Genome Analysis Centre) are establishing an automated field phenotyping platform in Norwich UK. In order to develop high-throughput bioimage analysis pipelines to analyse plant growth data based on high performance computing infrastructures, we are developing and translating our algorithms from Matlab-based codes to scipy software solutions. During this period of time, we have been heavily utilise scikit-image and scikit-learn libraries to speed up the implementation, which had generated convincing results for plant development studies.