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Today there is a rapid development taking place in phenotyping of plants using non-destructive image based machine vision techniques. Machine vision based plant phenotyping ranges from single plant trait estimation to broad assessment of crop canopy for thousands of plants in the field. Plant phenotyping systems either use single imaging method or integrative approach signifying simultaneous use of some of the imaging techniques like visible red, green and blue (RGB) imaging, thermal imaging, chlorophyll fluorescence imaging (CFIM), hyperspectral imaging, 3-dimensional (3-D) imaging or high resolution volumetric imaging. This paper provides an overview of imaging techniques and their applications in the field of plant phenotyping. This paper presents a comprehensive survey on recent machine vision methods for plant trait estimation and classification. In this paper, information about publicly available datasets is provided for uniform comparison among the state-of-the-art phenotyping methods. This paper also presents future research directions related to the use of deep learning based machine vision algorithms for structural (2-D and 3-D), physiological and temporal trait estimation, and classification studies in plants.