Stomatal morphology is a key phenotypic trait for plants' response analysis under various environmental stresses (e.g. Drought, salinity etc.). Stomata exhibit diverse characteristics with respect to orientation, size, shape and varying degree of papillae occlusion. Thus, the biologists currently rely on manual or semi-automatic approaches to accurately compute its morphological traits based on scanning electron microscopic (SEM) images of leaf surface. In contrast to these subjective and low-throughput methods, we propose a novel automated framework for stomata quantification. It is realized based on a hybrid approach where the candidate stomata region is first detected by a convolutional neural network (CNN) and the occlusion is dealt with an inpainting algorithm. In addition, we propose stomata segmentation based quantification framework to solve the problem of shape, scale and occlusion in an end-to-end manner. The performance of the proposed automated frameworks is evaluated by comparing the derived traits with manually computed morphological traits of stomata. With no prior information about its size and location, the hybrid and end-to-end machine learning frameworks shows a correlation of 0.94 and 0.93, respectively on rice stomata images. Furthermore, they successfully enable wheat stomata quantification showing generalizability in terms of cultivars. © 2018 IEEE.