Multi-leaf alignment from fluorescence plant images

In this paper, we propose a multi-leaf alignment framework based on Chamfer matching to study the problem of leaf alignment from fluorescence images of plants, which will provide a leaf-level analysis of photosynthetic activities. Different from the naive procedure of aligning leaves iteratively using the Chamfer distance, the new algorithm aims to find the best alignment of multiple leaves simultaneously in an input image. We formulate an optimization problem of an objective function with three terms: the average of chamfer distances of aligned leaves, the number of leaves, and the difference between the synthesized mask by the leaf candidates and the original image mask. Gradient descent is used to minimize our objective function. A quantitative evaluation framework is also formulated to test the performance of our algorithm. Experimental results show that the proposed multi-leaf alignment optimization performs substantially better than the baseline of the Chamfer matching algorithm in terms of both accuracy and efficiency.