Three dimensional reconstruction from optical microscopic plant slice images

Three dimensional (3D) visualization is efficient in representing the inside structure. Here we present a method for reconstructing plant stalk section slices to form a 3D volume to visualize the canaliculus inside the stalk of plant. In this preliminary work, one stalk from a study of heliconia plant was cut into sections which were photographed. A key technical problem in 3D reconstruction is registration. We explored a registration method based on the intensity of the image and compared with the traditional feature based methods. The mean square distance of the intensity was used as the similarity measure to search for the optimal parameters of rigid transformation and a multi-resolution approach was adopted to improve the accuracy and computation time. The between slice registration was then propagated through other slices. Slices were first registered, followed by building up the contour correspondence of stalks. We showed results of registration and the final 3D modal, which were encouraging.