We propose a light-field microscopy display system that provides improved image quality and realistic three-dimensional (3D) measurement information. Our approach acquires both high-resolution two-dimensional (2D) and light-field images of the specimen sequentially. We put forward a matting Laplacian-based depth estimation algorithm to obtain nearly realistic 3D surface data, allowing the calculation of depth data, which is relatively close to the actual surface, and measurement information from the light-field images of specimens. High-reliability area data of the focus measure map and spatial affinity information of the matting Laplacian are used to estimate nearly realistic depths. This process represents a reference value for the light-field microscopy depth range that was not previously available. A 3D model is regenerated by combining the depth data and the high-resolution 2D image. The element image array is rendered through a simplified direction-reversal calculation method, which depends on user interaction from the 3D model and is displayed on the 3D display device. We confirm that the proposed system increases the accuracy of depth estimation and measurement and improves the quality of visualization and 3D display images.