Extended depth from focus reconstruction using NIH ImageJ plugins: Quality and resolution of elevation maps

In this work, NIH ImageJ plugins for extended depth‐from‐focus reconstructions (EDFR) based on spatial domain operations were compared and tested for usage optimization. Also, some preprocessing solutions for light microscopy image stacks were evaluated, suggesting a general routine for the ImageJ user to get reliable elevation maps from grayscale image stacks. Two reflected light microscope image stacks were used to test the EDFR plugins: one bright‐field image stack for the fracture of carbon‐epoxy composite and its darkfield corresponding stack at same (x,y,z) spatial coordinates. Image quality analysis consisted of the comparison of signal‐to‐noise ratio and resolution parameters with the consistence of elevation maps, based on roughness and fractal measurements. Darkfield illumination contributed to enhance the homogeneity of images in stack and resulting height maps, reducing the influence of digital image processing choices on the dispersion of topographic measurements. The subtract background filter, as a preprocessing tool, contributed to produce sharper focused images. In general, the increasing of kernel size for EDFR spatial domain‐based solutions will produce smooth height maps. Finally, this work has the main objective to establish suitable guidelines to generate elevation maps by light microscopy. Microsc. Res. Tech. 2012. © 2012 Wiley Periodicals, Inc.     

MRT letter: A total variation based method for 3D shape recovery of microscopic objects through image focus

Generally, shape from focus methods use a single focus measure to compute focus quality and to obtain an initial depth map of an object. However, different focus measures perform differently in diverse conditions. Therefore, it is hard to get accurate 3D shape based on a single focus measure. In this article, we propose a total variation based method for recovering 3D shape of an object by combining multiple depth hypothesis obtained through different focus measures. Improved performance of the proposed method is evaluated by conducting several experiments using images of synthetic and real microscopic objects. Comparative analysis demonstrates the effectiveness of the proposed approach. Microsc. Res. Tech. 76:877–881, 2013. © 2013 Wiley Periodicals, Inc.     

A novel method for shape from focus in microscopy using Bezier surface approximation

In this article, we introduce a novel shape from focus method to compute 3D shape of microscopic objects, based on modified‐pixel intensities and Bezier surface approximations. A new and simple but effective focus measure is proposed. In our focus measure, the original intensities of a sequence of small neighborhood are modified by subtracting the maximum of the values of first and last frames. An initial depth map is calculated by finding the maximum of the pixel's focused energy and its corresponding frame number. Missing information between two consecutive frames, false depth detection, and enhancement of noise related intensities may provide inaccurate depth map. To overcome these problems and to produce an accurate depth map, we proposed Bezier surface approximation. The proposed method is tested using synthetic and real image sequences. The comparative analysis demonstrates the effectiveness of the proposed method. Microsc. Res. Tech., 2010. © 2009 Wiley‐Liss, Inc.