Image simulation for biological microscopy : microlith

Author Posting. © Optical Society, 2014. This article is posted here by permission of Optical Society for personal use, not for redistribution. The definitive version was published in Biomedical Optics Express 5 (2014): 1822-1838, doi:10.1364/BOE.5.001822.
Image simulation remains under-exploited for the most widely used biological phase microscopy methods, because of difficulties in simulating partially coherent illumination. We describe an open-source toolbox, microlith (https://code.google.com/p/microlith), which accurately predicts three-dimensional images of a thin specimen observed with any partially coherent imaging system, as well as images of coherently illuminated and self-luminous incoherent specimens. Its accuracy is demonstrated by comparing simulated and experimental bright-field and dark-field images of well-characterized amplitude and phase targets, respectively. The comparison provides new insights about the sensitivity of the dark-field microscope to mass distributions in isolated or periodic specimens at the length-scale of 10nm. Based on predictions using microlith, we propose a novel approach for detecting nanoscale structural changes in a beating axoneme using a dark-field microscope.
This study was funded by National Institutes of Health grant RO1 EB002583