  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, including coherently illuminated and incoherent,
self-luminous 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.
