title: Image simulation for biological microscopy: microlith.
abstract: 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.
authors.affiliation: Cellular Dynamics Program, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA.
authors.forename: Shalin B
authors.initials: SB
authors.lastname: Mehta
authors.affiliation: Cellular Dynamics Program, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA ; Physics Department, Brown University, Providence RI 02912, USA.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Oldenbourg
keywords: (110.2990) Image formation theory; (110.4980) Partial coherence in imaging; (170.0180) Microscopy; (170.3880) Medical and biological imaging; (350.5030) Phase