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Biomedical Optics Express

Biomedical Optics Express

  • Editor: Joseph A. Izatt
  • Vol. 5, Iss. 6 — Jun. 1, 2014
  • pp: 1822–1838

Image simulation for biological microscopy: microlith

Shalin B. Mehta and Rudolf Oldenbourg  »View Author Affiliations

Biomedical Optics Express, Vol. 5, Issue 6, pp. 1822-1838 (2014)

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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.

© 2014 Optical Society of America

OCIS Codes
(110.2990) Imaging systems : Image formation theory
(110.4980) Imaging systems : Partial coherence in imaging
(170.0180) Medical optics and biotechnology : Microscopy
(170.3880) Medical optics and biotechnology : Medical and biological imaging
(350.5030) Other areas of optics : Phase

ToC Category:

Original Manuscript: January 31, 2014
Revised Manuscript: March 26, 2014
Manuscript Accepted: April 18, 2014
Published: May 13, 2014

Shalin B. Mehta and Rudolf Oldenbourg, "Image simulation for biological microscopy: microlith," Biomed. Opt. Express 5, 1822-1838 (2014)

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