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microlith: Image simulation for microscopy and lithography systems

microlith (as defined in dictionary): a small stone tool that is sufficiently worked so as to be distinguishable from workshop waste or accidents.

microlith (this simulation package): a small simulation tool that is sufficiently accurate so as to allow investigation of image formation in microscopy and lithography systems.

This MATLAB package provides accurate algorithms for simulation of images produced by coherent, incoherent (fluorescence), and partially coherent microscopy methods. Arial images projected by optical lithography systems can also be simulated. If you are new to image simulation or partially coherent image simulation, please start by reading this tutorial and user guide.

The current source code and executable use cases can be downloaded here.

An in-depth discussion of accuracy of microlith and some intriguing results about dark-field microscopy can be found in our paper: Shalin B. Mehta and Rudolf Oldenbourg, “Image simulation for biological microscopy: microlith,” Biomedical Optics Express, Vol. 5, Issue 6, pp. 1822-1838 (2014).

If microlith proves useful in your research, please cite above paper.

Note: Future updates to microlith will be posted on this page, instead of now defunct google code site or github site.

Use cases:

  1. Which partially coherent model for differential interference contrast is correct?
  2. Through focus image of the MBL/NNF Siemens star target in a wide-field microscope.
  3. Image of the MBL/NNF Simens star target in the dark-field microscope.
  4. Three-dimensional amplitude point spread function, coherent transfer function, intensity point spread function, and optical transfer function for wide-field imaging.
  5. Simulation of spherical aberration and astigmatism in wide-field imaging.
  6. Radiometric consistency, i.e., effect of aperture size on the intensity.
  7. Comparison of images simulated using microlith with analytical images of simple objects.
  8. Fast computation of 1D specimens.