Software

microlith: Image simulation for microscopy and lithography systems.

I have been using image simulation to evaluate design of microscopes, to teach image formation, and to inform analysis algorithms of acquired data. The design and performance of the algorithm is described in Mehta and Oldenbourg, "Image simulation for biological microscopy: microlith", Biomedical Optics Express, Vol. 5, Issue 6, pp. 1822-1838 (2014).

OpenPolScope: Discover the order in living things

I contributed to conception and implementation of OpenPolScope resource at Marine Biological Laboratory in the laboratory of Rudolf Oldenbourg. It provides free Micro-Manager based software for acquisition and analysis of polarized light microscopy data.

Utility functions on Mathworks file exchange.
  • opticalLowpassInterpolation: Filter noise beyond the optical cutoff of the microscope and interpolate microscopy images without altering physical intensity distribution
  • imagecat: Display a catalog of images on individual axes and optionally link them. This is a handy function for visualizing various steps of image analysis pipeline such that the zoom and pan of images are synced.