Undergraduate Physics Honors Project:
Generating a Three-Dimensional Lattice of Photonic Spheres
to Track Fluorescently Labelled Chromatin

For the final year and a half of my undergraduate degree, I worked on developing a method for using a spatial light modulator (SLM) to create a three dimensional lattice of regularly spaced photonic spheres. In order to do this, we relied upon applying a pattern to the SLM generated by a collaborator via advanced computational optics. To work as intended, this pattern required a "flat" wavefront. By using a laser as our lightsource, we are able to begin with mostly coherent light. A spatial light modulator is a device which uses technology similar to that found in an LCD screen to apply voltage to various pixels, changing their index of refraction. If one can determine the phase pattern of an incoming light source, once can theoretically apply corrections to synchronize the phases of the beam to correct for the aberrations introduced by a non-ideal light sources and the optical train. We then tested various methods for flattening our wavefront, optimizing the phase corrections before adding the lattice-generating pattern. The method we focused on most was that of Dhalokia, which exploits the linearity of the system to optimize hundreds or even thousands of zones on the SLM individually before then applying the optimal pattern to each zone to create a full phase-correction mask. 

Figures 1-5 (left to right, top to bottom) below document the basic procedure. First test multiple phase patters (1), then apply those patterns simultaneously (2), testing the outcome by focusing the corrected wavefront (3). Optimally flattened wavefronts produce more regular (Gaussian) and smaller focal spots. We then add the 3-D lattice generation pattern of Dr. Zhu (4) atop our correction mask to produce a 3-D lattice in the focal plane (5, middle plane of pattern pictured).  For more detailed information, please read my full thesis, which is available as a PDF here. Additionally, for the more casual reader, a slideshow which I presented at my thesis defense gives a detailed summary of the project here.