Beads convolution/deconvolution simulation

Simulation of beads acquired with a 100x / 1.4 NA objective, the pixel size is 65 nm and the Z spacing is 200 nm. This is a simple "pixelated" simulation. Beads were 3 to 4 voxels laterally and 1 voxel axially. They were convolved with a PSF generated using the above parameters and assuming an embedding media of RI=1.4 and a depth below coverslip of 1 micron. Simulated phantom was convolved with PSF to produce a simluated "image", then deconvolved with 200 iterations of noncirculant Richardson Lucy. Low level code was written in Java (deconvolution, psf generation). High level code was written in Jython and can be found here - https://github.com/bnorthan/projects/tree/master/Scripts/Jython.