Meeting Experiments at the Diffraction Barrier with In Silico Fluorescence Microscopy

Fluorescence microscopy allows the
visualization of live cells
and their components, but even with advances in super-resolution microscopy,
atomic resolution remains unattainable. Contrarily, molecular simulations
can access atomic resolution, but comparison with experimental microscopy
images has not been possible. In this work, a novel in silico fluorescence
microscopy technique is proposed, which uses the physics-based point
spread function to generate images from molecular simulations. The
method allows the resolution of molecular simulation to be reduced
and made comparable to experiments, enabling direct cross-comparison
between in silico and experimental images. Simulation of a DNA-polyethylenimine
gene delivery system is used to demonstrate the production of in silico
images with a different optical axis, object focal planes, exposure
time, color combinations, resolution, brightness, and amount of out-of-focus
fluorescence. These images bridge the distinct worlds of molecular
simulation and experimental fluorescence microscopy by generating
new knowledge from direct cross-validation, determining equivalence
of properties extracted from molecular simulation and experimental
images, assessing and developing algorithms for experimental image
analysis, etc. The technique presented here can also be used as a
standalone visualization tool for molecular simulation and lays the
foundation for other in silico microscopy methods.