Fluorescence microscopies are widely used to study the structure and dynamics of live cells and its components. Although super-resolution microscopy has broken past the Abbe’s diffraction limit, atomistic resolution still remains out of reach. In order to study bio-chemical process at atomic/molecular resolution, molecular simulations are often used, however direct comparison with experiments is not always feasible. In this work, we developed an open-source software “siliscopy” that performs a novel in-silico widefield microscopy on molecular simulations. This adds a new avenue for direct comparison between simulations and experiments. Specifically, atomic/molecular positions are read from simulations and a microscopy image is generated using a point spread function. Images can be generated with different optical axis, object focal plane, exposure time, color combinations, full-width-at-half-maximum, brightness, and amount of out-of-focus fluorescence. A simple change in these setup parameters can generate images that resemble confocal, light-sheet, two-photon, super-resolution microscopy, etc. That is, it not only lays the foundation stones for other in-silico microscopy techniques but can also approximately emulate them. There are several other applications of this tool, such as verification of deconvolution algorithms, error analysis of properties determined from microscopy images, development of new image analysis techniques, use as a standalone visualisation technique for simulations at different scales, etc. While developing the in-silico microscopy, a new color mixing scheme is proposed that can mix any color (not limited to red, green, blue) assigned to fluorophores for generating the colocalized color. The ability to mix any color is significant because it can generate microscopy images with high color contrast and also images that are color-blind friendly. This new color mixing scheme is not limited to the in-silico microscopy and can be readily employed in experimental microscopies.

Siliscopy: Bridging molecular simulations and fluorescence microscopy

ACS Fall 2021

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