  Using bioimaging technology, biologists have attempted to identify and
document analytical interpretations that underlie biological phenomena in
biological cells. Theoretical biology aims at distilling those interpretations
into knowledge in the mathematical form of biochemical reaction networks and
understanding how higher level functions emerge from the combined action of
biomolecules. However, there still remain formidable challenges in bridging the
gap between bioimaging and mathematical modeling. Generally, measurements using
fluorescence microscopy systems are influenced by systematic effects that arise
from stochastic nature of biological cells, the imaging apparatus, and optical
physics. Such systematic effects are always present in all bioimaging systems
and hinder quantitative comparison between the cell model and bioimages.
Computational tools for such a comparison are still unavailable. Thus, in this
work, we present a computational framework for handling the parameters of the
cell models and the optical physics governing bioimaging systems. Simulation
using this framework can generate digital images of cell simulation results
after accounting for the systematic effects. We then demonstrate that such a
framework enables comparison at the level of photon-counting units.
