In this paper, we develop the mathematical framework for filtering problems arising from biophysical applications where data is collected from confocal laser scanning microscopy recordings of the space-time evolution of intracellular wave dynamics of biophysical quantities. In these applications, signals are described by stochastic partial differential equations (SPDEs) and observations can be modelled as functionals of marked point processes whose intensities depend on the underlying signal. We derive both the unnormalized and normalized filtering equations for these systems, demonstrate the asymptotic consistency and approximations of finite dimensional observation schemes respectively partial observations. Our theoretical results are validated through extensive simulations using synthetic and real data. These findings contribute to a deeper understanding of filtering with point process observations and provide a robust framework for future research in this area.