Particle beam microscopy uses a scanning beam of charged particles to create images of samples, and the quality of image reconstruction suffers when this beam current varies over time. Neither conventional reconstruction methods nor time-resolved sensing acknowledges beam current variation, although through sensitivity analysis, my project demonstrates that when the beam current variation is appreciable, time-resolved sensing has significant improvement compared to conventional methods in terms of image reconstruction quality, specifically mean-squared error (MSE). To more actively combat this unknown varying beam current's effects, my project further focuses on designing an algorithm that uses time-resolved sensing for even better image reconstruction quality in the presence of beam current variation. This algorithm works by simultaneously estimating the unknown beam current variation in addition to the underlying image, offering an alternative to more conventional methods, which exploit statistical assumptions of the image content without explicitly estimating the beam current. Using a concept of excess MSE due to beam current variation, this algorithm provides a factor of 7 improvement on average, which could lead to less expensive equipment in the future. Beyond improving the image estimation, this algorithm offers a novel estimation of the beam current, potentially providing more control in manufacturing and fabrication processes.