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Modern science is dependent on imaging on the nanoscale, often achieved through processes that detect secondary electrons created by a highly focused incident charged particle beam. Multiple types of measurement noise limit the ultimate trade-off between the image quality and the incident particle dose, which can preclude useful imaging of dose-sensitive samples. Existing methods to improve image quality do not fundamentally mitigate the noise sources. Furthermore, barriers to assigning a physically meaningful scale make the images qualitative. Here, we introduce ion count-aided microscopy (ICAM), which is a quantitative imaging technique that uses statistically principled estimation of the secondary electron yield. With a readily implemented change in data collection, ICAM substantially reduces source shot noise. In helium ion microscopy, we demonstrate 3 $\times$dose reduction and a good match between these empirical results and theoretical performance predictions. ICAM facilitates imaging of fragile samples and may make imaging with heavier particles more attractive. 

Most research on deep learning algorithms for image denoising has focused on signal-independent additive noise. Focused ion beam (FIB) microscopy with direct secondary electron detection has an unusual Neyman Type A (compound Poisson) measurement model, and sample damage poses fundamental challenges in obtaining training data. Model-based estimation is difficult and ineffective because of the nonconvexity of the negative log likelihood. In this paper, we develop deep learning-based denoising methods for FIB micrographs using synthetic training data generated from natural images. To the best of our knowledge, this is the first attempt in the literature to solve this problem with deep learning. Our results show that the proposed methods slightly outperform a total variation-regularized model-based method that requires time-resolved measurements that are not conventionally available. Improvements over methods using conventional measurements and less accurate noise modeling are dramatic - around 10 dB in peak signal-to-noise ratio.