Code and data for online beam current estimation in particle beam microscopy

In conventional particle beam microscopy, knowledge of the beam current is essential for accurate micrograph formation and sample milling. This generally necessitates offline calibration of the instrument. In this work, we establish that beam current can be estimated online, from the same secondary electron count data that is used to form micrographs. Our methods depend on the recently introduced time-resolved measurement concept, which combines multiple short measurements at a single pixel and has previously been shown to partially mitigate the effect of beam current variation on micrograph accuracy. We analyze the problem of jointly estimating beam current and secondary electron yield using the Cramer-Rao bound. Joint estimators operating at a single pixel and estimators that exploit models for inter-pixel correlation and Markov beam current variation are proposed and tested on synthetic microscopy data. Our estimates of secondary electron yield that incorporate explicit beam current estimation beat state-of-the-art methods, resulting in micrograph accuracy nearly indistinguishable from what is obtained with perfect beam current knowledge. Our novel beam current estimation could help improve milling outcomes, prevent sample damage, and enable online instrument diagnostics. This code reproduces results from paper Figures 6, 7, and 12.