We introduce a new method, rooted in estimation theory, to detect individual atoms in site-resolved images of microtrap arrays, such as optical lattices or optical tweezer arrays. Using labeled test images, we demonstrate drastic improvement of the detection accuracy, compared with the popular method based on Wiener deconvolution, when the intersite distance is comparable with the radius of the point spread function. The runtime of our method scales approximately linearly with the number of sites, and remains well below 100 ms for an array of $100\times 100$ sites on a desktop computer. It is therefore fully compatible with a real-time usage. Finally, we propose a rigorous definition for the signal-to-noise ratio of the problem and show that it can be used as a predictor for the detection error rate. Our work opens the prospect for future experiments with increased array sizes or reduced intersite distances.

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• Atom & ion cooling
• Cold gases in optical lattices
• Imaging & optical processing
• Optical lattices & traps
• Quantum engineering
• Quantum parameter estimation
• Quantum simulation