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We discuss the determination of energy region (bin) boundaries and decision metrics for gamma-ray spectra, acquired using a mid-resolution detector, that are useful for detecting illicit sources at low total counts. The bins are designed to produce the lowest minimum detectable counts using a spectral comparison ratio technique at a given false-positive rate for a specified population of benign-source spectra. Spectra from the benign source population consist of observations taken by a detector on a moving vehicle, as would be obtained during a search for a missing or hidden source. Raw counts in bins are transformed into a vector of background-corrected count differences. Bin boundaries are determined to yield large values of a standardized length of this vector for benign-plus-benchmark sources by applying an optimization technique. The objective function includes penalties for overlap with the spectral features of naturally occurring radioactive materials. We compare estimated minimum detectable count values for such bins applied to depleted uranium and barium-133 sources with those based on gross counting, and we examine the effect of nuisance potassium-, radium- and thorium-dominated sources. Using this methodology, we demonstrate that energy bins may be chosen to be sensitive to special nuclear materials, improving the likelihood of detection in low-count or masked-source searches.