The ability to tune an imaging system to be optimal for a specific task is an essential component of image quality. This article discusses the ability to tune the noise-equivalent quanta ͑NEQ͒ of cone-beam computed tomography ͑CBCT͒ by managing noise aliasing through binning of data at different points in the reconstruction cascade. The noise power spectrum, modulation transfer function, and NEQ for CBCT are calculated using cascaded systems analysis. Binning is treated as a modular process, insertable between any two stages ͑in both the 2D projection domain and in the 3D reconstruction domain͒, consisting of the application of an aperture, followed by the resampling of data ͑which introduces noise aliasing͒. Several conditions were examined to demonstrate the validity of the model and to describe the effect on the image quality of some common reconstruction and visualization techniques. It was found that when downsampling data for increased reconstruction speed, binning in 2D results in a superior low-frequency NEQ, while binning in 3D results in a superior high-frequency NEQ. Furthermore, visualization procedures such as slice averaging were found not to degrade the NEQ provided the sampling interval is unchanged. Finally methods for reducing noise aliasing by oversampling are examined, and a method to eliminate noise aliasing without increasing reconstruction time is proposed. These results demonstrate the ease with which the NEQ of CBCT can be modified and thus optimized for specific tasks and show how such analysis can be used to improve image quality.