Systems and methods for user control over the acquisition, processing, and presentation of medical data are provided. Some embodiments are particularly directed to controlling the display of multi-modality medical data in a multi-modality processing system. In one embodiment, a medical imaging system receives a set of medical data including a first data subset collected using a first sensor and a second data subset collected using a second sensor, where the first sensor and the second sensor are different. A display attribute to be applied to the first data subset independent of the second data subset is received. An instruction is generated that affects the processing of the first data subset based on the display attribute. The first data subset is processed according to the instruction. The processed first data subset is displayed according to the display attribute, and the second data subset is displayed independent of the display attribute.
