To get a more complete picture of the role of mitochondria in disease it is important to be able to both assess function in the intact system (in vivo) and dissect specific aspects of mitochondrial function without the complications of other cell systems (ex vivo). The tools of magnetic resonance spectroscopy and imaging and optical spectroscopy commonly associated with radiology provide a unique set of tools to measure in vivo mitochondrial function in humans and animal models. This metabolic spectroscopy approach allows us to measure mitochondrial ATP production, coupling, metabolite levels, resting metabolism (Amara et al., 2008; Campbell et al., 2015, see figure below) as well as muscle structural characteristics with MRI.  A main strategy in the lab is to integrate in vivo metabolic spectroscopy with ex vivo methods that allow us to dissect detailed structure-function relationships at the organelle and protein levels and evaluate mitochondrial function in skeletal muscle. We have found that these two approaches often provide different perspectives on the nature and extent of dysfunction. We are continually modifying both hardware and experimental protocols to make testing mitochondria in vivo more informative and easier to perform.