An important topic in medical research is the process of improving the images obtained from medical devices. As a consequence, there is also a need to improve medical image resolution and analysis. Another issue in this field is the large amount of stored medical data [16]. Human brain databases at medical institutes, for example, can accumulate tens of Terabytes of data per year. In this paper, we propose a novel medical image format representation based on multiple data structures that improve the information maintained in the medical images. The new representation keeps additional metadata information, such as the image class or tags for the objects found in the image. We defined our own ontology to help us classify the objects found in medical images using a multilayer neural network. As we generally deal with large data sets, we used the MapReduce paradigm in the Cloud environment to speed up the image processing. To optimize the transfer between Cloud nodes and to reduce the preprocessing time, we also propose a data compression method based on deduplication. We test our solution for image representation and efficient data transfer in a multisite cloud environment. Our proposed solution optimizes the data transfer with a time improvement of 27% on average.