Most hospitals today are dealing with the big data problem, as they generate and store petabytes of patient records most of which in form of medical imaging, such as pathological images, CT scans and X-rays in their datacenters. Analyzing such large amounts of biomedical imaging data to enable discovery and guide physicians in personalized care is becoming an important focus of data mining and machine learning algorithms developed for biomedical Informatics (BMI). Algorithms that are developed for BMI heavily rely on complex and computationally intensive machine learning and data mining methods to learn from large data. The high processing demand of big biomedical imaging data has given rise to their implementation in high-end server platforms running software ecosystems that are optimized for dealing with large amount of data including Apache Hadoop and Apache Spark. However, efficient processing of such large amount of imaging data running computational intensive learning methods is becoming a challenging problem using state-of-the-art high performance computing server architectures. To address this challenge, in this paper, we introduce a scalable and efficient hardware acceleration method using low cost commodity FPGAs that is interfaced with a server architecture through a high speed interface. In this work we present a full end-to-end implementation of big data image processing and machine learning applications in a heterogeneous CPU+FPGA architecture. We develop the MapReduce implementation of K-means and Laplacian Filtering in Hadoop Streaming environment that allows developing mapper functions in non-Java based languages suited for interfacing with FPGA-based hardware accelerating environment. We accelerate the mapper functions through hardware+software (HW+SW) co-design. We do a full implementation of the HW+SW mappers on the Zynq FPGA platform. The results show promising kernel speedup of up to 27× for large image data sets. This translate to 7.8× and 1.8× speedup in an end-to-end Hadoop MapReduce implementation of K-mean s and Laplacian Filtering algorithm, respectively.