There is growing awareness that weakness of muscle is a significant biomedical health issue associated with many different chronic diseases and aging. There are a variety of different diseases that affect muscle, including muscular dystrophy, fibromyalgia, cerebral palsy, amyotrophic lateral sclerosis, and myasthenia gravis, each of which carries its own unique set of symptoms, accompanied by a myriad of genetic and molecular abnormalities. There is agreement within the basic research and clinical communities that important morphological characteristics of muscle fibers, such as fiber cross sectional area, fiber type, the number and position of myonuclei, cellular infiltration, and fibrosis are among many critical factors that determine the health and functionality of the muscle. Until now, the imaging equipment available is relatively low throughput and the quantification is still largely based on manual or, at best, semi-automatic methods that require extensive human intervention. In Phase I, CytoInformatics LLC has developed a software called CytoQuant, which can accurately perform automatic segmentation and provide accurate boundaries of each muscle fiber for a cropped image patch. The goal of CytoInformatics LLC in Phase II is to 1) deliver the first version of the CytoQuant software to the market, 2) develop the second version of CytoQuant by continuously improving its performance, especially in handling large scale, whole slide images, and also 3) develop an integrated multiplexing imaging hardware and analysis software framework as a seamless solution for high throughput, automated image analysis of muscle specimens. After careful investigation in Phase I (please refer to the details in business plan), we conclude that this integrated software/hardware platform with cutting-edge technologies in advanced imaging, large scale machine learning, and big data is commercially attractive to the entire muscle community including research institutes, hospitals, and pharmaceutical and athletic companies, demonstrated by strong enthusiasm among end users and many supporting letters. The specific aims are: 1) Deliver the first version of CytoQuant developed in Phase I to the market, continue to develop the second version of CytoQuant, which will focus on improving the robustness and speed in handling whole slide images; 2) Develop an integrated platform that provides unified imaging hardware and image analysis software to handle whole slide images labeled with multiple bio-relevant markers. This unified whole-slide based software and hardware solution will deliver an efficient and specialized imaging platform that seamlessly integrates with a high throughput, multi-marker, and automatic image analysis software specifically designed for muscle.