Two possible system integration approaches for portable real time cytometry in microfluidic applications are discussed. An ocular mounted linear CMOS image sensor configured for real time detection of particles being transported in microfluidic channels is first described. This system delivers cytometry functionality utilizing standard microfluidic chips and conventional optics. While this approach affords a certain ease of integration, one significant drawback is the singular field of view onto the microfluidic substrate and the reliance on conventional microscopy. However, the microscopy resolution makes possible a simple device capable of determining precise position, size and trajectory information on a per particle basis. A second architecture comprises flip-chip integration of a custom CMOS active pixel sensor aboard a custom microfluidic glass substrate. At the expense of optical resolution, the near field sensor topology obviates the need for conventional microscopy, affords simultaneous multi-channel sensing and takes strides towards cost effective micro total analysis system (uTAS) deployment. The two platforms share a common microcontroller for processing, control and display as well as a unified host-side application programming interface; an approach which will enable side-by-side comparison of the two hardware architectures in real time. The common user interface, a platform independent .NET application, deploys to both desktop and compact framework pocket PC platforms.