Current uncertainties in the role of aerosols and clouds in the Earth's climate system limit our abilities to model the climate system and predict climate change. These limitations are due primarily to difficulties of adequately measuring aerosols and clouds on a global scale. The A-train satellites (Aqua, CALIPSO, CloudSat, PARASOL, and Aura) will provide an unprecedented opportunity to address these uncertainties. The various active and passive sensors of the A-train will use a variety of measurement techniques to provide comprehensive observations of the multi-dimensional properties of clouds and aerosols. However, to fully achieve the potential of this ensemble requires a robust data analysis framework to optimally and efficiently map these individual measurements into a comprehensive set of cloud and aerosol physical properties. In this work we introduce the Multi-Instrument Data Analysis and Synthesis (MIDAS) project, whose goal is to develop a suite of physically sound and computationally efficient algorithms that will combine active and passive remote sensing data in order to produce improved assessments of aerosol and cloud radiative and microphysical properties. These algorithms include (a) the development of an intelligent feature detection algorithm that combines inputs from both active and passive sensors, and (b) identifying recognizable multi-instrument signatures related to aerosol and cloud type derived from clusters of image pixels and the associated vertical profile information. Classification of these signatures will lead to the automated identification of aerosol and cloud types. Testing of these new algorithms is done using currently existing and readily available active and passive measurements from the Cloud Physics Lidar and the MODIS Airborne Simulator, which simulate, respectively, the CALIPSO and MODIS A-train instruments.