The Imaging Computational Microscope (ICM) is a suite of computational tools for automated analysis of functional imaging data that runs under the cross-platform MATLAB environment (The Mathworks, Inc.). ICM uses a semi-supervised framework, in which at every stage of analysis computers handle the routine work, which is then refined by user intervention. The main functionality of ICM is built upon automated extraction of component signals from imaging data, segmentation and clustering of component signals, and feature computation and visualization. Analysis of imaging data through ICM can also be done in real-time, enabling guided imaging experiments. ICM is built using MATLAB's object-oriented class design, which allows the tool to be used both as a graphic user interface (GUI) as well as in custom scripts. ICM is freely available under the GNU public license for non-commerical use and open source development, together with sample data, user tutorials and extensive documentation.