The Imaging Computational Microscope

TL;DR

The Imaging Computational Microscope (ICM) is a MATLAB-based suite that automates analysis of functional imaging data with semi-supervised methods, enabling real-time analysis and user-guided refinement.

Contribution

ICM introduces a semi-supervised, automated framework for functional imaging data analysis that supports real-time processing and is adaptable via object-oriented design.

Findings

Automated extraction of component signals from imaging data

Real-time analysis capability for guided experiments

Open-source tool with extensive documentation

Abstract

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.