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Technological advances in both hardware and software have made possible the realization of sophisticated biological imaging experiments using the optical microscope. As a result, modern microscopy experiments are capable of producing complex image datasets. For a given data analysis task, the images in a set are arranged, based on the requirements of the task, by attributes such as the time and focus levels at which they were acquired. Importantly, different tasks performed over the course of an analysis are often facilitated by the use of different arrangements of the images. We present a software framework that supports the use of different logical image arrangements to analyze a physical set of images. This framework, called the Microscopy Image Analysis Tool (MIATool), realizes the logical arrangements using arrays of pointers to the images, thereby removing the need to replicate and manipulate the actual images in their storage medium. In order that they may be tailored to the specific requirements of disparate analysis tasks, these logical arrangements may differ in size and dimensionality, with no restrictions placed on the number of dimensions and the meaning of each dimension. MIATool additionally supports processing flexibility, extensible image processing capabilities, and data storage management.