Within the current clinical setting and healthcare technology development, medical imaging is a vital component of a large number of medical application and health diagnosis. Since information gained from two images acquired in the clinical track of events is usually of a complementary nature, proper integration of useful data obtained from the separate images are often desired. The first step in this integration process is to bring the modalities involved into spatial alignment, a procedure referred to as image registration.
The intent of image registration is to align images with respect to each other. The input for this process is two images: the original image is known as the template/ reference image while the image that will be aligned with the respect of template/ reference image is known as the target image.
In this research the application of various automated image registration framework for solving multi-dimensional medical image registration problems are presented which consisting of image registration for multiple protein maps at single cell resolution , 3-dimensional serial section microscopy images, and multimodal image registration on 3-dimensional CT and MRI image.

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