A method and system for image-based region detection. Transformation matrices are computed by performing image registration between a target image and each of one or more reference images. Each transformation matrix is for transforming each of the reference images into a coordinate system of the target image. An optimal reference image is selected from among the reference images based on similarity measures between the target image and each reference image. The transformation matrix of the selected reference image is applied to a reference map associated with the reference image in order to generate a target map for the target image. The target map includes region labels indicating regions shown in the target image.