Image pair co-registration systems and methods include receiving a pair of multi-modal images, defining a parametric deformation model, defining a loss function that is minimized when the pair of images are aligned, and performing a multi-scale search to determine deformation parameters that minimize the loss function. The optimized deformation parameters define an alignment of the pair of images. The pair of images may include visible spectrum image and an infrared image. The method further includes resizing the visible spectrum image to match the infrared image, applying at least one lens distortion correction model, and normalizing a dynamic range of each of the pair of images. The multi-scale search may further include resizing the pair of images to a current processing scale, applying adaptive histogram equalization to the pair of images to generate equalized images, applying Gaussian Blur to the equalized images, and optimizing the deformation parameters.