Disclosed herein are systems, methods, and non-transitory computer-readable storage media that allow a user to easily generate survey mission plans for one or more UAVs and to capture high quality survey images, including those in the near infra-red, and stitch them into an orthomosaic having reduced geometric distortion. The generation of such orthomosaics allows the systems and methods disclosed herein to be particularly useful in applications where separation from the background of high reflective near infrared surfaces is important, such as identifying plants on soil and generating vegetation indices for precision agriculture applications.