Abstract: A method for processing images of an agricultural field is disclosed that enables accurate phenotype measurements for crops planted in each research plot of the agricultural field. The method comprises receiving a plurality of input images of the agricultural field, calculating and refining object space coordinates for matched key points in the input images and an object space camera pose for each input image, calculating and refining object space center points for the research plots based on a user-defined plot layout, and generating output images of individual research plots that are centered, cropped, orthorectified, and oriented in alignment with planted rows of crops. Based on the output images, accurate phenotype measurements for crops planted in each research plot can be determined.