An object of the invention is to provide an image processing technique for generating an all-in-focus image with less distortion from images obtained by imaging an imaging object carried together with a liquid in a well at different focus positions. An image processing method of the invention includes obtaining a plurality of images captured by imaging an imaging object carried together with a liquid in a well with a focus position changed in a direction substantially perpendicular to a liquid surface, calculating a local movement amount between the plurality of images, determining a correlation between a distance from a center of the well and an image distortion amount based on the local movement amount, and synthesizing the plurality of images by correcting pixels in each image based on the correlation and generating an all-in-focus image.