There are provided an information processing apparatus, an information processing method, a program, and a microscope system which can compose a microscopically observed image having a wide field of view and a high resolution by highly accurately stitching a plurality of digital images together.
An image acquisition unit provided in the information processing apparatus acquires a first partial image and a second partial image each formed by imaging a part of an observation target area, and a stitching position adjustment unit adjusts a stitching position of the second partial image with respect to the first partial image. The image acquisition unit controls drive of the microscope such that a partial image including a specimen is acquired as the second partial image when the first partial image includes a foreign matter.