Microscope system

A microscope system comprising:

• an irradiation optical system configured to irradiate a surface of a sample on a stage with light from an oblique direction;
• an observation optical system configured to form an image of scattered light from the surface of the sample;
• a focus mechanism configured to change height positions of focuses of the irradiation optical system and the observation optical system with respect to the surface of the sample;
• and
• a computer system configured to control the irradiation optical system, the observation optical system and the focus mechanism, and acquire the image formed by the observation optical system, wherein
• the computer system is configured to
• regarding the sample, acquire a first image in a first focus state at a first time point and a second image in a second focus state at a second time point, the first image and the second image having different focus heights,
• calculate a position of a spot pattern in the first image as a first spot position, and calculate a position of a spot pattern in the second image as a second spot position,
• calculate an amount of change between the first spot position and the second spot position as an amount of change in spot position,
• calculate an amount of change in height of the sample as an amount of change in sample height based on an incident angle between the oblique direction of the irradiating light and a normal to the surface of the sample and the amount of change in spot position, and
• adjust the height positions of the focuses by using the amount of change in sample height so as to focus on the surface of the sample.