An observation apparatus comprising: an imaging unit adapted to image an observation target accommodated in an accommodation part of a container in a field of view (R, R1, .... R54) smaller than the accommodation part at a series of predetermined imaging positions and to acquire a series of partial images along a scanning trajectory; a measurement unit adapted to measure a distance from the imaging unit to the accommodation part before each imaging performed by the imaging unit at the series of imaging positions; a storage unit adapted to store shape information representing a shape of the container and imaging position information representing the series of imaging positions; characterized by a calculation unit adapted to calculate effective range information indicating an effective range (F01-F03) in the scanning trajectory along said scanning trajectory based on the shape information and the imaging position information, the effective range being a range in which the distance is measurable by the measurement unit before imaging within a range of the field of view (R, R1, .... R54) of the imaging unit at the imaging positions; and a control unit adapted to compare the effective range information (e.g. F01) with a predetermined threshold value and to control a focus of imaging using a measurement result measured by the measurement unit in the effective range (F01) and a measurement result of the measurement unit in a field of view (R2) adjacent to the field of view (R1) including the effective range (F01) in a case where the effective range information (F01) is smaller than or equal to the threshold value. an imaging unit adapted to image an observation target accommodated in an accommodation part of a container in a field of view (R, R1, .... R54) smaller than the accommodation part at a series of predetermined imaging positions and to acquire a series of partial images along a scanning trajectory; a measurement unit adapted to measure a distance from the imaging unit to the accommodation part before each imaging performed by the imaging unit at the series of imaging positions; a storage unit adapted to store shape information representing a shape of the container and imaging position information representing the series of imaging positions; characterized by a calculation unit adapted to calculate effective range information indicating an effective range (F01-F03) in the scanning trajectory along said scanning trajectory based on the shape information and the imaging position information, the effective range being a range in which the distance is measurable by the measurement unit before imaging within a range of the field of view (R, R1, .... R54) of the imaging unit at the imaging positions; and a control unit adapted to compare the effective range information (e.g. F01) with a predetermined threshold value and to control a focus of imaging using a measurement result measured by the measurement unit in the effective range (F01) and a measurement result of the measurement unit in a field of view (R2) adjacent to the field of view (R1) including the effective range (F01) in a case where the effective range information (F01) is smaller than or equal to the threshold value. <EOS>