1. An image acquisition apparatus, comprising: a combination unit; a record unit; a preprocess unit; an analog/digital unit; a pixel shifting unit, implemented at least in part by hardware, moving a relative position between a luminous flux entering an image pickup device and the image pickup device to a plurality of predetermined positions in a predetermined order; a shooting unit, implemented at least in part by hardware, shooting an image of a subject image formed by the luminous flux on a photoreception surface of the image pickup device when the relative position is placed in any of the plurality of predetermined positions; a high-resolution image generation unit combining a plurality of images obtained by shooting the images by the shooting unit and generating a high-resolution image of the subject having higher resolution than the images; a prediction unit predicting a shooting environment when the shooting unit afterwards shoots the images of the subject on a basis of a change of at least two images obtained by shooting the images by the shooting unit; and a shooting condition setting control unit controlling a setting of a shooting condition when the shooting unit shoots an image of the subject image on a basis of a result of predicting the shooting environment by the prediction unit; the shooting condition setting control unit further comprises: a determination unit determining whether or not a reduction of a brightness value in two images continuously shot by the shooting unit under control of the shooting condition setting control unit is within a predetermined change threshold; a shooting condition setting reproduction unit reproducing a setting of a same shooting condition as in shooting a first shot image in the two continuous images when the determination unit determines that a reduction of a brightness value in the two images is within the predetermined change threshold; and a reshooting control unit controlling reshooting of the shooting unit under a setting of a shooting condition reproduced by the shooting condition setting reproduction unit, and reshooting a last shot image in the two continuous images; wherein the subject is a fluorescent observation sample; and the prediction unit predicting a change with time of the amount of light of the luminous flux by fading on the fluorescent observation sample after pumping on a basis of a change of a brightness value in at least two images and a shooting interval of the image by the shooting unit.