An image pickup device 1A is constructed with a photodetecting section 10 having a plurality of pixels; a charge transfer section 12 having 16 segmental charge transfer sections T01 to T16; an A/D converting section 15 that converts signals from the charge transfer section 12 to digital data signals; and a digital signal processing section 20. The digital signal processing section 20 carries out, to a correction target of a data signal outputted first in a signal array from the segmental charge transfer section, a data correction by use of a plurality of correcting data signals including at least one of a first correcting data signal included in the signal array and a second correcting data signal included in another signal array from a segmental charge transfer section adjacent to an output end side of the segmental charge transfer section. Thereby, realized are an image pickup device that is capable of favorably reducing influence of an abnormal output produced in data signals and a microscope apparatus using the same.