1. An imaging apparatus comprising: a position reference image creation unit for applying reference light to plural imaging targets each having the same shape, and creating silhouettes of the imaging targets, thereby to obtain a position reference image utilized for obtaining positions at which the respective imaging targets are present; a luminance reference image creation unit for applying an excitation light to the imaging targets, and creating luminance images of the imaging targets for respective optical filters each having a predetermined passing wavelength band, thereby to obtain plural luminance reference images utilized for obtaining luminance of respective imaging targets for each optical filter; a first vibration detection unit for detecting at least one among a change amount of the number or the area and a shape change of the imaging targets on the position reference image, and judging whether vibrations have occurred in the respective imaging targets during imaging the imaging target by the position reference image creation unit on the basis of the detected result; a mask image creation unit for creating a mask image that shows areas where the imaging targets are present from the position reference image for which the first vibration detection unit has detected no vibrations; and a second vibration detection unit for overlay-displaying the mask image on the respective luminance reference images, detecting whether or not the imaging targets are present outside the existing areas of the respective imaging targets, and judging whether or not vibrations have occurred in the respective imaging targets during imaging the imaging target by the luminance reference image creation unit on the basis of the detected result.