To provide an endoscope system and a method for operating the endoscope system which, even when using a plurality of index values, can narrow down the index values to index values to be remarkable at the time of diagnosis and exhibit the narrowed index values.SOLUTION: An image processing unit 60 includes an image acquisition unit 70, an extraction unit 72, an index value calculation unit 74, a determination unit 76, a color information setting unit 78, and an image generation unit 80. The image acquisition unit 70 acquires an image captured by an endoscope 12. The extraction unit 72 extracts a blood vessel to be observed. The index value calculation unit 74 calculates a plurality of blood vessel index values on the basis of the blood vessel. The color information setting part 78 sets color information on an abnormal index value or a normal index value among the index values. The image generation unit 80 generates an enhanced image on the basis of the color information.SELECTED DRAWING: Figure 4
