An endoscope system capable of improving an S / N ratio and reliability of an oxygen saturation image, a processor device of the endoscope system, and a method of operating the endoscope system. First and second illumination lights having different spectral characteristics are alternately irradiated on the specimen via the extinguishing period, and in each extinguishing period, signal reading is performed on the G pixel from the image pickup element (39) without pixel addition , B pixels and R pixels are subjected to pixel addition and signal reading is performed. A first image pickup signal read out from the image pickup element in a light extinguishing period after illumination of the first illumination light and a second image pickup signal read out from the image pickup element in the extinguishing period after irradiation with the second illumination light are converted into G Based on the signals of the pixels, comparison is made to calculate the amount of positional shift between the images based on the first and second imaging signals. Based on the amount of positional deviation, the images are aligned between the first and second imaging signals, and an oxygen saturation image is generated based on the first and second imaging signals after alignment.酸素飽和度画像のS/N比及び信頼性を向上させることを可能とする内視鏡システム、内視鏡システムのプロセッサ装置、及び内視鏡システムの作動方法を提供する。 分光特性が異なる第1及び第2照明光を、消灯期間を介して交互に検体に照射し、各消灯期間に、撮像素子(39)からG画素を、画素加算を行わずに信号読み出しを行い、B画素及びR画素を、画素加算を行って信号読み出しを行う。第1照明光の照射後の消灯期間に撮像素子から読み出された第1撮像信号と、第2照明光の照射後の消灯期間に撮像素子から読み出された第2撮像信号とを、G画素の信号に基づいて比較することにより、第1及び第2撮像信号に基づく画像間の位置ずれ量を算出する。位置ずれ量に基づいて、第1及び第2撮像信号間の画像の位置合わせを行い、位置合わせ後の第1及び第2撮像信号に基づいて酸素飽和度画像を生成する。
