A medical system comprising: a treatment tool including a treatment portion that is configured to perform treatment on a living body, a joint portion that is configured to move the treatment portion, a flexible tube portion that is connected to the joint portion, and a drive unit that is connected to the flexible tube portion and is configured to displace the joint portion; an endoscope device including a flexible outer sheath that has a distal end and a proximal end, the outer sheath being configured to hold the treatment tool such that the treatment portion protrudes from the distal end, and an imaging unit that is capable of acquiring at least an image including at least the joint portion in an imaging field of view; and a control unit that is configured to control an operation of the treatment tool based on the image, wherein the control unit includes: a table that has a parameter for causing the joint portion to move; and a controller that is configured to issue a command according to the parameter to the drive unit for driving the drive unit so as to displace the joint portion, characterized in that the control unit further includes an image processing unit that is configured to calculate at least one of a position and an orientation of the joint portion based on the image; and a compensation value calculating unit that is configured to detect a displacement of the joint portion according to at least one of the position and the orientation of the joint portion calculated by the image processing unit, generate a compensation value for compensating for a difference between the command and the displacement of the joint portion, and incorporate the compensation value into the parameter, wherein the control unit is configured to use the compensation value to perform a calibration of the treatment tool by determining a relationship between a driven movement amount of the drive unit and the displacement of the joint portion, the driven movement amount of the drive unit being instructed by the command issued by the controller. a treatment tool including a treatment portion that is configured to perform treatment on a living body, a joint portion that is configured to move the treatment portion, a flexible tube portion that is connected to the joint portion, and a drive unit that is connected to the flexible tube portion and is configured to displace the joint portion; an endoscope device including a flexible outer sheath that has a distal end and a proximal end, the outer sheath being configured to hold the treatment tool such that the treatment portion protrudes from the distal end, and an imaging unit that is capable of acquiring at least an image including at least the joint portion in an imaging field of view; and a control unit that is configured to control an operation of the treatment tool based on the image, wherein the control unit includes: a table that has a parameter for causing the joint portion to move; and a controller that is configured to issue a command according to the parameter to the drive unit for driving the drive unit so as to displace the joint portion, a table that has a parameter for causing the joint portion to move; and a controller that is configured to issue a command according to the parameter to the drive unit for driving the drive unit so as to displace the joint portion, characterized in that the control unit further includes an image processing unit that is configured to calculate at least one of a position and an orientation of the joint portion based on the image; and a compensation value calculating unit that is configured to detect a displacement of the joint portion according to at least one of the position and the orientation of the joint portion calculated by the image processing unit, generate a compensation value for compensating for a difference between the command and the displacement of the joint portion, and incorporate the compensation value into the parameter, wherein an image processing unit that is configured to calculate at least one of a position and an orientation of the joint portion based on the image; and a compensation value calculating unit that is configured to detect a displacement of the joint portion according to at least one of the position and the orientation of the joint portion calculated by the image processing unit, generate a compensation value for compensating for a difference between the command and the displacement of the joint portion, and incorporate the compensation value into the parameter, wherein the control unit is configured to use the compensation value to perform a calibration of the treatment tool by determining a relationship between a driven movement amount of the drive unit and the displacement of the joint portion, the driven movement amount of the drive unit being instructed by the command issued by the controller.