Controlling robotic manipulators via visual feedback requires a known coordinate frame transformation between the robot and the camera. Uncertainties in mechanical systems as well as camera calibration create errors in this coordinate frame transformation. These errors result in poor localization of robotic manipulators and create a significant challenge for applications that rely on precise interactions between manipulators and the environment. In this work, we estimate the camera-to-base transform and joint angle measurement errors for surgical robotic tools using an image based insertion-shaft detection algorithm and probabilistic models. We apply our proposed approach in both a structured environment as well as an unstructured environment and measure to demonstrate the efficacy of our methods.