A non-transitory computer readable storage medium comprising computer program instructions that when executed by a processor cause the processor to perform a method comprising: accessing robotic data regarding physical manipulation of an elongated medical instrument inserted into a tubular network of a patient; accessing image data captured by an imaging device located proximal to an instrument tip of the elongated medical instrument; accessing electromagnetic data captured using an EM sensor located proximal to the instrument tip as well as using at least one external EM sensor or EM generated located external to the patient; determining a robot-based estimated state for the instrument tip based on the robotic data, the robot-based estimated state associated with a first confidence value; determining an image-based estimated state for the instrument tip based on the image data, the image-based estimated state associated with a second confidence value; determining an EM-based estimated state for the instrument tip based on the EM data, the EM-based estimated state associated with a third confidence value; wherein the confidence value associated with each of the estimated states represents a degree of confidence in the determination of the corresponding estimated state; and determining a combined estimated state for the instrument tip based on the robot-based, image-based, and EM-based estimated states and wherein the combined estimated state is generated by, for each of the robot-based, EM-based, and image-based estimated states: representing the corresponding estimated state as a probability distribution including a set of possible values; and weighting the corresponding estimated state represented by the set of possible values using the corresponding confidence values applied to each value of the set of possible values. accessing robotic data regarding physical manipulation of an elongated medical instrument inserted into a tubular network of a patient; accessing image data captured by an imaging device located proximal to an instrument tip of the elongated medical instrument; accessing electromagnetic data captured using an EM sensor located proximal to the instrument tip as well as using at least one external EM sensor or EM generated located external to the patient; determining a robot-based estimated state for the instrument tip based on the robotic data, the robot-based estimated state associated with a first confidence value; determining an image-based estimated state for the instrument tip based on the image data, the image-based estimated state associated with a second confidence value; determining an EM-based estimated state for the instrument tip based on the EM data, the EM-based estimated state associated with a third confidence value; wherein the confidence value associated with each of the estimated states represents a degree of confidence in the determination of the corresponding estimated state; and determining a combined estimated state for the instrument tip based on the robot-based, image-based, and EM-based estimated states and wherein the combined estimated state is generated by, for each of the robot-based, EM-based, and image-based estimated states: representing the corresponding estimated state as a probability distribution including a set of possible values; and weighting the corresponding estimated state represented by the set of possible values using the corresponding confidence values applied to each value of the set of possible values. representing the corresponding estimated state as a probability distribution including a set of possible values; and weighting the corresponding estimated state represented by the set of possible values using the corresponding confidence values applied to each value of the set of possible values.