Embodiments of the disclosure comprise a vision-based robotic manipulation system that identifies, singulates, and removes an individual surgical instrument from a cluttered environment. A computer-vision algorithm incorporated with the system is robust against optical challenges such as changing light conditions, specularities, and inter-reflections among various surgical instruments. The system estimates 2D pose (as opposed to a more challenging 3D pose) using a camera with normal room lighting to identify each object, including its specified data matrix barcode; and incorporates the use of a robotic arm with a compliant electromagnetic gripper to handle objects having large shape variance. The system can then relocate the objects as desired. The robot manipulator is utilized in hospital and research settings, manufacturing, and sterile environments.