The current disclosure is directed to the field of pathology, and the automated handling of biological specimens from containers containing clear solutions wherein the biological specimens reside. A computer-implemented method is disclosed for extracting specimens from such containers via an extraction device attached to a robotic arm. The robotic arm is controlled by a robotic system controller. The three-dimensional location of all specimens are estimated using image analysis techniques using images obtained from a plurality of imaging systems. Image analysis is used to simultaneously guide the extraction device and track the location of specimens inside the container.
