A method of tube slot localization is provided using a tray coordinate system and a camera coordinate system. The method includes receiving, a series of images from at least one camera of a tray comprising tube slots arranged in a matrix of rows and columns. Each tube slot is configured to receive a sample tube. The method also includes automatically detecting fiducial markers disposed on cross sectional areas between the tube slots on the tray and receiving an encoder value indicating when each row of the tray is substantially at the center of the camera's field of view. The method further includes determining calibration information to provide mapping of locations from the tray coordinate system to locations from the camera coordinate system and automatically aligning the tray based on the encoder value and calibration information.