Systems and methods for automated analysis

A system, comprising:

• a first module comprising a sample analysis component and a first internal container rack conveyor system;
• a second module comprising a second internal container rack conveyor system, wherein the first and second modules are positioned adjacent to each other such that the first and the second internal container conveyor systems are aligned to transport containers from the first module to the second module;
• a container rack positioned within the first or the second internal container rack conveyer system, wherein the container rack comprises one or more sensing windows;
• and
• a tracking system that detects the location of the container rack within the first or the second internal container conveyor system, the tracking system disposed along the length of the internal container conveyor systems and comprising a plurality of pairs of optical emitters and optical detectors, each pair comprising an optical emitter and an optical detector situated on the opposite sides of the container conveyor system in a manner that the one or more sensing windows of the container rack permit optical communication between one or more optical emitters with the corresponding one or more optical detectors, and wherein the tracking system detects the location of the container rack within the first or the second internal container conveyor system based on the location of the one or more optical emitters that are in communication with the corresponding one or more optical detectors through the one or more sensing windows of the container rack,
• wherein optical communication between the one or more optical emitters and the corresponding one or more optical detectors is blocked when the one or more sensing windows are not aligned with the one or more optical emitters and the corresponding one or more optical detectors.