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In order to elicit the maximum performance of a multi-spectral imaging system designed for plant health mapping under field operating conditions, a multi-threaded approach was used in creating software modules to interface and integrate the use of a FireWire_A camera capable of 100 fps at 640x480 pixels (8-bit gray levels) and a Liquid Crystal Tunable Filter having a cycle time of 17 ms to switch between 692 and 755 nm. Due to the discrete-event nature of the multi-spectral imaging system, a multi-threaded software package was developed to distribute the workload of camera control, calibration, image capture, and image analysis over multiple worker threads implemented in the Microsoft Foundation Classes. The implementation of a priority-based, multi-threaded system achieved maximum efficiency by minimizing system downtime during processes that are timeintensive but computationally simple. In this system, computationally expensive routines such as image analysis are preformed while image capturing routines are suspended awaiting an event that is independent of the system.