The environmental sample processor (ESP) software design: software for detection and quantification of microorganisms

The Environmental Sample Processor (ESP) instrument has been designed by the Monterey Bay Aquarium Research Institute (MBARI) for ocean sampling and monitoring. The ESP is an in situ sampling and processing device that enables near real-time detection of specific microorganisms through the application of molecular probes. The intended use of ESP is a 1 to 3 month deployment in 50 meters maximum depth for detection of harmful algal blooms. The authors present an overview of the software architecture deployed on the ESP instrument. The ESP software design is applied on two prototype instruments with similar mechanical design, but different control electronics. Presented in this work is the software architectural framework used that allows for controlled start up, shutdown, task and event handling in a concurrent software environment. They discuss how object-oriented design patterns such as the Adapter pattern are used to solve design problems and how testing improved reliability. A description and examples are given of the flexible ESP macro language that allows scientists to automate chemical processing steps. And finally, an algorithm for DNA probe array image registration and data extraction involving low-pass filtering, connected components, rotational translation, and component recognition and interpretation is presented.