An abstract virtual instrument system for high throughput automatic microscopy

Modern biomedical therapies often involve disease specific drug development and may require observing cells at a very high resolution. Existing commercial microscopes behave very much like their traditional counterparts, where a user controls the microscope and chooses the areas of interest manually on a given specimen scan. This mode of discovery is suited to problems where it is easy for a user to draw a conclusion from observations by finding a small number of areas that might require further investigation. However, observations by an expert can be very time consuming and error prone when there are a large number of potential areas of interest (such as cells or vessels in a tumour), and compute intensive image processing is required to analyse them. In this paper, we propose an Abstract Virtual Instrument (AVI) system for accelerating scientific discovery. An AVI system is a novel software architecture for building an hierarchical scientific instrument – one in which a virtual instrument could be defined in terms of other physical instruments, and in which significant processing is required in producing the illusion of a single virtual scientific discovery instrument. We show that an AVI can be implemented using existing scientific workflow tools that both control the microscope and perform image analysis operations. The resulting solution is a flexible and powerful system for performing dynamic high throughput automatic microscopy. We illustrate the system using a case study that involves searching for blood vessels in an optical tissue scan, and automatically instructing the microscope to rescan these vessels at