Visual parameter optimisation for biomedical image processing

Background: Biomedical image processing methods require users to optimise input parameters to ensure high quality output. This presents two challenges. First, it is difficult to optimise multiple input parameters for multiple input images. Second, it is difficult to achieve an understanding of underlying algorithms, in particular, relationships between input and output. Results: We present a visualisation method that transforms users’ ability to understand algorithm behaviour by integrating input and output, and by supporting exploration of their relationships. We discuss its application to a colour deconvolution technique for stained histology images and show how it enabled a domain expert to identify suitable parameter values for the deconvolution of two types of images, and metrics to quantify deconvolution performance. It also enabled a breakthrough in understanding by invalidating an underlying assumption about the algorithm. Conclusions: The visualisation method presented here provides analysis capability for multiple inputs and outputs in biomedical image processing that is not supported by previous analysis software. The analysis supported by our method is not feasible with conventional trial-and-error approaches

Vismon: Facilitating Analysis of Trade-Offs, Uncertainty, and Sensitivity In Fisheries Management Decision Making

In this design study, we present an analysis and abstraction of the data and task in the domain of fisheries management, and the design and implementation of the Vismon tool to address the identified requirements. Vismon was designed to support sophisticated data analysis of simulation results by managers who are highly knowledgeable about the fisheries domain but not experts in simulation software and statistical data analysis. The previous workflow required the scientists who built the models to spearhead the analysis process. The features of Vismon include sensitivity analysis, comprehensive and global trade-offs analysis, and a staged approach to the visualization of the uncertainty of the underlying simulation model. The tool was iteratively refined through a multi-year engagement with fisheries scientists with a two-phase approach, where an initial diverging experimentation phase to test many alternatives was followed by a converging phase where the set of multiple linked views that proved effective were integrated together in a useable way. Several fisheries scientists have used Vismon to communicate with policy makers, and it is scheduled for deployment to policy makers in Alaska