Xerogel package

Many articles have been written and much exploratory work has been done regarding how VOC's (volatile organic compounds) in the exhaled breath of people may serve as biomarkers in detecting certain types of lung and breast cancer [M. McCulloch, T. Jezierski, M. Broffman, et al., Diagnostic accuracy of canine scent detection in early- and late-stage lung and breast cancers, Integr. Cancer Ther. 5 (2006) 30-39]. Xerogel chips are based on this idea. Xerogels are porous glass-like materials formed from drying silica gels in air. Xerogels have properties like optical transparency that enable them to act as a chemical sensor [S.S. Karri, A.H. Titus, E.C. Tehan, Z. Tao, Y. Tang, F.V. Bright, Image Analysis for Multi-Analyte Xerogel based Sensor Arrays, Proceedings of the 4th IEEE Conference on Sensors, vol. 1, 2005, pp. 373-376]. Chips are spotted on an array by a microscopic pin with xerogel infused with a fluroscein material. The fluroscein used depends on the targeted VOC. The xerogel chip is analyzed based on the intensity of light emitted by the fluroscein compound as it is exposed to varying amounts of the VOC. A TIFF format image of emitted light is taken using an epifluroscence microscope interfaced to a charge coupled device. This image is then analyzed using the Xerogel package written in the statistical software language, R [R Development Core Team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2006, ISBN 3-900051-07-0, 2006, URL: http://www.R-project.org]. The images can be stored as 8, 16, 24 or 48 bit TIFF format depending on the resolution required. The Xerogel package consists of routines that import the TIFF format image, read the image into a matrix, binarize the image matrix, identify the position and structure of the spots, and return statistics such as the mean, median, and total intensity for these spots. The summary statistics provide information on how the intensity of light varies with varying amounts of the VOC.