Xerogel

Version 0.0
License GPL (version 2 or later)
Requirements R (version 2.4.1 or higher)
packages:rtiff, rimage, pixmap and the free software ImageMagick
DLLs: libtiff3, jpeg62, zlib1
Installation
  1. Download the Xerogel package from the website.
  2. Unzip the downloaded file and save it under R/library or use the R function install.packages.
  3. Load the library into R using the command “library(Xerogel)”
Description The Xerogel package is written in R. R is a complete statistical software package and programming language for data manipulation, calculation and professional graphical display. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Sources, binaries and documentation for R can be obtained via CRAN, the “Comprehensive R Archive Network.”

Abstract

Many articles have been written and exploratory work has been done about the presence or increase in certain VOCs (Volatile organic compounds) in the exhaled breath of people suffering from lung and breast cancer compared to those who do not suffer from the same. Xerogel chips are based on this idea. Xerogels are materials with certain properties that enable it to act as a chemical sensor. Chips are spotted in an array by a microscopic pin with Xerogel infused with a fluroscein material. The fluroscein to be 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 and is analyzed using the Xerogel package. The images can be stored as 8, 16, 24 or 48 bit TIFF format. The Xerogel package consists of routines that import the TIFF format image, reads the image into a matrix that can be processed, binarizes the image matrix, identifies the position and structure of the spots and returns statistics such as mean, median and total intensity for these spots. Binary morphological operators such as erode and dilate which are used to identify spots and boundaries in the image are also present. The statistics generated help in understanding how the intensity of light varies with varying amounts of the VOC. Xerogel chips can be infused with fluroscein that react to the presence of the VOC's linked to the presence of lung and breast cancer and these can be analyzed. The statistics generated can be compared with the same from the control group and inference can be made.