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Title:  Plugins to the ImageJ software for capture of filter-based microarray data

Speaker: Mary Pat Reeve-Daly 

Place: Microarray Algorithms and Statistical Analysis: Methods and Standards, Tahoe  City, CA.

Date:  November, 1999

Abstract:

ImageJ is a Java application written and distributed by NIH  (http://rsb.info.nih.gov/ij/) and designed to replace the older NIH Image.  ImageJ comes with many of the features expected of an image package  (filtering, color handling, working with regions of interest, etc.) and also has an added facility for adding your own analysis components as plugins.

We have created a plugins for working with the duplicate gridding system used on many filter-based microarrays (spots are placed in 4x4 grids with 8 samples that are duplicated in a particular pattern).  After manually  placing the first grid using a tool added to ImageJ the software automatically will fill and quantitate the rest of the grid.  To increase the accuracy of the grid placement, first the two images to be compared are overlayed using registration points. Then we run a difference of Gaussian filter to sharpen the spots.  Last, the optimal position of the subgrid is located using a scoring algorithm that takes into account local intensities as well as the position of local subgrids (this helps correct for some of the warping that occurs in filter-based systems).