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Colocalization Distribution Data Analysis Script

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posted on 17.12.2019, 14:50 by Joseph Cabral, Hyung Oh, David Knipe
MATLAB script uses nuclear masks and foci center x,y coordinate data from each channel (results from Foci Detection and Colocalization software) to determine distances of nearest neighbor foci in a second channel from foci in the reference channel and generate distance frequency data. The script then generates the same number of random x,y points within the nuclear mask as were detected in the second channel. The distances from the centers of reference channel foci to nearest neighbor random points is then calculated and reported to within a user defined user defined radius of each reference focus. The resulting frequency distributions of reference-to-test channel distances and reference-to-random points are compared by the non-parametric Kolmogorov-Smirnov test. If the test rejects the null hypothesis at 5% significance, the test returns a value of 1, and 0 if the null hypothesis is not rejected. The test also returns an asymptotic p-value and a list of distances in pixel values which can then be plotted and further analyzed using GraphPad Prism (as it was here) or other data analysis packages.