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The first part of this tutorial is the basic user documentation of the Coloc_2 plugin which is found in the Analyze - Colocalization Analysis menu.
Coloc_2 implements and performs the pixel intensity correlation over space methods of [http://en.wikipedia.org/wiki/Pearson_product-moment_correlation_coefficient Pearson], [[Media:Manders.pdf|Manders]], [[Media:Costes etalColoc.pdf|Costes]], Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing.
None of this gives sensible results unless you have your imaging hardware set up appropriately and have acquired images properly, and have performed appropriate controls for bleed-through and chromatic shift etc. See [[Colocalization_-_hardware_setup_and_image_acquisition|here for hardware set up guidelines]]