Andrew L. Barlow et al. Table 1. Results of a global PCC colocalization analysis of synthetic Gaussian spot patterns similar to those used by Manders et al., 1993. Test pattern M1 M2 A B C D E F G H I J 1 0.75 0.5 0.25 0 0.33 0.5 1.0 0.75 1.0 1 0.75 0.5 0.25 0 0.25 0.25 0.25 0.083 0.992 Global PCC Volocity 5.3 1.0 0.742 0.483 0.225 -0.034 0.268 0.339 0.494 0.244 0.495 PCC JACoP 1.0 0.741 0.483 0.224 -0.033 0.268 0.338 0.493 0.243 0.495 1 Andrew L. Barlow et al. Table 2. Results of a thresholded analysis of the synthetic spot patterns in Table 1. Test Pattern Combination M1 M2 Thresholded PCC A 1 1 B C D E Uncorrelated F G H 0.75 0.5 0.25 0 0.33 0.5 1.0 Description Interpretation 1.0 36 green spots. 36 red spots Perfect correlation for all intensities 1.0 36 green spots. 36 red spots. 9 green spots displaced. Perfect correlation for 75% of green and red intensities. 1.0 36 green spots. 36 red spots. 18 green spots displaced. Perfect correlation for 50% of green and red intensities. 0.25 1.0 36 green spots. 36 red spots. 27 green spots displaced. Perfect correlation for 25% of green and red intensities. 0 No relationship. 36 green spots. 36 red spots. All 36 green spots displaced. No relationship. 1.0 27 green spots. 36 red spots. 18 green spots displaced. Perfect correlation between 33% of the green intensities and 25% of the red intensities. 1.0 18 green spots. 36 red spots. 9 green spots displaced. Perfect correlation between 50% of the green intensities and 25% of red intensities. 9 green spots. 36 red spots Perfect correlation between all of the green intensities and 25% of red intensities. 1.0 4 green spots. 36 red spots 1 green spot displaced. Perfect correlation between 75% of green intensities and 0.08% of red intensities. -1 36 green spots. 36 inverse red spots. A perfect inverse correlation between all green and 99.2% of red intensities. 0.75 0.5 0.25 0.25 0.25 1.0 I 0.75 1.0 J Anticorrelated 0.083 0.992 2 Andrew L. Barlow et al. Table 3. Results of thresholded and global PCC analysis of an experiment where Gaussian spots were progressively displaced. Number of pixels Thresholded PCC Global PCC shifted Volocity 5.3 JACoP 0 1.0 1 M1 M2 1.0 1.0 1.0 0.886 0.951 0.994 0.994 2 0.549 0.817 0.957 0.957 3 0.121 0.632 0.877 0.877 4 -0.235 0.433 0.752 0.752 5 -0.397 0.257 0.595 0.595 6 -0.465 0.123 0.425 0.425 7 -0.500 0.037 0.286 0.286 8 -0.561 -0.009 0.144 0.144 9 -0.544 -0.028 0.060 0.060 10 -0.914 -0.033 0.017 0.017 11 1.00 -0.034 0.002 0.002 12 No Relationship -0.034 0.000 0.000 13 No Relationship -0.034 0.000 0.000 3 Andrew L. Barlow et al. Table 4. The effect of background on global PCC, MOC and thresholded PCC. 20 X 20 60 X 60 120 X 120 4 Andrew L. Barlow et al. The effect of noncolocalized objects on correlation analysis. Table 5. Field Green Red Number of Red only Green only Mx Threshold Threshold Multispeck Beads Beads A‐C 29 29 8 13 14 0.36 D‐F 1 15 7 0 1 G‐I 28 26 1 10 5 My Global Thresholded PCC PCC 0.37 0.354 0.924 0.86 1 0.923 0.954 0.14 0.09 0.098 0.939 5 Andrew L. Barlow et al. Figure 1. Colocalization and exclusion in biological samples. 6 Andrew L. Barlow et al. Figure 2. Colocalization in a subset of transduced cells. 7