Or estimating parameters values by matching to simulated images. 2D real Autophagy images are shown on the left, and center slices of the best-matching 3D synthetic images are shown on the right. (A) A-431 cell line, Number of microtubules = 250, Mean of length distribution = 30 microns, Collinearity = 0.97000; (B) U2OS cell line, Number of microtubules = 250, Mean of length distribution = 30 microns, Collinearity = 0.98466; (C) U-251MG cell line, Number of microtubules = 250, Mean of length distribution = 20 microns, Collinearity = 0.99610. doi:10.1371/journal.pone.0050292.gComparison of Microtubule DistributionsFigure 5. Frequency distributions of all estimated parameters from real 2D images for all cell lines. There are two sets of three columns for the model parameters (number of microtubules, mean of the length distribution and collinearity) in each row. The cell lines (from top to bottom) are 1326631 U-251MG, A-549, MCF-7, Hep-G2, A-431 and HeLa in the left column, and CaCo2, PC-3, RT-4, Hek-293, and U-20S in the right. doi:10.1371/journal.pone.0050292.gintact cells across different cell lines. Methods such as electron microscopy can image intact cells, but have interference from other cell components [11]. More invasive methods of preparation such as extraction of the microtubule network can allow electron microscopy to generate traceable images, but are no longer representative of intact cells [12]. Fluorescence microscopy, on the other hand, can be used to obtain information about proteins atmonomer-level resolution of localization without interference from other cell components in intact cells with high-throughput data. One reason for studying microtubule distributions across cell lines is to begin to search for explanations of how expression of microtubule-associated proteins (MAPs) may account for any differences observed. The expression levels of many proteins vary across cell lines [13], and there are cell-specific proteins thatComparison of Microtubule DistributionsFigure 6. Comparison of the bivariate distributions of the estimated model parameters of the eleven cell lines. The ellipses are centered at the bivariate means of the two parameters and contain about 67 to 80 of the cells for a particular cell line (at most 1.5 standard deviations from the means). doi:10.1371/journal.pone.0050292.gFigure 7. Hierarchical clustering trees of eleven cell lines. The trees were built on the pairwise Hotelling’s T2 statistics from (A) the testing of the bivariate distributions of the estimated number of microtubules and mean length and (B) from the testing of the bivariate distributions of the first two principal components of the 24786787 multivariate Autophagy features computed from the real images. doi:10.1371/journal.pone.0050292.gComparison of Microtubule DistributionsTable 3. Statistical tests of the model parameters and the features between cell lines.p-valuesU-251MG (94) CaCo2(77) A-549(66) PC-3(110) MCF-7(54) RT-4(38) Hep-G2(51) Hek-293(70) A-431(112) U-2OS(114) HeLa(35)U-251MG NA 1 0.077 1 1 0.11 5.7e-4* 4.3e-3* 1.5e-4* 2.6e-7* 0*CaCo2 0* NA 1 1 1 0.030* 1 0.92 8.7e-6* 1.1e-5* 0*A-549 0* 1 NA 1 1 5.4e-4* 1 1 2.7e-9* 1.9e-4* 0*PC-3 0* 1 1 NA 1 0.067 2.0e-3* 0.26 0.012* 0.12 0*MCF-7 0* 0.86 0.012* 0.62 NA 1 0.081 0.12 0.059 4.1e-3* 0*RT-4 0* 0.045* 0.32 1 4.9e-5* NA 1.0e-4* 2.0e-9* 7.1e-3* 8.6e-6* 0*Hep-G2 6.1e-13* 6.3e-6* 0.12 7.6e-4* 9.2e-12* 7.3e-5* NA 1 0* 0* 0*Hek-293 1.1e-10* 5.5e-3* 1 1 3.1e-6* 1 0.020* NA 0* 2.9e-11* 0*A-431 5.8e-6* 0* 0* 0* 0* 0* 0*.Or estimating parameters values by matching to simulated images. 2D real images are shown on the left, and center slices of the best-matching 3D synthetic images are shown on the right. (A) A-431 cell line, Number of microtubules = 250, Mean of length distribution = 30 microns, Collinearity = 0.97000; (B) U2OS cell line, Number of microtubules = 250, Mean of length distribution = 30 microns, Collinearity = 0.98466; (C) U-251MG cell line, Number of microtubules = 250, Mean of length distribution = 20 microns, Collinearity = 0.99610. doi:10.1371/journal.pone.0050292.gComparison of Microtubule DistributionsFigure 5. Frequency distributions of all estimated parameters from real 2D images for all cell lines. There are two sets of three columns for the model parameters (number of microtubules, mean of the length distribution and collinearity) in each row. The cell lines (from top to bottom) are 1326631 U-251MG, A-549, MCF-7, Hep-G2, A-431 and HeLa in the left column, and CaCo2, PC-3, RT-4, Hek-293, and U-20S in the right. doi:10.1371/journal.pone.0050292.gintact cells across different cell lines. Methods such as electron microscopy can image intact cells, but have interference from other cell components [11]. More invasive methods of preparation such as extraction of the microtubule network can allow electron microscopy to generate traceable images, but are no longer representative of intact cells [12]. Fluorescence microscopy, on the other hand, can be used to obtain information about proteins atmonomer-level resolution of localization without interference from other cell components in intact cells with high-throughput data. One reason for studying microtubule distributions across cell lines is to begin to search for explanations of how expression of microtubule-associated proteins (MAPs) may account for any differences observed. The expression levels of many proteins vary across cell lines [13], and there are cell-specific proteins thatComparison of Microtubule DistributionsFigure 6. Comparison of the bivariate distributions of the estimated model parameters of the eleven cell lines. The ellipses are centered at the bivariate means of the two parameters and contain about 67 to 80 of the cells for a particular cell line (at most 1.5 standard deviations from the means). doi:10.1371/journal.pone.0050292.gFigure 7. Hierarchical clustering trees of eleven cell lines. The trees were built on the pairwise Hotelling’s T2 statistics from (A) the testing of the bivariate distributions of the estimated number of microtubules and mean length and (B) from the testing of the bivariate distributions of the first two principal components of the 24786787 multivariate features computed from the real images. doi:10.1371/journal.pone.0050292.gComparison of Microtubule DistributionsTable 3. Statistical tests of the model parameters and the features between cell lines.p-valuesU-251MG (94) CaCo2(77) A-549(66) PC-3(110) MCF-7(54) RT-4(38) Hep-G2(51) Hek-293(70) A-431(112) U-2OS(114) HeLa(35)U-251MG NA 1 0.077 1 1 0.11 5.7e-4* 4.3e-3* 1.5e-4* 2.6e-7* 0*CaCo2 0* NA 1 1 1 0.030* 1 0.92 8.7e-6* 1.1e-5* 0*A-549 0* 1 NA 1 1 5.4e-4* 1 1 2.7e-9* 1.9e-4* 0*PC-3 0* 1 1 NA 1 0.067 2.0e-3* 0.26 0.012* 0.12 0*MCF-7 0* 0.86 0.012* 0.62 NA 1 0.081 0.12 0.059 4.1e-3* 0*RT-4 0* 0.045* 0.32 1 4.9e-5* NA 1.0e-4* 2.0e-9* 7.1e-3* 8.6e-6* 0*Hep-G2 6.1e-13* 6.3e-6* 0.12 7.6e-4* 9.2e-12* 7.3e-5* NA 1 0* 0* 0*Hek-293 1.1e-10* 5.5e-3* 1 1 3.1e-6* 1 0.020* NA 0* 2.9e-11* 0*A-431 5.8e-6* 0* 0* 0* 0* 0* 0*.