Extended Data Fig. 3: Image analysis software QUANTEX and feature comparison for maximum linear dimension.
From: Stabilization of chromatin topology safeguards genome integrity
a, QUANTEX 3D image analysis workflow to analyse spatial features of 53BP1-MDs at sites of DNA damage. Step 1: 3D-SIM images were processed and segmented for cell nuclei and 53BP1-MDs using a slice-by-slice segmentation approach. Step 2: measurements of texture, morphology and geometry features were automatically derived for all segmented structures and 3D models for visual inspection were generated. Step 3: Data analysis and statistics. For more information, see Methods. b, QUANTEX analysis of principal axis length metric of 53BP1-MDs in cells treated with control or RIF1 siRNAs. Principal axis length data were derived from the same experiments as in Fig. 1a, d and represent a parallel data analysis to the metric mean breadth in Fig. 1f; n = 60. Box plots: centre lines, medians; box limits, 25th and 75th centiles; whiskers, minimum and maximum; dots, outliers. ****P = 9.4329 × 10−6 (left), 2.3092 × 10–9 (right); two-tailed non-parametric Wilcoxon rank-sum test. The experiment was biologically replicated twice with similar results. c, Spearman’s Correlation R2 value was calculated for mean breadth and principal axis length metrics derived from control (negative class, n = 90) and RIF1 depletion (positive class, n = 87) experiments combined, in order to test association. ****P = 2.74 × 10−35; two-sided Spearman’s rank correlation coefficient method.
