All images were obtained with a Leica TCS SP8 confocal microscope and with a 40× objective. The voxel size is 0.0946 × 0.0946 × 0.3463 μm. Propidium Iodide staining was applied according to the manufacturer’s protocol. A detailed protocol of the experiment can be found in the STARmap PLUS paperWe used 3D chromatin images to obtain nuclear features and associated these features to plaque size using the regression gradient.
. For each cell, we used all the z-stack images and cropped the horizontal directions to 37.84 × 37.84 µmcentered at the cell centroid. After min-max scaling to [0, 1], the 3D stack of each cell was further cropped to 18.92 × 18.92 µmin the horizontal directions. The images were resampled in the z-direction to have isotropic voxels. Then we applied Gaussian blur, spot detection, a second Gaussian blur with sigma set to 3, Otsu thresholding, and Voronoi labeling.
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