Extended Data Fig. 7: Comparing location stereotypy and concordance throughout the cell and nuclear shape space.

a. Box plots of the diagonal values for each of the 25 cellular structures in the 3D voxel-wise Pearson correlation matrix heat map for all cells in the 8-dimensional sphere (Extended Data Fig. 6a). The thicker and shorter horizontal black line inside the box is the location stereotypy, the average of all the values in that structure’s block in the correlation matrix. Dots represent the raw data (one dot per correlation value; 1,000 randomly selected points are shown). The box extends from the first quartile (Q1) to the third quartile (Q3) of the data, with a line at the median. The whiskers extend from the box by 1.5x the interquartile range (IQR). Numbers of cells are in Supplementary Data  1. Colour bars along the bottom (x axis) indicate the cellular structure. Numbers above the colour bar indicate structures ranked by their stereotypy from greatest to least. The structures with the greatest location stereotypy were the nuclear envelope (lamin B1) and the plasma membrane (via CAAX domain of K-Ras, “CAAX”). These observations are effectively positive controls, because these two structures should be very similar to the cell and nuclear boundary shapes that were used as fixed points in the SHE interpolation. In decreasing order of stereotypy, the next highest were two nucleolar compartments, the Dense Fibrillar Component (DFC, via fibrillarin) and the Granular Component (GC, via nucleophosmin), followed by the ER (both Sec61 beta and SERCA) and microtubules. Structures with the least location stereotypy included those with a low number of discrete separated locations near the top or bottom of the cell such as centrioles (via centrin-2), desmosomes (desmoplakin), and matrix adhesions (paxillin) as well as structures with sparse, punctate locations such as cohesins (SMC-1A), endosomes (Rab-5A) and peroxisomes (PMP34). b. The process to create the Pearson correlation matrix for the 8-dimensional sphere (Extended Data Fig. 6a) was repeated for the reconstructed cell and nuclear shapes at each of the nine map points for each of the eight shape modes. Shown here are the resulting correlation matrices along Shape Mode 1. Each entry in this matrix represents the correlation between the cellular structure PILR of two cells. Thicker black lines within the matrix indicate the regions (blocks) of the matrix corresponding to cells with a tagged structure. The size of each dimension of each block corresponds to the number of cells. c. Heat maps of the difference in location stereotypy for each of the eight shape modes (SM). Each heat map represents a shape mode, each column represents the nine binned map points along that shape mode (Fig. 2b), and each row represents a different cellular structure. Each heat map value corresponds to the stereotypy difference between the mean cell shape and the cell shape in the indicated shape mode bin for that cellular structure. d. Heat maps of the difference in location concordance between the mean cell shape and either, the −2σ and 2σ shape space map points (bottom and top triangles, respectively), for each of the eight shape modes. Numbers of cells are in Supplementary Data 1. Colour bars on the left of heat maps indicate the cellular structure. Additional concordance difference heat maps are available in Supplementary Data 1.

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