Extended Data Fig. 9: ALPs in shape-matched non-edge and edge cells.

a. Cell and nuclear SHE coefficients from a comparison dataset (e.g., edge cells; red dots) are transformed according to the SHE PCA of a baseline dataset (e.g. interphase cells; black + grey dots) resulting in the embedding of the comparison dataset cells into the baseline 8D shape space. Each cell in the comparison dataset is matched to its nearest neighbour in the shape space that is also in the baseline dataset (lines connecting black and red dots), creating the shape-matched dataset. b. Average morphed cells for six cellular structures in shape-matched non-edge and edge cells. For five of these structures, the ALP is a redistribution of the structure towards the outer edge of the colony, while for adherens junctions (via beta-catenin) the ALP is a redistribution of junctions away from the colony edge. c. Dimensionality of PILRs of cells in the shape-matched dataset is first reduced to 32 via PCA (see Methods). LDA is then applied to these 32 PCs to find the axis of greatest separation (solid purple line) between the two groups of cells in the dataset (black and red dots). Data points are projected along the discriminant axis to determine the frequency of cells. d. Average morphed cells for actin bundles (via alpha-actinin-1) in non-edge and edge cells. e. PILR-LDA based reconstructions of actin bundles in average morphed cells at five positions (in σ units) along the LDA axis. Dotted lines correspond to the locations of the mean non-edge (black) and edge (red) cells in (d). f. Frequency of cells along the LDA axis within non-edge and edge cell populations. Dotted vertical lines indicate the means. g. Top view and side view 1 of three examples of each non-edge and edge cells along the LDA axis. Top row shows the original and bottom row the morphed visualizations for each of these cells. Images are average projections of the segmented structure. h. Frequency of cells along the LDA axis within non-edge and edge cell populations for the five structures in (b). Dotted vertical lines indicate the means. PILR-LDA based reconstructions of average morphed cells at five positions (in σ units) along the LDA axis for all 25 cellular structures as well as single-cell examples available in Supplementary Video 3. i. Heat maps of the differences in average location similarity (left), stereotypy (centre) and concordance (right) for the 25 cellular structures in shape-matched non-edge vs. edge cells (numbers of cells and heat map data in Supplementary Data 1).

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