Extended Data Fig. 10: Integrated intracellular reorganization in early mitosis (supporting figure).

a. We investigated two stages of early mitosis—prophase (m1) and early prometaphase (m2), when the condensing chromosomes still largely form an aggregated, nuclear-like structure that could be biologically interpreted in the context of our cell and nuclear shape-based coordinate system. Due to the breakdown of the nucleus and the condensation of DNA in these early stages of mitosis, the outline of the DNA-dye-based segmentation was no longer appropriate for SHE-based parameterization. Instead, we replaced the nuclear segmentation of cells in both datasets with their convex-hull counterpart. b. Mean cell (magenta or purple) and nuclear (cyan or green) shape for all interphase cells (1^st column), cells in prophase (m1), shape-matched interphase 1 and m1 cells (i1 + m1), cells in early prometaphase (m2), and shape-matched interphase 2 and m2 cells (i2 + m2), respectively. c. Frequency of cells for the eight shape modes (SM) for all interphase (grey), i1 (black) and m1 (red) cells (top two rows), i2 (black) and m2 (red) cells (bottom two rows). d. Concordance heat maps for interphase cells in the two shape-matched interphase datasets (i1, i2) and their corresponding prophase (m1) and early prometaphase (m2) mitotic cells. e. Heat maps of the differences in concordance in early mitosis for i1–i2, i1–m1, m1–m2, and i2–m2 stages. f. Flagged significant concordance differences (black boxes) for each of the difference heat maps shown in (e). g. Average structure similarity heat maps for interphase cells in the two shape-matched interphase datasets (i1, i2) and their corresponding prophase (m1) and early prometaphase (m2) mitotic cells. Due to the low number of cells in mitosis for some structures, we did not quantitatively analyse differences in the average location similarities, although their qualitative results matched those based on the concordance values. Heat maps in Supplementary Data 1.

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