Extended Data Fig. 5: Overview panel for creating aggregated morphed cells for all 25 cellular structures.

a. Each row represents one of the 25 cellular structures (indicated by the colour bar on the far left). From left to right, on the left side of the large arrow, the first three sets of three images each show top view and side view 1 of three examples of individual cells with shapes similar to the mean cell shape (origin of the 8-dimensional sphere). For each set of three images, the left is the maximum intensity projection (MIP) of the original FP image (grayscale on black background), the centre is the average intensity projection of the structure segmentation image (AIP; binary on white background), and the right is the AIP for the structure segmentation-based PILR for that cell morphed into the mean cell shape. For nuclear envelope and nuclear pores, the centre slice, through the centre of the nucleus, of the original FP image is shown instead of the MIP. For these two structures and for histones, the cyan DNA outline has been left out to see the location of these structures at the nuclear periphery. b. On the right side of the large arrow are three different types of aggregations of the indicated number of individual morphed cells based on the structure segmentation PILRs. On the left is the average morphed cell, the centre is the standard deviation (std.) morphed cell, and the right is the “structure-localized coefficient of variation” (SLCV) morphed cell, representing a quantitative measure of how variable the location of a structure is at any given voxel (Supplementary Methods). Contrast settings for FP and AIP images were adjusted per cellular structure to best represent its location. Heat maps for average morphed cells indicate relative likelihood of a structure being at a given location in the cell. Heat map ranges for standard deviation morphed cell and SLCV morphed cell are as described (Supplementary Methods). Scale bars are 5 µm.