Extended Data Fig. 5: The effect of anchor density on FICTURE performance.

(a) A representative example of the simulated spatial pattern with random cell type assignment. Colors indicate cell types. (b) Sliding hexagonal grids that generate the anchors. Top left shows a regular hexagonal tiling of the space. Black lines represent the axes along which we will slide the grid the yellow line segment marks the distance (d) between the centers of adjacent hexagons. The other three subplots on the left show the three possible tiling when we slide the grid with a step size s = d/2. The subplot on the right shows the resulting anchors, which are centers of the hexagons, where the distance between adjacent anchors equals to s. (c) The pixel level cell type assignment error rate (y-axis, with different ranges across rows) across analyses with different hexagon sizes (color) and distances between adjacent anchors (x-axis), stratified by the transcript density of the simulation (rows) and the shape of the simulated cells where the error is located (columns). ‘Background’ means the pixels located outside of the simulated cell boundaries. The transcript density outside cells is 20% of that within cells. The transcript densities indicated in the figure are the within-cell densities. (d) Total runtime (in seconds) of FICTURE when using different number of anchors in a 0.5 mm x 0.5 mm area, stratified by the transcript density. Data are presented as mean +/- SD with n = 10 in (C, D).