Extended Data Fig. 4: Benchmarking analysis under various simulation settings.

(a) Cell shape parameters used in all benchmarking simulations for comparison between FICTURE, Baysor and GraphST. (b) The pixel level error rate under two scenarios with different cell packing settings across 20 simulations with randomly sampled cell types. Apart from the three methods compared in the main results, we included grid-based LDA analysis performed on hexagons. (c-h) A visualization similar to Fig. 3b, but instead of simulating transcripts assuming sparse background outside cell boundaries, this simulation uses the uniform transcript density across the entire region. We refer to this simulation as ‘densely packed’ while ‘sparse background’ represents the simulation in Fig. 3b. (c-e): All pixels are visualized with colors representing their inferred factors from (c) FICTURE, (d) Baysor, and (e) Graph ST. (f-h): Pixels where the factors inferred from (f) FICTURE, (g) Baysor, and (h) GraphST differ from the ground truth are visualized with colors representing their true generating factors.