Paper Figures
Interactive notebooks reproducing the main figures from the SAME paper.
Synthetic Benchmark (Fig 2, S1)
411 template / 372 query cells, 3 cell types, 4 quadrants with distinct alignment challenges.
ISS Heart (Fig 3, S4–S7)
Human embryonic heart, ~3160 cells, 8 cell types. Includes parameter sweeps, noise robustness, and kNN analysis.
MERSCOPE Tongue — Protein + RNA (Fig 4, S9–S14)
Human tongue, 3608 RNA cells (MERSCOPE) + 4671 protein cells (PCF), 5 cell types. Cross-modal alignment with matrixplot and differential expression.
LUAD33 — Protein + Xenium (Fig 5, S15–S19)
Lung adenocarcinoma, ~94K PCF protein + ~100K Xenium RNA cells, 5 cell types. Penalty sweep, cross-modal matrixplot, and T cell exhaustion analysis.