Single-Cell Pseudotime Trajectory Explorer

Real single-cell sequencing experiments capture a snapshot of thousands of cells frozen at different points along a developmental process — not a time-lapse. Pseudotime analysis reconstructs the missing time axis by connecting cells that are close together in expression space into a lineage graph and measuring distance along that graph. This simulator builds a synthetic branching population, computes its minimum-spanning-tree lineage graph in real 3D, and colors every cell by its pseudotime — click any cell to re-root the tree and watch the whole population re-order around its new developmental origin.