Interactive analysis of single-cell trajectories in 3D space with Cell Journey

Cell Journey is an interactive platform for 3D visualization and analysis of RNA velocity trajectories in single-cell datasets, addressing the limitations of 2D representations by providing a more accurate depiction of cellular transitions. It supports unimodal and multimodal data, offering extensive customization for trajectory visualization and computes RNA velocity vector fields using Euler integration or the Runge–Kutta method. The platform's intuitive interface allows researchers to explore cellular dynamics and state transitions, demonstrated with datasets from mouse pancreatic endocrinogenesis and human bone marrow mononuclear cell progenitors. Cell Journey is Python-based, integrates with tools like Scanpy, and excels in visualizing cellular transitions with customizable volume plots. It is optimized for speed, capable of handling large-scale datasets, and supports various experimental and computational approaches, with ongoing development to expand its functionality.