StaVia Tutorial Videos

StaVia Installation

  • Via can also be run on Linux and MAC, setup is similar. with hnswlib potentially needing to be installed using pip or conda forge prior to pip install via

StaVia Implementation and Basic Usage

Main sections covered in usage tutorial

  • Initializing StaVia: setting the root, key parameters

  • Visualization: cluster level trajectory and terminals states

  • Visualization: hi-resolution edge drawings

  • Visualization: Mapping trajectory paths onto single-cell embeddings

  • Visualization: Animations of trajectories

  • Gene trends: along pseudotime

  • Lineage probabilistic pathways

StaVia for Spatial MERFISH data

Main sections

  • Initializing spatial parameters

  • Visualization on different levels (cluster graph, single cell and Atlas View)