Tutorials

• Tutorial to generate checkerbord cell simulation with an artbitray expression
  • 1) Generate checkerboard
  • 2) Add nuclei in the checker board
  • 3) Simulation of arbitrary cell expression
  • Plot of final simulation
  • Save and load simulation
• Tutorial for tissue simulation with transcriptomic profile sample from scRNAseq data
  • download test data at :
  • 1) Generate the cytoplasm with simulate_single_cell_mask()
  • 2) (optional) Remove a percentage of nuclei with remove_nuclei
  • 3) sample transcriptomic profile with sim_spots_from_ref_anndata() and simulate position
  • Plot final simulation