unravel.allen_institute.abca.merfish package

• unravel.allen_institute.abca.merfish.utils module
  • filter_neurons()
  • load_cell_metadata()
  • load_cell_metadata_og()
  • join_reconstructed_coords()
  • join_cluster_details()
  • join_cluster_colors()
  • join_parcellation_annotation()
  • join_parcellation_color()
  • filter_brain_section()
  • load_expression_data()
  • select_gene()
  • join_expression_to_section()
  • genes_in_merfish_data()
  • genes_in_imputed_merfish_data()
  • prepare_cells_table()
  • build_neuron_subset()
  • slice_index_dict()
  • load_region_boundaries()
  • auto_zoom()
  • plot_slice_color()
  • plot_slice_gene()
• unravel.allen_institute.abca.merfish.merfish module
• unravel.allen_institute.abca.merfish.merfish_slice module
  • Usage for color mode (choose cell_metadata.csv color column):
  • Usage for gene expression mode:
  • Usage for overlaying neurons:
  • parse_args()
  • join_cell_metadata()
  • legend_prep()
  • main()
• unravel.allen_institute.abca.merfish.merfish_filter module
• unravel.allen_institute.abca.merfish.merfish_filter_by_mask module
• unravel.allen_institute.abca.merfish.merfish_cells_to_nii module
  • Usage:
  • parse_args()
  • merfish_cells_to_img()
  • main()
• unravel.allen_institute.abca.merfish.merfish_expression_to_nii module
• unravel.allen_institute.abca.merfish.merfish_join_expression module
• unravel.allen_institute.abca.merfish.merfish_check_genes module
• unravel.allen_institute.abca.merfish.merfish_regions module
  • Usage:
  • Usage with piping to grep:
  • parse_args()
  • main()