unravel.allen_institute.abca package

• unravel.allen_institute.abca.cache module
• unravel.allen_institute.abca.merfish package
  • unravel.allen_institute.abca.merfish.utils module
    • filter_neurons()
    • load_cell_metadata()
    • 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_gene module
• unravel.allen_institute.abca.sunburst package
  • unravel.allen_institute.abca.sunburst.sunburst module
    • Usage:
    • parse_args()
    • filter_non_neuronal_cells()
    • main()
  • unravel.allen_institute.abca.sunburst.sunburst_expression module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.sunburst_filter_by_expression module
    • Usage for first run:
    • Usage to apply filtering from another dataset:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.sunburst_filter_by_proportion module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.mean_expression_color_scale module
    • Usage:
    • parse_args()
    • main()
  • unravel.allen_institute.abca.sunburst.percent_expression_color_scale module
    • Usage:
    • parse_args()
    • main()
• unravel.allen_institute.abca.scRNA_seq package
  • unravel.allen_institute.abca.scRNA_seq.filter module
  • unravel.allen_institute.abca.scRNA_seq.expression module
  • unravel.allen_institute.abca.scRNA_seq.join_gene module