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
  • Usage for gene expression:
  • Usage for color:
  • parse_args()
  • load_cell_metadata()
  • join_reconstructed_coords()
  • join_cluster_details()
  • join_cluster_colors()
  • join_parcellation_annotation()
  • join_parcellation_color()
  • filter_brain_section()
  • load_region_boundaries()
  • load_expression_data()
  • filter_expression_data()
  • create_expression_dataframe()
  • genes_in_merfish_data()
  • genes_in_imputed_merfish_data()
  • slice_index_dict()
  • section_to_zindex()
  • plot_section()
  • points_to_img_sum()
  • main()
• 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
  • Usage:
  • parse_args()
  • sanitize_filename()
  • save_filtered_value()
  • filter_all_values()
  • filter_dataframe()
  • main()
• unravel.allen_institute.abca.merfish.merfish_filter_by_mask module
  • Usage:
  • parse_args()
  • check_cells_in_mask()
  • merfish_filter_by_mask()
  • main()
• 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
  • Notes:
  • Usage:
  • Usage for one gene:
  • Usage for selected genes:
  • Usage for all genes:
  • GeneJobResult
  • parse_args()
  • unique_preserve_order()
  • get_requested_genes_from_args()
  • format_gene_preview()
  • find_expression_h5ad()
  • default_output_path()
  • get_var_symbols()
  • get_gene_to_cols()
  • load_and_prepare_cell_metadata()
  • infer_cell_id_column()
  • align_cells_to_adata()
  • precompute_linear_indices()
  • load_X_fully_into_memory()
  • subset_matrix_after_memory_load()
  • get_gene_values()
  • expression_values_to_img()
  • save_nii()
  • process_gene_job()
  • run_gene_jobs()
  • main()
• unravel.allen_institute.abca.merfish.merfish_join_expression module
  • Usage:
  • parse_args()
  • main()
• unravel.allen_institute.abca.merfish.merfish_check_genes module
  • Usage:
  • parse_args()
  • normalize_gene_names()
  • main()
• unravel.allen_institute.abca.merfish.merfish_regions module
  • Usage:
  • Usage with piping to grep:
  • parse_args()
  • main()