Reference

• COLM pipeline
  • run_colm_pipeline()
• Intensity Correction
  • correct_stitched_data()
  • process_slice()
• Cloud Storage Input/Output
  • download_data()
  • get_mip_at_res()
• Stitching
  • generate_stitching_commands()
  • get_metadata()
  • get_scanned_cells()
  • run_terastitcher()
  • write_import_xml()
  • write_terastitcher_commands()
  • * Change Log *
  • check_double_quote()
  • check_flag()
  • collect_instructions()
  • create_commands()
  • create_sizes()
  • create_starts_end()
  • eliminate_double_quote()
  • extract_params()
  • generate_final_command()
  • generate_first_command()
  • generate_parallel_command()
  • main()
  • opt_algo()
  • pop_left()
  • prep_array()
  • read_item()
  • read_params()
  • score_function()
  • search_for_entry()
  • sort_elaborations()
  • sort_list()
  • sort_start_end()
  • sort_work()
  • subordinate()
  • worker()
  • * Change Log *
  • check_double_quote()
  • check_flag()
  • collect_instructions()
  • create_commands()
  • create_sizes()
  • create_starts_end()
  • do_additional_partition()
  • eliminate_double_quote()
  • extract_np()
  • extract_params()
  • find_last_slash()
  • generate_final_command()
  • generate_first_command()
  • generate_parallel_command()
  • main_step2()
  • main_step6()
  • opt_algo()
  • partition()
  • pop_left()
  • prep_array()
  • read_input()
  • read_item()
  • read_params()
  • score_function()
  • search_for_entry()
  • sort_elaborations()
  • sort_list()
  • sort_start_end()
  • sort_work()
  • subordinate()
  • worker()
• Registration
  • run_registration()
  • get_affine_matrix()
  • register()
• Utility Functions
  • S3Url
  • aws_cli()
  • calc_hierarchy_levels()
  • chunks()
  • download_terastitcher_files()
  • get_bias_field()
  • get_matching_s3_keys()
  • get_reorientations()
  • imgResample()
  • run_command_on_server()
  • start_ec2_instance()
  • tqdm_joblib()
  • upload_file_to_s3()
  • S3Url
  • create_viz_link()
  • get_layer_json()
  • get_neuroglancer_json()
  • get_output_dimensions_json()