CloudReg
  • Setup
    • Setup (Cloud)
      • Requirements
      • Create AWS account
      • Create IAM Role
      • Create IAM User
      • Create S3 Bucket
      • Set up CORS on S3 Bucket containing processed data/results
      • Set up Docker EC2 instance
      • Set up MATLAB EC2 instance
      • Set up AWS CloudFront
      • Set up AWS Web Application Firewall
      • Local machine setup
    • Setup (Local)
      • Requirements
      • Local Machine Setup
  • Run
    • Cloud
      • Preprocessing
      • Registration
      • Visualization
    • Local
      • Convert 2D image series to precomputed format
      • Registration
      • Visualization
  • 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()
  • License

Useful Links

  • CloudReg @ GitHub
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© Copyright 2020, Vikram Chandrashekhar.

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