allensdk.internal.pipeline_modules package

Subpackages

• allensdk.internal.pipeline_modules.gbm package
  • Submodules
    • allensdk.internal.pipeline_modules.gbm.generate_gbm_analysis_run_records module
      • main()
    • allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap module
      • create_gene_fpkm_table()
      • create_genes_for_transcripts()
      • create_sample_metadata()
      • create_transcript_fpkm_table()
      • create_transcripts_for_genes()
      • main()
    • allensdk.internal.pipeline_modules.gbm.generate_gbm_sample_metadata module
      • main()
  • Module contents

Submodules

• allensdk.internal.pipeline_modules.run_annotated_region_metrics module
  • debug()
  • load_arrays()
  • main()
• allensdk.internal.pipeline_modules.run_demixing module
  • assert_exists()
  • debug()
  • get_path()
  • main()
  • parse_input()
• allensdk.internal.pipeline_modules.run_dff_computation module
  • main()
  • parse_input()
• allensdk.internal.pipeline_modules.run_eye_tracking module
• allensdk.internal.pipeline_modules.run_neuropil_correction module
  • adjust_r_for_negativity()
  • debug()
  • debug_plot()
  • main()
• allensdk.internal.pipeline_modules.run_observatory_analysis module
  • debug()
  • get_experiment_nwb_file()
  • get_experiment_session()
  • main()
• allensdk.internal.pipeline_modules.run_observatory_container_thumbnails module
• allensdk.internal.pipeline_modules.run_observatory_thumbnails module
  • build_cell_plots()
  • build_correlation_plots()
  • build_drifting_gratings()
  • build_experiment_thumbnails()
  • build_eye_tracking_plots()
  • build_locally_sparse_noise()
  • build_natural_movie()
  • build_natural_scenes()
  • build_plots()
  • build_receptive_field()
  • build_speed_tuning()
  • build_static_gratings()
  • build_type()
  • debug()
  • get_experiment_analysis_file()
  • get_experiment_files()
  • get_experiment_nwb_file()
  • get_input_data()
  • lsna_check_hvas()
  • main()
  • parse_input()
• allensdk.internal.pipeline_modules.run_ophys_eye_calibration module
  • debug()
  • get_wkf()
  • main()
  • parse_input_data()
  • write_output()
• allensdk.internal.pipeline_modules.run_ophys_session_decomposition module
  • convert_frame()
  • create_fake_metadata()
  • debug()
  • main()
  • parse_input()
• allensdk.internal.pipeline_modules.run_ophys_time_sync module
  • TimeSyncOutputs
    • TimeSyncOutputs.behavior_alignment
    • TimeSyncOutputs.behavior_delta
    • TimeSyncOutputs.behavior_times
    • TimeSyncOutputs.experiment_id
    • TimeSyncOutputs.eye_alignment
    • TimeSyncOutputs.eye_delta
    • TimeSyncOutputs.eye_times
    • TimeSyncOutputs.ophys_delta
    • TimeSyncOutputs.ophys_times
    • TimeSyncOutputs.stimulus_alignment
    • TimeSyncOutputs.stimulus_delay
    • TimeSyncOutputs.stimulus_delta
    • TimeSyncOutputs.stimulus_times
  • TimeSyncWriter
    • TimeSyncWriter.validate_paths()
    • TimeSyncWriter.write()
    • TimeSyncWriter.write_output_h5()
    • TimeSyncWriter.write_output_json()
  • check_stimulus_delay()
  • main()
  • run_ophys_time_sync()
• allensdk.internal.pipeline_modules.run_roi_filter module
• allensdk.internal.pipeline_modules.run_tissuecyte_projection_thumbnail_from_json module
• allensdk.internal.pipeline_modules.run_tissuecyte_stitching_classic module
• allensdk.internal.pipeline_modules.run_tissuecyte_unionize_cav_from_json module
• allensdk.internal.pipeline_modules.run_tissuecyte_unionize_classic_counts_from_json module
• allensdk.internal.pipeline_modules.run_tissuecyte_unionize_classic_from_json module
  • main()

Module contents