allensdk package

Subpackages

• allensdk.api package
  • Subpackages
    • allensdk.api.cloud_cache package
      • Submodules
        • allensdk.api.cloud_cache.cloud_cache module
        • allensdk.api.cloud_cache.file_attributes module
        • allensdk.api.cloud_cache.manifest module
        • allensdk.api.cloud_cache.utils module
      • Module contents
    • allensdk.api.queries package
      • Submodules
        • allensdk.api.queries.annotated_section_data_sets_api module
        • allensdk.api.queries.biophysical_api module
        • allensdk.api.queries.brain_observatory_api module
        • allensdk.api.queries.cell_types_api module
        • allensdk.api.queries.connected_services module
        • allensdk.api.queries.glif_api module
        • allensdk.api.queries.grid_data_api module
        • allensdk.api.queries.image_download_api module
        • allensdk.api.queries.mouse_atlas_api module
        • allensdk.api.queries.mouse_connectivity_api module
        • allensdk.api.queries.ontologies_api module
        • allensdk.api.queries.reference_space_api module
        • allensdk.api.queries.rma_api module
        • allensdk.api.queries.rma_pager module
        • allensdk.api.queries.rma_template module
        • allensdk.api.queries.svg_api module
        • allensdk.api.queries.synchronization_api module
        • allensdk.api.queries.tree_search_api module
      • Module contents
    • allensdk.api.warehouse_cache package
      • Submodules
        • allensdk.api.warehouse_cache.cache module
        • allensdk.api.warehouse_cache.caching_utilities module
      • Module contents
  • Submodules
    • allensdk.api.api module
  • Module contents
• allensdk.brain_observatory package
  • Subpackages
    • allensdk.brain_observatory.behavior package
      • Subpackages
        • allensdk.brain_observatory.behavior.behavior_project_cache package
          • Subpackages
            • allensdk.brain_observatory.behavior.behavior_project_cache.external package
              • Submodules
                • allensdk.brain_observatory.behavior.behavior_project_cache.external.behavior_project_metadata_writer module
              • Module contents
            • allensdk.brain_observatory.behavior.behavior_project_cache.tables package
              • Subpackages
                • allensdk.brain_observatory.behavior.behavior_project_cache.tables.util package
                  • Submodules
                    • allensdk.brain_observatory.behavior.behavior_project_cache.tables.util.experiments_table_utils module
                    • allensdk.brain_observatory.behavior.behavior_project_cache.tables.util.image_presentation_utils module
                    • allensdk.brain_observatory.behavior.behavior_project_cache.tables.util.prior_exposure_processing module
                  • Module contents
              • Submodules
                • allensdk.brain_observatory.behavior.behavior_project_cache.tables.experiments_table module
                • allensdk.brain_observatory.behavior.behavior_project_cache.tables.ophys_mixin module
                • allensdk.brain_observatory.behavior.behavior_project_cache.tables.ophys_sessions_table module
                • allensdk.brain_observatory.behavior.behavior_project_cache.tables.project_table module
                • allensdk.brain_observatory.behavior.behavior_project_cache.tables.sessions_table module
              • Module contents
          • Submodules
            • allensdk.brain_observatory.behavior.behavior_project_cache.behavior_neuropixels_project_cache module
            • allensdk.brain_observatory.behavior.behavior_project_cache.behavior_project_cache module
            • allensdk.brain_observatory.behavior.behavior_project_cache.project_cache_base module
            • allensdk.brain_observatory.behavior.behavior_project_cache.utils module
          • Module contents
        • allensdk.brain_observatory.behavior.data_files package
          • Submodules
            • allensdk.brain_observatory.behavior.data_files.avg_projection_file module
            • allensdk.brain_observatory.behavior.data_files.demix_file module
            • allensdk.brain_observatory.behavior.data_files.dff_file module
            • allensdk.brain_observatory.behavior.data_files.event_detection_file module
            • allensdk.brain_observatory.behavior.data_files.eye_tracking_file module
            • allensdk.brain_observatory.behavior.data_files.eye_tracking_metadata_file module
            • allensdk.brain_observatory.behavior.data_files.eye_tracking_video module
            • allensdk.brain_observatory.behavior.data_files.max_projection_file module
            • allensdk.brain_observatory.behavior.data_files.neuropil_corrected_file module
            • allensdk.brain_observatory.behavior.data_files.neuropil_file module
            • allensdk.brain_observatory.behavior.data_files.rigid_motion_transform_file module
            • allensdk.brain_observatory.behavior.data_files.stimulus_file module
            • allensdk.brain_observatory.behavior.data_files.sync_file module
          • Module contents
        • allensdk.brain_observatory.behavior.data_objects package
          • Subpackages
            • allensdk.brain_observatory.behavior.data_objects.cell_specimens package
              • Subpackages
                • allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces package
                  • Submodules
                    • allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.corrected_fluorescence_traces module
                    • allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.demixed_traces module
                    • allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.dff_traces module
                    • allensdk.brain_observatory.behavior.data_objects.cell_specimens.traces.neuropil_traces module
                  • Module contents
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.cell_specimens.cell_specimens module
                • allensdk.brain_observatory.behavior.data_objects.cell_specimens.events module
                • allensdk.brain_observatory.behavior.data_objects.cell_specimens.rois_mixin module
              • Module contents
            • allensdk.brain_observatory.behavior.data_objects.eye_tracking package
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.eye_tracking.eye_tracking_table module
                • allensdk.brain_observatory.behavior.data_objects.eye_tracking.rig_geometry module
              • Module contents
            • allensdk.brain_observatory.behavior.data_objects.metadata package
              • Subpackages
                • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata package
                  • Submodules
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_metadata module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_session_id module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.behavior_session_uuid module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.date_of_acquisition module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.equipment module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.foraging_id module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.project_code module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.session_type module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_metadata.stimulus_frame_rate module
                  • Module contents
                • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata package
                  • Subpackages
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata package
                      • Submodules
                        • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.imaging_plane_group module
                        • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.multi_plane_metadata.multi_plane_metadata module
                      • Module contents
                  • Submodules
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.field_of_view_shape module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_depth module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.imaging_plane module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_container_id module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_experiment_metadata module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_project_code module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.ophys_session_id module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.ophys_experiment_metadata.targeted_imaging_depth module
                  • Module contents
                • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata package
                  • Submodules
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.age module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.driver_line module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.full_genotype module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.mouse_id module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.reporter_line module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.sex module
                    • allensdk.brain_observatory.behavior.data_objects.metadata.subject_metadata.subject_metadata module
                  • Module contents
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.metadata.behavior_ophys_metadata module
              • Module contents
            • allensdk.brain_observatory.behavior.data_objects.running_speed package
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.running_speed.multi_stim_running_processing module
                • allensdk.brain_observatory.behavior.data_objects.running_speed.running_acquisition module
                • allensdk.brain_observatory.behavior.data_objects.running_speed.running_processing module
                • allensdk.brain_observatory.behavior.data_objects.running_speed.running_speed module
              • Module contents
            • allensdk.brain_observatory.behavior.data_objects.stimuli package
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.stimuli.fingerprint_stimulus module
                • allensdk.brain_observatory.behavior.data_objects.stimuli.presentations module
                • allensdk.brain_observatory.behavior.data_objects.stimuli.stimuli module
                • allensdk.brain_observatory.behavior.data_objects.stimuli.stimulus_templates module
                • allensdk.brain_observatory.behavior.data_objects.stimuli.templates module
                • allensdk.brain_observatory.behavior.data_objects.stimuli.util module
              • Module contents
            • allensdk.brain_observatory.behavior.data_objects.timestamps package
              • Subpackages
                • allensdk.brain_observatory.behavior.data_objects.timestamps.stimulus_timestamps package
                  • Submodules
                    • allensdk.brain_observatory.behavior.data_objects.timestamps.stimulus_timestamps.stimulus_timestamps module
                    • allensdk.brain_observatory.behavior.data_objects.timestamps.stimulus_timestamps.timestamps_processing module
                  • Module contents
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.timestamps.ophys_timestamps module
                • allensdk.brain_observatory.behavior.data_objects.timestamps.util module
              • Module contents
            • allensdk.brain_observatory.behavior.data_objects.trials package
              • Submodules
                • allensdk.brain_observatory.behavior.data_objects.trials.trial module
                • allensdk.brain_observatory.behavior.data_objects.trials.trials module
              • Module contents
          • Submodules
            • allensdk.brain_observatory.behavior.data_objects.licks module
            • allensdk.brain_observatory.behavior.data_objects.motion_correction module
            • allensdk.brain_observatory.behavior.data_objects.projections module
            • allensdk.brain_observatory.behavior.data_objects.rewards module
            • allensdk.brain_observatory.behavior.data_objects.task_parameters module
          • Module contents
        • allensdk.brain_observatory.behavior.sync package
          • Submodules
            • allensdk.brain_observatory.behavior.sync.process_sync module
          • Module contents
        • allensdk.brain_observatory.behavior.write_behavior_nwb package
          • Submodules
            • allensdk.brain_observatory.behavior.write_behavior_nwb.schemas module
          • Module contents
        • allensdk.brain_observatory.behavior.write_nwb package
          • Subpackages
            • allensdk.brain_observatory.behavior.write_nwb.extensions package
              • Subpackages
                • allensdk.brain_observatory.behavior.write_nwb.extensions.event_detection package
                  • Submodules
                    • allensdk.brain_observatory.behavior.write_nwb.extensions.event_detection.extension_builder module
                    • allensdk.brain_observatory.behavior.write_nwb.extensions.event_detection.ndx_ophys_events module
                  • Module contents
                • allensdk.brain_observatory.behavior.write_nwb.extensions.stimulus_template package
                  • Submodules
                    • allensdk.brain_observatory.behavior.write_nwb.extensions.stimulus_template.extension_builder module
                    • allensdk.brain_observatory.behavior.write_nwb.extensions.stimulus_template.ndx_stimulus_template module
                  • Module contents
              • Module contents
          • Module contents
      • Submodules
        • allensdk.brain_observatory.behavior.behavior_ophys_analysis module
        • allensdk.brain_observatory.behavior.behavior_ophys_experiment module
        • allensdk.brain_observatory.behavior.behavior_ophys_session module
        • allensdk.brain_observatory.behavior.behavior_session module
        • allensdk.brain_observatory.behavior.criteria module
        • allensdk.brain_observatory.behavior.dprime module
        • allensdk.brain_observatory.behavior.event_detection module
        • allensdk.brain_observatory.behavior.eye_tracking_processing module
        • allensdk.brain_observatory.behavior.image_api module
        • allensdk.brain_observatory.behavior.mtrain module
        • allensdk.brain_observatory.behavior.rewards_processing module
        • allensdk.brain_observatory.behavior.schemas module
        • allensdk.brain_observatory.behavior.session_metrics module
        • allensdk.brain_observatory.behavior.stimulus_processing module
        • allensdk.brain_observatory.behavior.trial_masks module
        • allensdk.brain_observatory.behavior.trials_processing module
      • Module contents
    • allensdk.brain_observatory.data_release_utils package
      • Subpackages
        • allensdk.brain_observatory.data_release_utils.metadata_utils package
          • Submodules
            • allensdk.brain_observatory.data_release_utils.metadata_utils.id_generator module
            • allensdk.brain_observatory.data_release_utils.metadata_utils.utils module
          • Module contents
      • Module contents
    • allensdk.brain_observatory.ecephys package
      • Subpackages
        • allensdk.brain_observatory.ecephys.align_timestamps package
          • Submodules
            • allensdk.brain_observatory.ecephys.align_timestamps.barcode module
            • allensdk.brain_observatory.ecephys.align_timestamps.barcode_sync_dataset module
            • allensdk.brain_observatory.ecephys.align_timestamps.channel_states module
            • allensdk.brain_observatory.ecephys.align_timestamps.probe_synchronizer module
          • Module contents
        • allensdk.brain_observatory.ecephys.copy_utility package
          • Module contents
        • allensdk.brain_observatory.ecephys.current_source_density package
          • Module contents
        • allensdk.brain_observatory.ecephys.data_objects package
          • Submodules
            • allensdk.brain_observatory.ecephys.data_objects.trials module
          • Module contents
        • allensdk.brain_observatory.ecephys.ecephys_project_api package
          • Submodules
            • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_api module
            • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_fixed_api module
            • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_lims_api module
            • allensdk.brain_observatory.ecephys.ecephys_project_api.ecephys_project_warehouse_api module
            • allensdk.brain_observatory.ecephys.ecephys_project_api.http_engine module
            • allensdk.brain_observatory.ecephys.ecephys_project_api.rma_engine module
            • allensdk.brain_observatory.ecephys.ecephys_project_api.utilities module
          • Module contents
        • allensdk.brain_observatory.ecephys.ecephys_session_api package
          • Submodules
            • allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_nwb1_session_api module
            • allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_nwb_session_api module
            • allensdk.brain_observatory.ecephys.ecephys_session_api.ecephys_session_api module
          • Module contents
        • allensdk.brain_observatory.ecephys.file_io package
          • Submodules
            • allensdk.brain_observatory.ecephys.file_io.continuous_file module
            • allensdk.brain_observatory.ecephys.file_io.ecephys_sync_dataset module
            • allensdk.brain_observatory.ecephys.file_io.stim_file module
          • Module contents
        • allensdk.brain_observatory.ecephys.lfp_subsampling package
          • Submodules
            • allensdk.brain_observatory.ecephys.lfp_subsampling.subsampling module
          • Module contents
        • allensdk.brain_observatory.ecephys.nwb package
          • Submodules
            • allensdk.brain_observatory.ecephys.nwb.ecephys_nwb_extension_builder module
          • Module contents
        • allensdk.brain_observatory.ecephys.optotagging_table package
          • Module contents
        • allensdk.brain_observatory.ecephys.stimulus_analysis package
          • Submodules
            • allensdk.brain_observatory.ecephys.stimulus_analysis.dot_motion module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.drifting_gratings module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.flashes module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.natural_movies module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.natural_scenes module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.receptive_field_mapping module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.static_gratings module
            • allensdk.brain_observatory.ecephys.stimulus_analysis.stimulus_analysis module
          • Module contents
        • allensdk.brain_observatory.ecephys.stimulus_table package
          • Subpackages
            • allensdk.brain_observatory.ecephys.stimulus_table.visualization package
              • Submodules
                • allensdk.brain_observatory.ecephys.stimulus_table.visualization.view_blocks module
              • Module contents
          • Submodules
            • allensdk.brain_observatory.ecephys.stimulus_table.ephys_pre_spikes module
            • allensdk.brain_observatory.ecephys.stimulus_table.naming_utilities module
            • allensdk.brain_observatory.ecephys.stimulus_table.output_validation module
            • allensdk.brain_observatory.ecephys.stimulus_table.stimulus_parameter_extraction module
          • Module contents
        • allensdk.brain_observatory.ecephys.visualization package
          • Module contents
        • allensdk.brain_observatory.ecephys.write_nwb package
          • Subpackages
            • allensdk.brain_observatory.ecephys.write_nwb.vbn package
              • Module contents
          • Submodules
            • allensdk.brain_observatory.ecephys.write_nwb.nwb_writer module
            • allensdk.brain_observatory.ecephys.write_nwb.schemas module
          • Module contents
      • Submodules
        • allensdk.brain_observatory.ecephys.behavior_ecephys_session module
        • allensdk.brain_observatory.ecephys.ecephys_project_cache module
        • allensdk.brain_observatory.ecephys.ecephys_session module
        • allensdk.brain_observatory.ecephys.nwb_util module
        • allensdk.brain_observatory.ecephys.optotagging module
        • allensdk.brain_observatory.ecephys.probes module
        • allensdk.brain_observatory.ecephys.stimulus_sync module
        • allensdk.brain_observatory.ecephys.utils module
      • Module contents
    • allensdk.brain_observatory.extract_running_speed package
      • Module contents
    • allensdk.brain_observatory.gaze_mapping package
      • Module contents
    • allensdk.brain_observatory.multi_stimulus_running_speed package
      • Submodules
        • allensdk.brain_observatory.multi_stimulus_running_speed.multi_stimulus_running_speed module
      • Module contents
    • allensdk.brain_observatory.nwb package
      • Subpackages
        • allensdk.brain_observatory.nwb.eye_tracking package
          • Submodules
            • allensdk.brain_observatory.nwb.eye_tracking.extension_builder module
            • allensdk.brain_observatory.nwb.eye_tracking.ndx_ellipse_eye_tracking module
          • Module contents
      • Submodules
        • allensdk.brain_observatory.nwb.behavior_ophys_nwb_extension_builder module
        • allensdk.brain_observatory.nwb.metadata module
        • allensdk.brain_observatory.nwb.nwb_api module
        • allensdk.brain_observatory.nwb.nwb_utils module
        • allensdk.brain_observatory.nwb.schemas module
      • Module contents
    • allensdk.brain_observatory.ophys package
      • Subpackages
        • allensdk.brain_observatory.ophys.trace_extraction package
          • Module contents
      • Module contents
    • allensdk.brain_observatory.receptive_field_analysis package
      • Submodules
        • allensdk.brain_observatory.receptive_field_analysis.chisquarerf module
        • allensdk.brain_observatory.receptive_field_analysis.eventdetection module
        • allensdk.brain_observatory.receptive_field_analysis.fit_parameters module
        • allensdk.brain_observatory.receptive_field_analysis.fitgaussian2D module
        • allensdk.brain_observatory.receptive_field_analysis.postprocessing module
        • allensdk.brain_observatory.receptive_field_analysis.receptive_field module
        • allensdk.brain_observatory.receptive_field_analysis.tools module
        • allensdk.brain_observatory.receptive_field_analysis.utilities module
        • allensdk.brain_observatory.receptive_field_analysis.visualization module
      • Module contents
    • allensdk.brain_observatory.sync_utilities package
      • Module contents
    • allensdk.brain_observatory.vbn_2022 package
      • Subpackages
        • allensdk.brain_observatory.vbn_2022.input_json_writer package
          • Submodules
            • allensdk.brain_observatory.vbn_2022.input_json_writer.input_json_writer module
            • allensdk.brain_observatory.vbn_2022.input_json_writer.schemas module
            • allensdk.brain_observatory.vbn_2022.input_json_writer.utils module
          • Module contents
        • allensdk.brain_observatory.vbn_2022.metadata_writer package
          • Submodules
            • allensdk.brain_observatory.vbn_2022.metadata_writer.dataframe_manipulations module
            • allensdk.brain_observatory.vbn_2022.metadata_writer.lims_queries module
            • allensdk.brain_observatory.vbn_2022.metadata_writer.metadata_writer module
            • allensdk.brain_observatory.vbn_2022.metadata_writer.schemas module
          • Module contents
        • allensdk.brain_observatory.vbn_2022.utils package
          • Submodules
            • allensdk.brain_observatory.vbn_2022.utils.schemas module
          • Module contents
      • Module contents
    • allensdk.brain_observatory.visualization package
      • Module contents
  • Submodules
    • allensdk.brain_observatory.argschema_utilities module
    • allensdk.brain_observatory.brain_observatory_exceptions module
    • allensdk.brain_observatory.brain_observatory_plotting module
    • allensdk.brain_observatory.chisquare_categorical module
    • allensdk.brain_observatory.circle_plots module
    • allensdk.brain_observatory.comparison_utils module
    • allensdk.brain_observatory.demixer module
    • allensdk.brain_observatory.dff module
    • allensdk.brain_observatory.drifting_gratings module
    • allensdk.brain_observatory.findlevel module
    • allensdk.brain_observatory.locally_sparse_noise module
    • allensdk.brain_observatory.natural_movie module
    • allensdk.brain_observatory.natural_scenes module
    • allensdk.brain_observatory.observatory_plots module
    • allensdk.brain_observatory.r_neuropil module
    • allensdk.brain_observatory.roi_masks module
    • allensdk.brain_observatory.running_speed module
    • allensdk.brain_observatory.session_analysis module
    • allensdk.brain_observatory.session_api_utils module
    • allensdk.brain_observatory.static_gratings module
    • allensdk.brain_observatory.stimulus_analysis module
    • allensdk.brain_observatory.stimulus_info module
    • allensdk.brain_observatory.sync_dataset module
      • Dependencies
    • allensdk.brain_observatory.sync_stim_aligner module
  • Module contents
• allensdk.config package
  • Subpackages
    • allensdk.config.app package
      • Submodules
        • allensdk.config.app.application_config module
      • Module contents
    • allensdk.config.model package
      • Subpackages
        • allensdk.config.model.formats package
          • Submodules
            • allensdk.config.model.formats.hdf5_util module
            • allensdk.config.model.formats.json_description_parser module
            • allensdk.config.model.formats.pycfg_description_parser module
          • Module contents
      • Submodules
        • allensdk.config.model.description module
        • allensdk.config.model.description_parser module
      • Module contents
  • Submodules
    • allensdk.config.manifest module
    • allensdk.config.manifest_builder module
  • Module contents
• allensdk.core package
  • Subpackages
    • allensdk.core.lazy_property package
      • Submodules
        • allensdk.core.lazy_property.lazy_property module
        • allensdk.core.lazy_property.lazy_property_mixin module
      • Module contents
  • Submodules
    • allensdk.core.auth_config module
    • allensdk.core.authentication module
    • allensdk.core.brain_observatory_cache module
    • allensdk.core.brain_observatory_nwb_data_set module
    • allensdk.core.cache_method_utilities module
    • allensdk.core.cell_types_cache module
    • allensdk.core.dat_utilities module
    • allensdk.core.dataframe_utils module
    • allensdk.core.exceptions module
    • allensdk.core.h5_utilities module
    • allensdk.core.json_utilities module
    • allensdk.core.mouse_connectivity_cache module
    • allensdk.core.nwb_data_set module
    • allensdk.core.obj_utilities module
    • allensdk.core.ontology module
    • allensdk.core.ophys_experiment_session_id_mapping module
    • allensdk.core.pickle_utils module
    • allensdk.core.reference_space module
    • allensdk.core.reference_space_cache module
    • allensdk.core.simple_tree module
    • allensdk.core.sitk_utilities module
    • allensdk.core.structure_tree module
    • allensdk.core.swc module
    • allensdk.core.typing module
    • allensdk.core.utilities module
  • Module contents
• allensdk.ephys package
  • Submodules
    • allensdk.ephys.ephys_extractor module
    • allensdk.ephys.ephys_features module
    • allensdk.ephys.extract_cell_features module
    • allensdk.ephys.feature_extractor module
  • Module contents
• allensdk.internal package
  • Subpackages
    • allensdk.internal.api package
      • Subpackages
        • allensdk.internal.api.queries package
          • Submodules
            • allensdk.internal.api.queries.behavior_lims_queries module
            • allensdk.internal.api.queries.biophysical_module_api module
            • allensdk.internal.api.queries.biophysical_module_reader module
            • allensdk.internal.api.queries.compound_lims_queries module
            • allensdk.internal.api.queries.ecephys_lims_queries module
            • allensdk.internal.api.queries.equipment_lims_queries module
            • allensdk.internal.api.queries.grid_data_api_prerelease module
            • allensdk.internal.api.queries.mouse_connectivity_api_prerelease module
            • allensdk.internal.api.queries.optimize_config_reader module
            • allensdk.internal.api.queries.pre_release module
            • allensdk.internal.api.queries.utils module
            • allensdk.internal.api.queries.wkf_lims_queries module
          • Module contents
      • Submodules
        • allensdk.internal.api.api_prerelease module
        • allensdk.internal.api.lims_api module
        • allensdk.internal.api.mtrain_api module
      • Module contents
    • allensdk.internal.brain_observatory package
      • Subpackages
        • allensdk.internal.brain_observatory.resources package
          • Module contents
        • allensdk.internal.brain_observatory.util package
          • Submodules
            • allensdk.internal.brain_observatory.util.multi_session_utils module
          • Module contents
      • Submodules
        • allensdk.internal.brain_observatory.annotated_region_metrics module
        • allensdk.internal.brain_observatory.demix_report module
        • allensdk.internal.brain_observatory.demixer module
        • allensdk.internal.brain_observatory.eye_calibration module
        • allensdk.internal.brain_observatory.fit_ellipse module
        • allensdk.internal.brain_observatory.frame_stream module
        • allensdk.internal.brain_observatory.itracker module
        • allensdk.internal.brain_observatory.itracker_utils module
        • allensdk.internal.brain_observatory.mask_set module
        • allensdk.internal.brain_observatory.mouse module
        • allensdk.internal.brain_observatory.ophys_session_decomposition module
        • allensdk.internal.brain_observatory.roi_filter module
        • allensdk.internal.brain_observatory.roi_filter_utils module
        • allensdk.internal.brain_observatory.run_itracker module
        • allensdk.internal.brain_observatory.time_sync module
      • Module contents
    • allensdk.internal.core package
      • Submodules
        • allensdk.internal.core.lims_pipeline_module module
        • allensdk.internal.core.lims_utilities module
        • allensdk.internal.core.mouse_connectivity_cache_prerelease module
        • allensdk.internal.core.simpletree module
        • allensdk.internal.core.swc module
      • Module contents
    • allensdk.internal.ephys package
      • Submodules
        • allensdk.internal.ephys.core_feature_extract module
        • allensdk.internal.ephys.plot_qc_figures module
        • allensdk.internal.ephys.plot_qc_figures3 module
      • Module contents
    • allensdk.internal.model package
      • Subpackages
        • allensdk.internal.model.biophysical package
          • Subpackages
            • allensdk.internal.model.biophysical.fits package
              • Subpackages
                • allensdk.internal.model.biophysical.fits.fit_styles package
                  • Module contents
              • Module contents
            • allensdk.internal.model.biophysical.passive_fitting package
              • Subpackages
                • allensdk.internal.model.biophysical.passive_fitting.passive package
                  • Module contents
              • Submodules
                • allensdk.internal.model.biophysical.passive_fitting.neuron_passive_fit module
                • allensdk.internal.model.biophysical.passive_fitting.neuron_passive_fit2 module
                • allensdk.internal.model.biophysical.passive_fitting.neuron_passive_fit_elec module
                • allensdk.internal.model.biophysical.passive_fitting.neuron_utils module
                • allensdk.internal.model.biophysical.passive_fitting.output_grabber module
                • allensdk.internal.model.biophysical.passive_fitting.preprocess module
              • Module contents
          • Submodules
            • allensdk.internal.model.biophysical.biophysical_archiver module
            • allensdk.internal.model.biophysical.check_fi_shift module
            • allensdk.internal.model.biophysical.deap_utils module
            • allensdk.internal.model.biophysical.ephys_utils module
            • allensdk.internal.model.biophysical.fit_stage_1 module
            • allensdk.internal.model.biophysical.fit_stage_2 module
            • allensdk.internal.model.biophysical.make_deap_fit_json module
            • allensdk.internal.model.biophysical.neuron_parallel module
            • allensdk.internal.model.biophysical.optimize module
            • allensdk.internal.model.biophysical.run_optimize module
            • allensdk.internal.model.biophysical.run_optimize_workflow module
            • allensdk.internal.model.biophysical.run_passive_fit module
            • allensdk.internal.model.biophysical.run_simulate_lims module
            • allensdk.internal.model.biophysical.run_simulate_workflow module
          • Module contents
        • allensdk.internal.model.glif package
          • Submodules
            • allensdk.internal.model.glif.ASGLM module
            • allensdk.internal.model.glif.MLIN module
            • allensdk.internal.model.glif.are_two_lists_of_arrays_the_same module
            • allensdk.internal.model.glif.configure_model module
            • allensdk.internal.model.glif.error_functions module
            • allensdk.internal.model.glif.find_spikes module
            • allensdk.internal.model.glif.find_sweeps module
            • allensdk.internal.model.glif.glif_experiment module
            • allensdk.internal.model.glif.glif_optimizer module
            • allensdk.internal.model.glif.glif_optimizer_neuron module
            • allensdk.internal.model.glif.optimize_neuron module
            • allensdk.internal.model.glif.plotting module
            • allensdk.internal.model.glif.preprocess_neuron module
            • allensdk.internal.model.glif.rc module
            • allensdk.internal.model.glif.spike_cutting module
            • allensdk.internal.model.glif.threshold_adaptation module
          • Module contents
      • Submodules
        • allensdk.internal.model.AIC module
        • allensdk.internal.model.GLM module
        • allensdk.internal.model.data_access module
      • Module contents
    • allensdk.internal.morphology package
      • Submodules
        • allensdk.internal.morphology.compartment module
        • allensdk.internal.morphology.morphology module
        • allensdk.internal.morphology.morphvis module
        • allensdk.internal.morphology.node module
        • allensdk.internal.morphology.validate_swc module
      • Module contents
    • allensdk.internal.mouse_connectivity package
      • Subpackages
        • allensdk.internal.mouse_connectivity.interval_unionize package
          • Submodules
            • allensdk.internal.mouse_connectivity.interval_unionize.cav_unionize module
            • allensdk.internal.mouse_connectivity.interval_unionize.cav_unionizer module
            • allensdk.internal.mouse_connectivity.interval_unionize.data_utilities module
            • allensdk.internal.mouse_connectivity.interval_unionize.interval_unionizer module
            • allensdk.internal.mouse_connectivity.interval_unionize.run_tissuecyte_unionize_cav module
            • allensdk.internal.mouse_connectivity.interval_unionize.run_tissuecyte_unionize_classic module
            • allensdk.internal.mouse_connectivity.interval_unionize.tissuecyte_unionize_record module
            • allensdk.internal.mouse_connectivity.interval_unionize.tissuecyte_unionizer module
            • allensdk.internal.mouse_connectivity.interval_unionize.unionize_record module
          • Module contents
        • allensdk.internal.mouse_connectivity.projection_thumbnail package
          • Submodules
            • allensdk.internal.mouse_connectivity.projection_thumbnail.generate_projection_strip module
            • allensdk.internal.mouse_connectivity.projection_thumbnail.image_sheet module
            • allensdk.internal.mouse_connectivity.projection_thumbnail.projection_functions module
            • allensdk.internal.mouse_connectivity.projection_thumbnail.visualization_utilities module
            • allensdk.internal.mouse_connectivity.projection_thumbnail.volume_projector module
            • allensdk.internal.mouse_connectivity.projection_thumbnail.volume_utilities module
          • Module contents
        • allensdk.internal.mouse_connectivity.tissuecyte_stitching package
          • Submodules
            • allensdk.internal.mouse_connectivity.tissuecyte_stitching.stitcher module
            • allensdk.internal.mouse_connectivity.tissuecyte_stitching.tile module
          • Module contents
      • Module contents
    • allensdk.internal.notebooks package
      • Submodules
        • allensdk.internal.notebooks.execute_notebooks module
      • Module contents
    • allensdk.internal.pipeline_modules package
      • Subpackages
        • allensdk.internal.pipeline_modules.gbm package
          • Submodules
            • allensdk.internal.pipeline_modules.gbm.generate_gbm_analysis_run_records module
            • allensdk.internal.pipeline_modules.gbm.generate_gbm_heatmap module
            • allensdk.internal.pipeline_modules.gbm.generate_gbm_sample_metadata module
          • Module contents
      • Submodules
        • allensdk.internal.pipeline_modules.run_annotated_region_metrics module
        • allensdk.internal.pipeline_modules.run_demixing module
        • allensdk.internal.pipeline_modules.run_dff_computation module
        • allensdk.internal.pipeline_modules.run_eye_tracking module
        • allensdk.internal.pipeline_modules.run_neuropil_correction module
        • allensdk.internal.pipeline_modules.run_observatory_analysis module
        • allensdk.internal.pipeline_modules.run_observatory_container_thumbnails module
        • allensdk.internal.pipeline_modules.run_observatory_thumbnails module
        • allensdk.internal.pipeline_modules.run_ophys_eye_calibration module
        • allensdk.internal.pipeline_modules.run_ophys_session_decomposition module
        • allensdk.internal.pipeline_modules.run_ophys_time_sync module
        • 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
      • Module contents
  • Module contents
• allensdk.model package
  • Subpackages
    • allensdk.model.biophys_sim package
      • Subpackages
        • allensdk.model.biophys_sim.neuron package
          • Submodules
            • allensdk.model.biophys_sim.neuron.hoc_utils module
          • Module contents
        • allensdk.model.biophys_sim.scripts package
          • Module contents
      • Submodules
        • allensdk.model.biophys_sim.bps_command module
        • allensdk.model.biophys_sim.config module
      • Module contents
    • allensdk.model.biophysical package
      • Submodules
        • allensdk.model.biophysical.run_simulate module
        • allensdk.model.biophysical.runner module
        • allensdk.model.biophysical.utils module
      • Module contents
    • allensdk.model.glif package
      • Submodules
        • allensdk.model.glif.glif_neuron module
        • allensdk.model.glif.glif_neuron_methods module
        • allensdk.model.glif.simulate_neuron module
      • Module contents
  • Module contents
• allensdk.morphology package
  • Submodules
    • allensdk.morphology.validate_swc module
  • Module contents
• allensdk.mouse_connectivity package
  • Subpackages
    • allensdk.mouse_connectivity.grid package
      • Subpackages
        • allensdk.mouse_connectivity.grid.subimage package
          • Submodules
            • allensdk.mouse_connectivity.grid.subimage.base_subimage module
            • allensdk.mouse_connectivity.grid.subimage.cav_subimage module
            • allensdk.mouse_connectivity.grid.subimage.classic_subimage module
            • allensdk.mouse_connectivity.grid.subimage.count_subimage module
          • Module contents
        • allensdk.mouse_connectivity.grid.utilities package
          • Submodules
            • allensdk.mouse_connectivity.grid.utilities.downsampling_utilities module
            • allensdk.mouse_connectivity.grid.utilities.image_utilities module
          • Module contents
        • allensdk.mouse_connectivity.grid.writers package
          • Module contents
      • Submodules
        • allensdk.mouse_connectivity.grid.image_series_gridder module
      • Module contents
  • Module contents
• allensdk.test_utilities package
  • Submodules
    • allensdk.test_utilities.custom_comparators module
    • allensdk.test_utilities.regression_fixture module
    • allensdk.test_utilities.temp_dir module
  • Module contents

Submodules

• allensdk.deprecated module

Module contents

exception allensdk.OneResultExpectedError

Bases: RuntimeError

allensdk.one(x)