Index

_

__init__() (ibl_alignment_gui.backends.allen.anatomical_atlas.BrainAtlasAnatomical method) (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) (ibl_alignment_gui.plugins.channel_prediction.ChannelPrediction method)

A

activate_data_button() (ibl_alignment_gui.app.widgets.custom_widgets.SelectionWidget method) activate_selection_button() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) add_actions() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget static method) add_all_button() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) add_extra_alignments() (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) add_filters() (in module ibl_alignment_gui.plugins.allen.custom_filters) add_grid_layout() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) add_header() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) add_lut() (ibl_alignment_gui.app.widgets.custom_widgets.LutWidget method) add_options() (ibl_alignment_gui.app.widgets.custom_widgets.CheckBoxGroup method) add_plots() (in module ibl_alignment_gui.plugins.additional_plots) (in module ibl_alignment_gui.plugins.allen.additional_plots_allen) add_point() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) add_points_to_display() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) add_popup() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) add_reference_lines_to_display() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) add_regions() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) add_shanks() (ibl_alignment_gui.plugins.upload_dialog.UploadDialog method) add_shortcuts_to_menu() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) add_tab_layout() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) adjust_extremes_linear() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) adjust_extremes_uniform() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) align_reference_lines() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method)

align_reference_lines_and_points() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) aligned (ibl_alignment_gui.plugins.ephys_features.EphysFeatures property) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView property) AlignmentGUIController (class in ibl_alignment_gui.app.controllers.app_controller) AlignmentGUIView (class in ibl_alignment_gui.app.views.app_view) AlignmentHandler (class in ibl_alignment_gui.handlers.alignment_handler) AlignmentLoader (class in ibl_alignment_gui.loaders.alignment_loader) AlignmentLoaderDocDB (class in ibl_alignment_gui.loaders.alignment_loader) AlignmentLoaderLocal (class in ibl_alignment_gui.loaders.alignment_loader) AlignmentLoaderOne (class in ibl_alignment_gui.loaders.alignment_loader) AlignmentUploader (class in ibl_alignment_gui.loaders.alignment_uploader) AlignmentUploaderDocDB (class in ibl_alignment_gui.loaders.alignment_uploader) AlignmentUploaderLocal (class in ibl_alignment_gui.loaders.alignment_uploader) AlignmentUploaderOne (class in ibl_alignment_gui.loaders.alignment_uploader) AlignmentYAML (class in ibl_alignment_gui.utils.parse_yaml) AnatomicalSliceLoader (class in ibl_alignment_gui.loaders.histology_loader) AntsTransformChainFiles (class in ibl_alignment_gui.loaders.transform_loader) apply_fit() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) apply_to_all (ibl_alignment_gui.plugins.qc_dialog.QCDialog property) apply_to_shanks() (in module ibl_alignment_gui.plugins.qc_dialog) arrange_channels_into_banks() (in module ibl_alignment_gui.loaders.geometry_loader) arrange_into_regions() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) as_list() (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles method) atlas_image_path (ibl_alignment_gui.loaders.histology_loader.ImageSpacePaths attribute) atlas_labels_path (ibl_alignment_gui.loaders.histology_loader.ImageSpacePaths attribute) average_chns_at_same_depths() (in module ibl_alignment_gui.loaders.geometry_loader)

B

boundaries (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) BrainAtlasAnatomical (class in ibl_alignment_gui.backends.allen.anatomical_atlas)

build_anatomical_atlas() (in module ibl_alignment_gui.loaders.histology_loader) build_atlas() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) ButtonWidget (class in ibl_alignment_gui.app.widgets.custom_widgets)

C

callback() (in module ibl_alignment_gui.plugins.cluster_features) (in module ibl_alignment_gui.plugins.datoviz_3d) (in module ibl_alignment_gui.plugins.ephys_features) (in module ibl_alignment_gui.plugins.qc_dialog) (in module ibl_alignment_gui.plugins.range_controller) ChannelGeometry (class in ibl_alignment_gui.loaders.geometry_loader) ChannelPrediction (class in ibl_alignment_gui.plugins.channel_prediction) CheckBoxGroup (class in ibl_alignment_gui.app.widgets.custom_widgets) chn_max (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) chn_min (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) CircularIndexTracker (class in ibl_alignment_gui.handlers.alignment_handler) classes (ibl_alignment_gui.plugins.ephys_atlas.inference.InferenceModel attribute) clear_channels() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_feature() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_fit() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_histology() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_line() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_plots() (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView method) clear_probe() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_scale_factor() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_scatter() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_selection_dropdown() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) clear_slice() (ibl_alignment_gui.app.views.shank_view.ShankView method) clear_tabs() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) client (ibl_alignment_gui.backends.allen.docdb_api.DocDB property) close_popups() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) closeEvent() (ibl_alignment_gui.app.widgets.custom_widgets.PopupWindow method) cluster (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) ClusterPopup (class in ibl_alignment_gui.plugins.cluster_features) ClusterPopupManager (class in ibl_alignment_gui.plugins.cluster_features) cmap (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) ColorBar (class in ibl_alignment_gui.app.widgets.custom_widgets) COLOURS (ibl_alignment_gui.app.views.shank_view.ShankView attribute) colours (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) complete_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) compute_avg_cluster_activity() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) compute_bincount() (in module ibl_alignment_gui.loaders.plot_loader) compute_cumulative_predictions() (in module ibl_alignment_gui.plugins.channel_prediction) compute_inference_predictions() (in module ibl_alignment_gui.plugins.channel_prediction) compute_mapping_predictions() (in module ibl_alignment_gui.plugins.channel_prediction) compute_rasters() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method)

compute_spatial_encoder_predictions() (in module ibl_alignment_gui.plugins.channel_prediction) compute_spike_average() (in module ibl_alignment_gui.loaders.plot_loader) compute_timescales() (in module ibl_alignment_gui.plugins.cluster_features) Configuration (class in ibl_alignment_gui.utils.parse_yaml) configurations (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute) ConfigWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) connect_button() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) connect_cluster_plugin() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) connect_docdb_checkbox() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) connect_lin_fit() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) connect_selection_button() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) connect_selection_dropdown() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) connect_selection_menu() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) connect_tabs() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) create_checkbox_group() (ibl_alignment_gui.plugins.range_controller.RangeControllerView static method) create_combobox() (ibl_alignment_gui.app.widgets.custom_widgets.SelectionWidget static method) create_ephys_figure_layout() (ibl_alignment_gui.app.widgets.custom_widgets.ConfigWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.DualConfigFeatureWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.DualConfigWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SingleConfigFeatureWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SingleConfigWidget method) create_ephys_plots() (ibl_alignment_gui.app.views.shank_view.ShankView method) create_field_widget() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) create_figure_area() (ibl_alignment_gui.app.widgets.custom_widgets.ConfigWidget static method) create_figures() (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView static method) create_fit_items() (ibl_alignment_gui.app.views.shank_view.ShankView method) create_hist_figure_layout() (ibl_alignment_gui.app.widgets.custom_widgets.ConfigWidget static method) create_histology_plots() (ibl_alignment_gui.app.views.shank_view.ShankView method) create_line_edit() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) create_line_style() (ibl_alignment_gui.app.views.shank_view.ShankView static method) create_random_color() (in module ibl_alignment_gui.plugins.datoviz_3d) create_reference_line() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) create_reference_line_and_point() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) create_reference_lines() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) create_shanks() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) create_slice_items() (ibl_alignment_gui.app.views.shank_view.ShankView method) create_tabs() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget method) create_widgets() (ibl_alignment_gui.app.widgets.custom_widgets.ButtonWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.CheckBoxGroup method) (ibl_alignment_gui.app.widgets.custom_widgets.SelectionWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) current_idx (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property)

D

data (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) data_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) data_to_colors() (in module ibl_alignment_gui.plugins.datoviz_3d) DataLoader (class in ibl_alignment_gui.loaders.data_loader) DataLoaderLocal (class in ibl_alignment_gui.loaders.data_loader) DataLoaderOne (class in ibl_alignment_gui.loaders.data_loader) DatasetPaths (class in ibl_alignment_gui.utils.parse_yaml) Datasets (class in ibl_alignment_gui.utils.parse_yaml) datasets (ibl_alignment_gui.utils.parse_yaml.Probe attribute) deactivate_data_button() (ibl_alignment_gui.app.widgets.custom_widgets.SelectionWidget method) deactivate_selection_button() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) default_levels (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.LineData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) defaults (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute)

delete_progress() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploader method) delete_reference_line() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) delete_reference_line_and_point() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) delete_widgets() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) disable_sliders() (ibl_alignment_gui.plugins.range_controller.RangeController method) display() (in module ibl_alignment_gui.plugins.qc_dialog) (in module ibl_alignment_gui.plugins.upload_dialog) DocDB (class in ibl_alignment_gui.backends.allen.docdb_api) download_features() (ibl_alignment_gui.loaders.data_loader.FeatureLoaderOne method) download_histology() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocal method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocalYaml method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) download_histology_data() (in module ibl_alignment_gui.loaders.histology_loader) DualConfigFeatureWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) DualConfigWidget (class in ibl_alignment_gui.app.widgets.custom_widgets)

E

enterEvent() (ibl_alignment_gui.app.widgets.custom_widgets.PopupWindow method) EphysAlignment (class in ibl_alignment_gui.core.ephys_alignment) EphysFeatures (class in ibl_alignment_gui.plugins.ephys_features)

EphysFeatureView (class in ibl_alignment_gui.plugins.ephys_features) execute_plugins() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) exists (ibl_alignment_gui.loaders.transform_loader.TransformLoader property)

F

feature (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) feature2track() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) feature2track_lin() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) feature_ephys_atlas() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) feature_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) feature_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) feature_prev (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) FeatureLoader (class in ibl_alignment_gui.loaders.data_loader) FeatureLoaderLocal (class in ibl_alignment_gui.loaders.data_loader) FeatureLoaderOne (class in ibl_alignment_gui.loaders.data_loader) features (ibl_alignment_gui.plugins.ephys_atlas.inference.InferenceModel attribute) (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) Features3D (class in ibl_alignment_gui.plugins.datoviz_3d) FIELDS (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget attribute) filter_aind_qc() (in module ibl_alignment_gui.plugins.allen.custom_filters) filter_raw_by_chns() (ibl_alignment_gui.loaders.data_loader.DataLoader method)

filter_spikes_by_chns() (ibl_alignment_gui.loaders.data_loader.DataLoader method) filter_spikes_by_fr() (ibl_alignment_gui.loaders.data_loader.DataLoader static method) filter_unit_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) filter_unit_refine_neural() (in module ibl_alignment_gui.plugins.allen.custom_filters) filter_unit_refine_sua() (in module ibl_alignment_gui.plugins.allen.custom_filters) filter_units() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) find_actions() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget static method) find_geometry_mismatches() (in module ibl_alignment_gui.loaders.geometry_loader) fit_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) FitWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) FloatLineEdit (class in ibl_alignment_gui.app.widgets.custom_widgets) focus() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) focusOutEvent() (ibl_alignment_gui.app.widgets.custom_widgets.FloatLineEdit method) format_label() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget static method) format_value() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget static method) from_folder() (ibl_alignment_gui.loaders.histology_loader.ImageSpacePaths class method) (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles class method)

G

Geometry (class in ibl_alignment_gui.loaders.geometry_loader) GeometryLoader (class in ibl_alignment_gui.loaders.geometry_loader) GeometryLoaderLocal (class in ibl_alignment_gui.loaders.geometry_loader) GeometryLoaderOne (class in ibl_alignment_gui.loaders.geometry_loader) get() (ibl_alignment_gui.loaders.histology_loader.LazySliceDict method) get_autocorr() (in module ibl_alignment_gui.plugins.cluster_features) get_brain_locations() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_brain_regions() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) get_brush() (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar method) get_ccf_channels() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) get_channel_locations() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_channels() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) get_checked() (ibl_alignment_gui.app.widgets.custom_widgets.CheckBoxGroup method) get_color() (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar static method) get_colour_map() (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar method) get_config() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) get_current_shank() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) get_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) get_feature_and_track_coords() (ibl_alignment_gui.app.views.shank_view.ShankView method) get_features() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) get_geometry() (ibl_alignment_gui.loaders.geometry_loader.GeometryLoader method) get_histology_regions() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) get_image_plot_type() (ibl_alignment_gui.plugins.range_controller.RangeController method) get_insertion() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) get_insertion_track() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_layout() (ibl_alignment_gui.app.widgets.custom_widgets.ConfigWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.DualConfigFeatureWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.DualConfigWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SingleConfigFeatureWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SingleConfigWidget method) get_levels() (in module ibl_alignment_gui.plugins.range_controller) get_meta_data() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader method) get_model() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) get_nearest_boundary() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) get_passive_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) (ibl_alignment_gui.loaders.data_loader.DataLoaderLocal method) get_paths() (ibl_alignment_gui.loaders.histology_loader.AnatomicalSliceLoader method) (ibl_alignment_gui.loaders.histology_loader.NrrdSliceLoader method) (ibl_alignment_gui.loaders.histology_loader.SliceLoader method) (ibl_alignment_gui.loaders.histology_loader.TiffSliceLoader method) get_perp_vector() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_pids() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) get_plot() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) get_plot_group() (in module ibl_alignment_gui.plugins.range_controller) get_plot_keys() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) get_plots() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) get_previous_alignments() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method)

get_psd_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) get_qc() (ibl_alignment_gui.plugins.qc_dialog.QCDialog method) get_region_boundaries() (in module ibl_alignment_gui.plugins.channel_prediction) get_regions() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) (in module ibl_alignment_gui.plugins.datoviz_3d) get_rms_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) get_scale_factor() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_scaled_histology() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) get_selected_configs() (ibl_alignment_gui.plugins.range_controller.RangeControllerView method) get_selected_path() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) get_selected_shank() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) get_selected_shanks() (ibl_alignment_gui.plugins.range_controller.RangeControllerView method) get_selected_yaml() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) get_session_probe_name() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) get_sessions() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) get_shanks() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocal method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocalYaml method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) get_sites_for_shank() (ibl_alignment_gui.loaders.geometry_loader.GeometryLoader method) get_slices() (ibl_alignment_gui.loaders.histology_loader.SliceLoader method) get_slider_values() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) get_spike_sorting_path() (ibl_alignment_gui.loaders.data_loader.DataLoaderOne method) get_spikes_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) get_start_alignment_idx() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) get_starting_alignment() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) get_stored_alignment_idx() (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) get_subjects() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) get_template_wf() (in module ibl_alignment_gui.plugins.cluster_features) get_ticks() (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar method) get_time_snippets() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader static method) get_tip_location() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_track_and_feature() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) get_transforms() (ibl_alignment_gui.loaders.transform_loader.TransformLoader method) (ibl_alignment_gui.loaders.transform_loader.TransformLoaderAllen method) get_upload_info() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) get_xyz_picks() (in module ibl_alignment_gui.plugins.datoviz_3d) get_yaxis_lims() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) GridTabSwitcher (class in ibl_alignment_gui.app.widgets.custom_widgets) group_bincount() (in module ibl_alignment_gui.loaders.plot_loader)

H

has_allen() (in module ibl_alignment_gui.utils.optional) has_ibllib() (in module ibl_alignment_gui.utils.optional) has_menu_option() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method)

HEADER_STYLE (ibl_alignment_gui.app.views.shank_view.ShankView attribute) histology (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) histology_image_path (ibl_alignment_gui.loaders.histology_loader.ImageSpacePaths attribute) histology_space (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute)

I

ibl_alignment_gui module ibl_alignment_gui.app module ibl_alignment_gui.app.controllers module ibl_alignment_gui.app.controllers.app_controller module ibl_alignment_gui.app.controllers.shank_controller module ibl_alignment_gui.app.load_worker module ibl_alignment_gui.app.main module ibl_alignment_gui.app.views module ibl_alignment_gui.app.views.app_view module ibl_alignment_gui.app.views.shank_view module ibl_alignment_gui.app.widgets module ibl_alignment_gui.app.widgets.custom_widgets module ibl_alignment_gui.backends module ibl_alignment_gui.backends.allen module ibl_alignment_gui.backends.allen.anatomical_atlas module ibl_alignment_gui.backends.allen.docdb_api module ibl_alignment_gui.convertors module ibl_alignment_gui.core module ibl_alignment_gui.core.ephys_alignment module ibl_alignment_gui.handlers module ibl_alignment_gui.handlers.alignment_handler module ibl_alignment_gui.handlers.probe_handler module ibl_alignment_gui.handlers.shank_handler module ibl_alignment_gui.loaders module ibl_alignment_gui.loaders.alignment_loader module ibl_alignment_gui.loaders.alignment_uploader module ibl_alignment_gui.loaders.data_loader module ibl_alignment_gui.loaders.geometry_loader module ibl_alignment_gui.loaders.histology_loader module ibl_alignment_gui.loaders.plot_loader module ibl_alignment_gui.loaders.transform_loader module ibl_alignment_gui.plugins module ibl_alignment_gui.plugins.add_plugins module ibl_alignment_gui.plugins.additional_plots module ibl_alignment_gui.plugins.allen module

ibl_alignment_gui.plugins.allen.additional_plots_allen module ibl_alignment_gui.plugins.allen.custom_filters module ibl_alignment_gui.plugins.channel_prediction module ibl_alignment_gui.plugins.cluster_features module ibl_alignment_gui.plugins.datoviz_3d module ibl_alignment_gui.plugins.ephys_atlas module ibl_alignment_gui.plugins.ephys_atlas.inference module ibl_alignment_gui.plugins.ephys_features module ibl_alignment_gui.plugins.qc_dialog module ibl_alignment_gui.plugins.range_controller module ibl_alignment_gui.plugins.upload_dialog module ibl_alignment_gui.utils module ibl_alignment_gui.utils.helpers module ibl_alignment_gui.utils.optional module ibl_alignment_gui.utils.parse_yaml module idx (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) idx_prev (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) image_correlation() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_firing_rate() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) image_lfp_spectrum() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_passive_events() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) image_raw_ap_data() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_raw_lf_data() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_rms_ap() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_rms_ap_main() (in module ibl_alignment_gui.plugins.allen.additional_plots_allen) image_rms_lf() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_rms_lf_main() (in module ibl_alignment_gui.plugins.allen.additional_plots_allen) ImageData (class in ibl_alignment_gui.loaders.plot_loader) ImageSpacePaths (class in ibl_alignment_gui.loaders.histology_loader) img (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) indices_to_physical_points() (ibl_alignment_gui.backends.allen.anatomical_atlas.BrainAtlasAnatomical method) InferenceModel (class in ibl_alignment_gui.plugins.ephys_atlas.inference) init_plot_items() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) init_reference_line_arrays() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) init_shanks() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) init_tabs() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) init_view() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) initialise() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) initialise_shanks() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocal method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocalYaml method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) intensity_sitk_image (ibl_alignment_gui.backends.allen.anatomical_atlas.BrainAtlasAnatomical attribute) interpolate_along_track() (in module ibl_alignment_gui.core.ephys_alignment) invalidate_predictions() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) is_docdb_checked() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) is_grid (ibl_alignment_gui.app.views.app_view.AlignmentGUIView property) is_model_loaded() (in module ibl_alignment_gui.plugins.ephys_atlas.inference)

L

launch_app() (in module ibl_alignment_gui.app.main) launch_app_allen() (in module ibl_alignment_gui.app.main) launch_app_ibl() (in module ibl_alignment_gui.app.main) layout_widgets() (ibl_alignment_gui.app.widgets.custom_widgets.ButtonWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SelectionWidget method) (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) LazySliceDict (class in ibl_alignment_gui.loaders.histology_loader) leaveEvent() (ibl_alignment_gui.app.widgets.custom_widgets.PopupWindow method) levels (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.LineData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) levels_edited() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) levels_unchanged() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) lin_fit_option_changed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) line_amplitude() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) line_dead_channels() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) line_firing_rate() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) line_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) line_noisy_channels_coherence() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) line_noisy_channels_psd() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) line_outside_channels() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) line_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) LineData (class in ibl_alignment_gui.loaders.plot_loader) load_alignment_yaml() (in module ibl_alignment_gui.utils.parse_yaml) load_alignments() (ibl_alignment_gui.backends.allen.docdb_api.DocDB method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderDocDB method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderLocal method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderOne method) load_all() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) load_ap_data() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader method) (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderOne method) load_ap_snippets() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader method) load_channels() (ibl_alignment_gui.loaders.geometry_loader.GeometryLoader method) (ibl_alignment_gui.loaders.geometry_loader.GeometryLoaderLocal method) (ibl_alignment_gui.loaders.geometry_loader.GeometryLoaderOne method) load_data() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) (ibl_alignment_gui.loaders.data_loader.DataLoader static method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method)

load_dataframe() (ibl_alignment_gui.loaders.data_loader.FeatureLoaderOne method) load_ephys_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) (ibl_alignment_gui.loaders.data_loader.DataLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.DataLoaderOne method) load_features() (ibl_alignment_gui.loaders.data_loader.FeatureLoader method) (ibl_alignment_gui.loaders.data_loader.FeatureLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.FeatureLoaderOne method) load_inference_model() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) load_lf_data() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader method) (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderOne method) load_lf_snippets() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader method) load_meta_data() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader method) (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoaderOne method) (ibl_alignment_gui.loaders.geometry_loader.GeometryLoader method) (ibl_alignment_gui.loaders.geometry_loader.GeometryLoaderLocal method) (ibl_alignment_gui.loaders.geometry_loader.GeometryLoaderOne method) load_model_dialog() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) load_passive_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) (ibl_alignment_gui.loaders.data_loader.DataLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.DataLoaderOne method) load_pid() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) load_plots() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) load_previous_alignments() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) load_progress() (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) load_raw_passive_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) (ibl_alignment_gui.loaders.data_loader.DataLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.DataLoaderOne method) load_spikes_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) (ibl_alignment_gui.loaders.data_loader.DataLoaderLocal method) (ibl_alignment_gui.loaders.data_loader.DataLoaderOne method) load_trajectory() (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderOne method) load_volume() (ibl_alignment_gui.loaders.histology_loader.AnatomicalSliceLoader method) (ibl_alignment_gui.loaders.histology_loader.NrrdSliceLoader method) (ibl_alignment_gui.loaders.histology_loader.SliceLoader method) (ibl_alignment_gui.loaders.histology_loader.TiffSliceLoader method) load_xyz_picks() (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderLocal method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderOne method) loop_through_tabs() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) LutWidget (class in ibl_alignment_gui.app.widgets.custom_widgets)

M

make_slice_loader() (in module ibl_alignment_gui.loaders.histology_loader) make_transform() (ibl_alignment_gui.app.views.shank_view.ShankView static method) mask (ibl_alignment_gui.loaders.plot_loader.LineData attribute) mask_colour (ibl_alignment_gui.loaders.plot_loader.LineData attribute) mask_style (ibl_alignment_gui.loaders.plot_loader.LineData attribute) match_feature_line() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) match_linear_region() (ibl_alignment_gui.app.views.shank_view.ShankView method) match_track_line() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) MenuWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) MetaGeometry (class in ibl_alignment_gui.loaders.geometry_loader) minimise_popups() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) model_config (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute) (ibl_alignment_gui.utils.parse_yaml.Configuration attribute) (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) (ibl_alignment_gui.utils.parse_yaml.Datasets attribute) (ibl_alignment_gui.utils.parse_yaml.Probe attribute) model_path (ibl_alignment_gui.plugins.ephys_atlas.inference.InferenceModel attribute) module ibl_alignment_gui ibl_alignment_gui.app ibl_alignment_gui.app.controllers ibl_alignment_gui.app.controllers.app_controller ibl_alignment_gui.app.controllers.shank_controller ibl_alignment_gui.app.load_worker ibl_alignment_gui.app.main ibl_alignment_gui.app.views ibl_alignment_gui.app.views.app_view ibl_alignment_gui.app.views.shank_view ibl_alignment_gui.app.widgets ibl_alignment_gui.app.widgets.custom_widgets ibl_alignment_gui.backends ibl_alignment_gui.backends.allen ibl_alignment_gui.backends.allen.anatomical_atlas ibl_alignment_gui.backends.allen.docdb_api ibl_alignment_gui.convertors ibl_alignment_gui.core ibl_alignment_gui.core.ephys_alignment ibl_alignment_gui.handlers ibl_alignment_gui.handlers.alignment_handler ibl_alignment_gui.handlers.probe_handler ibl_alignment_gui.handlers.shank_handler ibl_alignment_gui.loaders ibl_alignment_gui.loaders.alignment_loader ibl_alignment_gui.loaders.alignment_uploader ibl_alignment_gui.loaders.data_loader ibl_alignment_gui.loaders.geometry_loader ibl_alignment_gui.loaders.histology_loader ibl_alignment_gui.loaders.plot_loader ibl_alignment_gui.loaders.transform_loader ibl_alignment_gui.plugins ibl_alignment_gui.plugins.add_plugins ibl_alignment_gui.plugins.additional_plots ibl_alignment_gui.plugins.allen ibl_alignment_gui.plugins.allen.additional_plots_allen ibl_alignment_gui.plugins.allen.custom_filters ibl_alignment_gui.plugins.channel_prediction ibl_alignment_gui.plugins.cluster_features ibl_alignment_gui.plugins.datoviz_3d ibl_alignment_gui.plugins.ephys_atlas ibl_alignment_gui.plugins.ephys_atlas.inference ibl_alignment_gui.plugins.ephys_features ibl_alignment_gui.plugins.qc_dialog ibl_alignment_gui.plugins.range_controller ibl_alignment_gui.plugins.upload_dialog ibl_alignment_gui.utils ibl_alignment_gui.utils.helpers ibl_alignment_gui.utils.optional ibl_alignment_gui.utils.parse_yaml

N

n_folds (ibl_alignment_gui.plugins.ephys_atlas.inference.InferenceModel attribute) next_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) next_idx() (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method)

next_idx_to_fill() (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker method) normalised (ibl_alignment_gui.plugins.ephys_features.EphysFeatures property) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView property) normalize_shank_label() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler static method) NrrdSliceLoader (class in ibl_alignment_gui.loaders.histology_loader)

O

offset (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) on_accept() (ibl_alignment_gui.plugins.qc_dialog.QCDialog method) (ibl_alignment_gui.plugins.upload_dialog.UploadDialog method) on_align_plots() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_alignment_selected() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_area_clicked() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_close() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) (ibl_alignment_gui.plugins.range_controller.RangeController method) on_cmap_chosen() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_config_button_clicked() (ibl_alignment_gui.plugins.range_controller.RangeControllerView method) on_config_selected() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_fig_size_changed() (ibl_alignment_gui.app.widgets.custom_widgets.FitWidget method) on_folder_selected() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_mouse_double_clicked() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_mouse_hover() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_next_page_pressed() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_normalise_plots() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method)

on_open_session_yaml() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_plot_changed() (ibl_alignment_gui.plugins.range_controller.RangeController method) on_plot_chosen() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_point_size_changed() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) on_prev_page_pressed() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_region_chosen() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_reset_button_pressed() (ibl_alignment_gui.plugins.range_controller.RangeController method) on_reset_levels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_session_selected() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_shank_button_clicked() (ibl_alignment_gui.plugins.range_controller.RangeControllerView method) (ibl_alignment_gui.plugins.upload_dialog.UploadDialog method) on_shank_selected() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_slider_moved() (ibl_alignment_gui.plugins.range_controller.RangeController method) on_slider_released() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_subject_selected() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_use_docdb_changed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) on_view_changed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) other_channel_paths (ibl_alignment_gui.loaders.histology_loader.ImageSpacePaths attribute) output (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute)

P

pad_data_to_full_chn_map() (in module ibl_alignment_gui.loaders.geometry_loader) page_step (ibl_alignment_gui.plugins.ephys_features.EphysFeatures property) paint() (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar method) parse_levels() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) path (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute) (ibl_alignment_gui.utils.parse_yaml.Configuration attribute) (ibl_alignment_gui.utils.parse_yaml.Datasets attribute) (ibl_alignment_gui.utils.parse_yaml.Probe attribute) pen (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) physical_points_to_indices() (ibl_alignment_gui.backends.allen.anatomical_atlas.BrainAtlasAnatomical method) picks (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) pipeline_image_path (ibl_alignment_gui.loaders.histology_loader.ImageSpacePaths attribute) pipeline_sitk_image (ibl_alignment_gui.backends.allen.anatomical_atlas.BrainAtlasAnatomical attribute) plot_all() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) plot_channel_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_channels() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) plot_clusters() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) plot_dual_colorbar() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_empty() (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_feature() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_feature_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_features() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) plot_fit() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_fit_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_histology() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_histology_cumulative() (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_histology_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_histology_ref() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) plot_histology_ref_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_image() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_image_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_line() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_line_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.plugins.range_controller.RangeController method) plot_picks() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) plot_probe() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView method) plot_probe_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_region() (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView method) plot_region_ref_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_regions() (ibl_alignment_gui.plugins.channel_prediction.ChannelPrediction method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method)

plot_scale_factor() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_scale_factor_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_scatter() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_scatter_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) plot_single_feature() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) plot_slice() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) plot_slice_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) PlotLoader (class in ibl_alignment_gui.loaders.plot_loader) Plugins (class in ibl_alignment_gui.plugins.add_plugins) points (ibl_alignment_gui.app.controllers.shank_controller.ShankController property) populate_combobox() (ibl_alignment_gui.app.widgets.custom_widgets.SelectionWidget static method) populate_exclusive_tab() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget method) populate_menu_tab() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) populate_menubar() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) populate_non_exclusive_tab() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget method) populate_selection_dropdown() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) popup_closed() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) popup_entered() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) popup_left() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) PopupWindow (class in ibl_alignment_gui.app.widgets.custom_widgets) predict() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) predict_cumulative() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) prepare_feature_data() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) prepare_offset_data() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) prepare_region_data() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) prev_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) prev_idx() (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) Probe (class in ibl_alignment_gui.utils.parse_yaml) probe_ephys_atlas() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) probe_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) probe_lfp_spectrum() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) probe_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) probe_rfmap() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) probe_rms_ap() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) probe_rms_ap_main() (in module ibl_alignment_gui.plugins.allen.additional_plots_allen) probe_rms_lf() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) probe_rms_lf_main() (in module ibl_alignment_gui.plugins.allen.additional_plots_allen) ProbeData (class in ibl_alignment_gui.loaders.plot_loader) ProbeHandler (class in ibl_alignment_gui.handlers.probe_handler) ProbeHandlerAllenYaml (class in ibl_alignment_gui.handlers.probe_handler) ProbeHandlerCSV (class in ibl_alignment_gui.handlers.probe_handler) ProbeHandlerLocal (class in ibl_alignment_gui.handlers.probe_handler) ProbeHandlerLocalYaml (class in ibl_alignment_gui.handlers.probe_handler) ProbeHandlerONE (class in ibl_alignment_gui.handlers.probe_handler) probes (ibl_alignment_gui.utils.parse_yaml.Configuration attribute) processed_ephys (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) progress_file (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploader property)

Q

QCDialog (class in ibl_alignment_gui.plugins.qc_dialog)

query_docdb_id() (ibl_alignment_gui.backends.allen.docdb_api.DocDB method)

R

RangeController (class in ibl_alignment_gui.plugins.range_controller) RangeControllerView (class in ibl_alignment_gui.plugins.range_controller) raw_ephys (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) raw_task (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) read_full_dataframe() (ibl_alignment_gui.loaders.data_loader.FeatureLoaderOne method) recovered_key (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader property) refresh_fields() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) remove_actions() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget static method) remove_fit_panels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) remove_grid_layout() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) remove_header() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) remove_items() (ibl_alignment_gui.app.views.shank_view.ShankView static method) remove_lut() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) (ibl_alignment_gui.app.widgets.custom_widgets.LutWidget method) remove_markers() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) remove_point() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) remove_points_from_display() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) remove_reference_line() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) remove_reference_lines_from_display() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method)

remove_regions() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) remove_tab_layout() (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method) reset_axis_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) reset_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) reset_default_levels() (in module ibl_alignment_gui.plugins.range_controller) reset_feature_and_tracks() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) reset_features_and_tracks() (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) reset_idx() (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker method) reset_levels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) reset_lut_levels() (ibl_alignment_gui.app.widgets.custom_widgets.LutWidget method) reset_pressed() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) reset_reference_line_arrays() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) reset_shanks() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) reset_slice_axis() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) reset_view() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) resolve_path() (in module ibl_alignment_gui.utils.parse_yaml) resolve_pid() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) run() (ibl_alignment_gui.app.load_worker.Worker method)

S

save_alignments() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) save_channels() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) save_progress() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploader method) save_progress_button_pressed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) scale (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) scale_hist_data() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) scale_histology_regions() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment method) scatter_amp_depth_duration() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) scatter_amp_depth_fr() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) scatter_amp_depth_prediction() (in module ibl_alignment_gui.plugins.additional_plots) scatter_firing_rate() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) scatter_fr_depth_amp() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) scatter_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) scatter_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) ScatterData (class in ibl_alignment_gui.loaders.plot_loader) SelectionWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) set_axis() (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar method) (in module ibl_alignment_gui.app.widgets.custom_widgets) set_checked() (ibl_alignment_gui.app.widgets.custom_widgets.CheckBoxGroup method) set_enabled() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) set_ephys_plots() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) set_feature_title() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) set_field() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) set_fig_scale_title() (ibl_alignment_gui.app.views.shank_view.ShankView method) set_font() (in module ibl_alignment_gui.app.widgets.custom_widgets) set_header_style() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) set_info() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocal method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerLocalYaml method) (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerONE method) set_init_alignment() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) set_init_feature_track() (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) set_init_levels() (ibl_alignment_gui.plugins.range_controller.RangeController method) set_init_reference_lines() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) set_labels() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) set_levels() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) (ibl_alignment_gui.app.widgets.custom_widgets.ColorBar method) (in module ibl_alignment_gui.plugins.range_controller) set_lut() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) (ibl_alignment_gui.app.widgets.custom_widgets.LutWidget method) set_lut_levels() (ibl_alignment_gui.app.widgets.custom_widgets.LutWidget method) set_markers() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) set_picks() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) set_point_size() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) set_points() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) set_probe_lims() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) set_scale_title() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) set_selected_path() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) set_selection_dropdown() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) set_shank_header() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) set_shank_tab() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) set_slice_tab() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) set_slider_intervals() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) set_slider_values() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method)

set_tabs() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) set_use_docdb() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerAllenYaml method) set_user_qc() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) set_xaxis_range() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) set_yaxis_lims() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) set_yaxis_range() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) setup() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.widgets.custom_widgets.PopupWindow method) (ibl_alignment_gui.plugins.cluster_features.ClusterPopup method) (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) (ibl_alignment_gui.plugins.datoviz_3d.Viewer3D method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView method) (ibl_alignment_gui.plugins.qc_dialog.QCDialog method) (ibl_alignment_gui.plugins.range_controller.RangeController method) (ibl_alignment_gui.plugins.range_controller.RangeControllerView method) (ibl_alignment_gui.plugins.upload_dialog.UploadDialog method) (in module ibl_alignment_gui.plugins.additional_plots) (in module ibl_alignment_gui.plugins.allen.additional_plots_allen) (in module ibl_alignment_gui.plugins.allen.custom_filters) (in module ibl_alignment_gui.plugins.channel_prediction) (in module ibl_alignment_gui.plugins.cluster_features) (in module ibl_alignment_gui.plugins.datoviz_3d) (in module ibl_alignment_gui.plugins.ephys_features) (in module ibl_alignment_gui.plugins.qc_dialog) (in module ibl_alignment_gui.plugins.range_controller) (in module ibl_alignment_gui.plugins.upload_dialog) setup_callback() (ibl_alignment_gui.app.widgets.custom_widgets.CheckBoxGroup method) setup_connections() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) setup_double_click() (ibl_alignment_gui.app.widgets.custom_widgets.ConfigWidget method) setup_mouse_hover() (ibl_alignment_gui.app.widgets.custom_widgets.ConfigWidget method) shank_loop() (in module ibl_alignment_gui.utils.helpers) shank_tab_changed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) ShankController (class in ibl_alignment_gui.app.controllers.shank_controller) ShankHandler (class in ibl_alignment_gui.handlers.shank_handler) ShankView (class in ibl_alignment_gui.app.views.shank_view) SingleConfigFeatureWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) SingleConfigWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) size (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) skip_missing() (in module ibl_alignment_gui.loaders.plot_loader) slice_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) slice_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) slice_tab_changed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) SliceLoader (class in ibl_alignment_gui.loaders.histology_loader) slider_released() (ibl_alignment_gui.app.widgets.custom_widgets.SliderWidget method) SliderWidget (class in ibl_alignment_gui.app.widgets.custom_widgets) smartspim_template_affine_transform (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles attribute) smartspim_template_warp_transform (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles attribute) space (ibl_alignment_gui.utils.parse_yaml.Datasets attribute) spike_amps (ibl_alignment_gui.loaders.plot_loader.PlotLoader property) spike_clusters (ibl_alignment_gui.loaders.plot_loader.PlotLoader property) spike_depths (ibl_alignment_gui.loaders.plot_loader.PlotLoader property) spike_sorting (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) spike_sorting_path (ibl_alignment_gui.loaders.data_loader.DataLoaderLocal property) (ibl_alignment_gui.loaders.data_loader.DataLoaderOne property) spike_times (ibl_alignment_gui.loaders.plot_loader.PlotLoader property) SpikeGLXLoader (class in ibl_alignment_gui.loaders.data_loader) SpikeGLXLoaderLocal (class in ibl_alignment_gui.loaders.data_loader) SpikeGLXLoaderOne (class in ibl_alignment_gui.loaders.data_loader) split_sites_per_shank() (ibl_alignment_gui.loaders.geometry_loader.Geometry method) symbol (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) sync_config_alignments() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method)

T

tab_layout_changed() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) task (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) teardown() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) template_to_ccf_affine_transform (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles attribute) template_to_ccf_warp_transform (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles attribute) tif2nrrd() (in module ibl_alignment_gui.loaders.histology_loader) TiffSliceLoader (class in ibl_alignment_gui.loaders.histology_loader) tip_location (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) title (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) toggle_action() (ibl_alignment_gui.app.widgets.custom_widgets.MenuWidget static method) toggle_channels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) toggle_labels() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) toggle_layout() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.app.widgets.custom_widgets.GridTabSwitcher method)

toggle_menu_option() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) toggle_picks() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) toggle_plots() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) toggle_reference_lines() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) toggle_regions() (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) toggle_tabs() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) total_idx (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) track (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) track2feature() (ibl_alignment_gui.core.ephys_alignment.EphysAlignment static method) track_lines (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) transform_to_ccf() (ibl_alignment_gui.loaders.transform_loader.TransformLoader method) (ibl_alignment_gui.loaders.transform_loader.TransformLoaderAllen method) TransformLoader (class in ibl_alignment_gui.loaders.transform_loader) TransformLoaderAllen (class in ibl_alignment_gui.loaders.transform_loader) transforms (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute) trigger_menu_option() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method)

U

update_channels() (in module ibl_alignment_gui.plugins.datoviz_3d) update_clusters() (in module ibl_alignment_gui.plugins.datoviz_3d) update_feature_reference_line() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) update_feature_reference_line_and_point() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) update_lut_levels() (ibl_alignment_gui.app.widgets.custom_widgets.LutWidget method) update_page_label() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) update_plots() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) (ibl_alignment_gui.plugins.datoviz_3d.Features3D method) update_string() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) update_track_reference_line() (ibl_alignment_gui.app.controllers.app_controller.AlignmentGUIController method) update_track_reference_line_and_point() (ibl_alignment_gui.app.controllers.shank_controller.ShankController method) (ibl_alignment_gui.app.views.shank_view.ShankView method) upload_alignments() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method)

upload_channels() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) upload_data() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploader method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderDocDB method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) upload_info() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) upload_prompt() (ibl_alignment_gui.app.views.app_view.AlignmentGUIView method) upload_qc() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) upload_shanks() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) uploadable_alignments (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader property) UploadDialog (class in ibl_alignment_gui.plugins.upload_dialog)

V

validate_features() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) validate_model() (in module ibl_alignment_gui.plugins.ephys_atlas.inference)

validate_model_folder() (in module ibl_alignment_gui.plugins.ephys_atlas.inference) Viewer3D (class in ibl_alignment_gui.plugins.datoviz_3d) vlines (ibl_alignment_gui.loaders.plot_loader.LineData attribute)

W

which_to_invert() (ibl_alignment_gui.loaders.transform_loader.AntsTransformChainFiles method)

Worker (class in ibl_alignment_gui.app.load_worker) write_output() (ibl_alignment_gui.backends.allen.docdb_api.DocDB method)

X

x (ibl_alignment_gui.loaders.plot_loader.LineData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) xaxis (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.LineData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute) xcorr() (in module ibl_alignment_gui.plugins.cluster_features) xrange (ibl_alignment_gui.loaders.plot_loader.ImageData attribute) (ibl_alignment_gui.loaders.plot_loader.LineData attribute) (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute)

xyz_channels (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) xyz_clusters (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) xyz_picks (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) xyz_samples (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) xyz_track (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property)

Y

y (ibl_alignment_gui.loaders.plot_loader.LineData attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute)

y_max (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) y_min (ibl_alignment_gui.handlers.shank_handler.ShankHandler property)