Index

A

activate_data_button() (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget method) activate_selection_button() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) AdaptedAxisItem (class in ibl_alignment_gui.utils.qt.adapted_axis) add_actions() (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget static method) add_all_button() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) add_extra_alignments() (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoader method) add_grid_layout() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) add_header() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) add_lut() (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget method) add_options() (ibl_alignment_gui.utils.qt.custom_widgets.CheckBoxGroup method) add_plots() (in module ibl_alignment_gui.plugins.additional_plots) add_point() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) add_points_to_display() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) add_popup() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) add_reference_lines_to_display() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) add_shanks() (ibl_alignment_gui.plugins.upload_dialog.UploadDialog method)

add_shortcuts_to_menu() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) add_tab_layout() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) align_reference_lines_and_points() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) aligned (ibl_alignment_gui.plugins.ephys_features.EphysFeatures property) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView property) AlignmentGUIView (class in ibl_alignment_gui.app.app_view) AlignmentHandler (class in ibl_alignment_gui.handlers.alignment_handler) AlignmentLoader (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) 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) allowMove() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) arrange_channels_into_banks() (in module ibl_alignment_gui.loaders.geometry_loader) average_chns_at_same_depths() (in module ibl_alignment_gui.loaders.geometry_loader)

B

backend (ibl_alignment_gui.utils.parse_yaml.Datasets attribute), [1] boundaries (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] brain_atlas (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler attribute) buffer (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler attribute)

button_style (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget attribute) buttons (ibl_alignment_gui.utils.qt.custom_widgets.ButtonWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget attribute) ButtonWidget (class in ibl_alignment_gui.utils.qt.custom_widgets)

C

callback() (in module ibl_alignment_gui.plugins.cluster_features) (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) checkboxes (ibl_alignment_gui.utils.qt.custom_widgets.CheckBoxGroup attribute) CheckBoxGroup (class in ibl_alignment_gui.utils.qt.custom_widgets) chn_max (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) chn_min (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) chosen_region (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) CircularIndexTracker (class in ibl_alignment_gui.handlers.alignment_handler) clear_channels() (ibl_alignment_gui.app.shank_view.ShankView method) clear_feature() (ibl_alignment_gui.app.shank_view.ShankView method) clear_fit() (ibl_alignment_gui.app.shank_view.ShankView method) clear_histology() (ibl_alignment_gui.app.shank_view.ShankView method) clear_line() (ibl_alignment_gui.app.shank_view.ShankView method) clear_plots() (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView method) clear_probe() (ibl_alignment_gui.app.shank_view.ShankView method) clear_scale_factor() (ibl_alignment_gui.app.shank_view.ShankView method) clear_scatter() (ibl_alignment_gui.app.shank_view.ShankView method) clear_selection_dropdown() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) clear_slice() (ibl_alignment_gui.app.shank_view.ShankView method) clear_tabs() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) close_popups() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) closed (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow attribute) closeEvent() (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow method) cluster (ibl_alignment_gui.app.shank_controller.ShankController attribute) (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] cluster_data (ibl_alignment_gui.app.shank_controller.ShankController attribute) cluster_popups (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager 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), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) ColorBar (class in ibl_alignment_gui.utils.qt.custom_widgets) COLOURS (ibl_alignment_gui.app.shank_view.ShankView attribute) colours (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] compute_avg_cluster_activity() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) compute_bincount() (in module ibl_alignment_gui.loaders.plot_loader) compute_cosmos_predictions() (in module ibl_alignment_gui.plugins.channel_prediction) compute_cumulative_distribution() (in module ibl_alignment_gui.plugins.channel_prediction) compute_random_predictions() (in module ibl_alignment_gui.plugins.channel_prediction)

compute_rasters() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) compute_spike_average() (in module ibl_alignment_gui.loaders.plot_loader) compute_timescales() (in module ibl_alignment_gui.plugins.cluster_features) config (ibl_alignment_gui.app.shank_controller.ShankController attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigWidget attribute) Configuration (class in ibl_alignment_gui.utils.parse_yaml) configurations (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute), [1] ConfigWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) connect_button() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) connect_lin_fit() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) connect_selection_button() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) connect_selection_dropdown() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) connect_tabs() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) controller (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView attribute) (ibl_alignment_gui.plugins.range_controller.RangeController attribute) create_combobox() (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget static method) create_ephys_figure_layout() (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigWidget method) create_ephys_plots() (ibl_alignment_gui.app.shank_view.ShankView method) create_figure_area() (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget static method) create_figures() (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView static method) create_fit_items() (ibl_alignment_gui.app.shank_view.ShankView method) create_hist_figure_layout() (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget static method) create_histology_plots() (ibl_alignment_gui.app.shank_view.ShankView method) create_line_style() (ibl_alignment_gui.app.shank_view.ShankView static method) create_reference_line_and_point() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) create_slice_items() (ibl_alignment_gui.app.shank_view.ShankView method) create_tabs() (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget method) create_widgets() (ibl_alignment_gui.utils.qt.custom_widgets.ButtonWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.CheckBoxGroup method) (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget method) current_idx (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) current_pids (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) custom_signal (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute), [1]

D

data (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] 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), [1] deactivate_data_button() (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget method) deactivate_selection_button() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) default_levels (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] defaults (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute), [1] delete_reference_line_and_point() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method)

delete_widgets() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) diff_idx (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) disable (ibl_alignment_gui.plugins.range_controller.RangeController attribute) 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) 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) drawPicture() (ibl_alignment_gui.utils.qt.adapted_axis.AdaptedAxisItem method) dropdowns (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget attribute) DualConfigFeatureWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) DualConfigWidget (class in ibl_alignment_gui.utils.qt.custom_widgets)

E

enter (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow attribute) enterEvent() (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow method) ephys_area (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget attribute)

ephysalign (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler attribute) EphysFeatures (class in ibl_alignment_gui.plugins.ephys_features) EphysFeatureView (class in ibl_alignment_gui.plugins.ephys_features)

F

feature (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) feature2track_lin() (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) feature_data (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) 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) FeatureLoaderOne (class in ibl_alignment_gui.loaders.data_loader) features (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler attribute)

fig_areas (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView attribute) fig_fit (ibl_alignment_gui.utils.qt.custom_widgets.FitWidget attribute) 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_units() (ibl_alignment_gui.app.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.utils.qt.custom_widgets.MenuWidget static method) FitWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) focus() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) format_label() (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget static method)

G

generateDrawSpecs() (ibl_alignment_gui.utils.qt.adapted_axis.AdaptedAxisItem method) 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_autocorr() (in module ibl_alignment_gui.plugins.cluster_features) get_brain_regions() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) get_brush() (ibl_alignment_gui.utils.qt.custom_widgets.ColorBar method) get_channels() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderLocal method) get_checked() (ibl_alignment_gui.utils.qt.custom_widgets.CheckBoxGroup method) get_color() (ibl_alignment_gui.utils.qt.custom_widgets.ColorBar static method) get_colour_map() (ibl_alignment_gui.utils.qt.custom_widgets.ColorBar method) get_config() (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.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_image_plot_type() (ibl_alignment_gui.plugins.range_controller.RangeController method) get_insertion() (ibl_alignment_gui.handlers.probe_handler.ProbeHandlerCSV method) get_layout() (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget method) (ibl_alignment_gui.utils.qt.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_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.NrrdSliceLoader method) (ibl_alignment_gui.loaders.histology_loader.SliceLoader 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) get_rms_data() (ibl_alignment_gui.loaders.data_loader.DataLoader method) get_scaled_histology() (ibl_alignment_gui.app.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.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_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_slice() (ibl_alignment_gui.loaders.histology_loader.SliceLoader method) get_slices() (ibl_alignment_gui.loaders.histology_loader.SliceLoader method) get_slider_values() (ibl_alignment_gui.utils.qt.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_starting_alignment() (ibl_alignment_gui.handlers.probe_handler.ProbeHandler method) (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.utils.qt.custom_widgets.ColorBar method) get_time_snippets() (ibl_alignment_gui.loaders.data_loader.SpikeGLXLoader static method) get_upload_info() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) get_yaxis_lims() (ibl_alignment_gui.app.shank_controller.ShankController method) grid_layout (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) grid_widget (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) GridTabSwitcher (class in ibl_alignment_gui.utils.qt.custom_widgets) group_bincount() (in module ibl_alignment_gui.loaders.plot_loader)

H

header (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigWidget attribute) HEADER_STYLE (ibl_alignment_gui.app.shank_view.ShankView attribute)

headers (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) high() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) hist_area (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget attribute) hist_mapping (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler attribute) histology (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute), [1]

I

ibl_alignment_gui module ibl_alignment_gui.app module ibl_alignment_gui.app.app_view module ibl_alignment_gui.app.shank_controller module ibl_alignment_gui.app.shank_view 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.plugins module ibl_alignment_gui.plugins.additional_plots module ibl_alignment_gui.plugins.channel_prediction module ibl_alignment_gui.plugins.cluster_features 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.parse_yaml module

ibl_alignment_gui.utils.qt module ibl_alignment_gui.utils.qt.adapted_axis module ibl_alignment_gui.utils.qt.custom_widgets module ibl_alignment_gui.utils.qt.qrange_slider module ibl_alignment_gui.utils.utils module idx (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigWidget attribute) idx_prev (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) 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_data() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_rms_ap() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) image_rms_lf() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) ImageData (class in ibl_alignment_gui.loaders.plot_loader) images (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget attribute) img (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] index (ibl_alignment_gui.app.shank_controller.ShankController attribute) init_plot_items() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) init_reference_line_arrays() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) init_tabs() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) init_view() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) initialise() (ibl_alignment_gui.utils.qt.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) intervals (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) is_grid (ibl_alignment_gui.app.app_view.AlignmentGUIView property) items (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigWidget attribute) items_default (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget attribute) items_non_default (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget attribute)

L

labels (ibl_alignment_gui.utils.qt.custom_widgets.ButtonWidget attribute) last_idx (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) layout (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) layout_widgets() (ibl_alignment_gui.utils.qt.custom_widgets.ButtonWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget method) (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget method) leave (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow attribute) leaveEvent() (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow method) levels (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) lin_fit_option (ibl_alignment_gui.utils.qt.custom_widgets.FitWidget attribute) 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.loaders.alignment_loader.AlignmentLoader method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderLocal method) (ibl_alignment_gui.loaders.alignment_loader.AlignmentLoaderOne 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_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.FeatureLoaderOne 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_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_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_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.NrrdSliceLoader method) (ibl_alignment_gui.loaders.histology_loader.SliceLoader 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) low() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) lut_layout (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget attribute) lut_levels (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget attribute) lut_status (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget attribute) LutWidget (class in ibl_alignment_gui.utils.qt.custom_widgets)

M

make_transform() (ibl_alignment_gui.app.shank_view.ShankView static method) mask (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] mask_colour (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] mask_style (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] match_feature_line() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) match_linear_region() (ibl_alignment_gui.app.shank_view.ShankView method) match_track_line() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) max_idx (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) max_levels (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) MenuWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) MetaGeometry (class in ibl_alignment_gui.loaders.geometry_loader) minimise_popups() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) model (ibl_alignment_gui.app.shank_controller.ShankController attribute) 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) module ibl_alignment_gui ibl_alignment_gui.app ibl_alignment_gui.app.app_view ibl_alignment_gui.app.shank_controller ibl_alignment_gui.app.shank_view 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.plugins ibl_alignment_gui.plugins.additional_plots ibl_alignment_gui.plugins.channel_prediction ibl_alignment_gui.plugins.cluster_features 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.parse_yaml ibl_alignment_gui.utils.qt ibl_alignment_gui.utils.qt.adapted_axis ibl_alignment_gui.utils.qt.custom_widgets ibl_alignment_gui.utils.qt.qrange_slider ibl_alignment_gui.utils.utils

mouseMoveEvent() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) mousePressEvent() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method)

N

name (ibl_alignment_gui.app.shank_controller.ShankController attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.DualConfigWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigFeatureWidget attribute) (ibl_alignment_gui.utils.qt.custom_widgets.SingleConfigWidget attribute) 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

offline (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget attribute) offset (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] offset_data (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) offset_hist_data() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) 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_area_clicked() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) on_close() (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_fig_size_changed() (ibl_alignment_gui.utils.qt.custom_widgets.FitWidget 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_plot_changed() (ibl_alignment_gui.plugins.range_controller.RangeController method) on_plot_chosen() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures 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.plugins.ephys_features.EphysFeatures method) on_shank_button_clicked() (ibl_alignment_gui.plugins.range_controller.RangeControllerView method) (ibl_alignment_gui.plugins.upload_dialog.UploadDialog method) on_slider_moved() (ibl_alignment_gui.plugins.range_controller.RangeController method) on_slider_released() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) output (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute), [1]

P

pad_data_to_full_chn_map() (in module ibl_alignment_gui.loaders.geometry_loader) page_idx (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) page_num (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) paint() (ibl_alignment_gui.utils.qt.custom_widgets.ColorBar method) paintEvent() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) panel_names (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) panels (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) parent (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget attribute) parent_view (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager attribute) path (ibl_alignment_gui.utils.parse_yaml.AlignmentYAML attribute), [1] (ibl_alignment_gui.utils.parse_yaml.Configuration attribute), [1] (ibl_alignment_gui.utils.parse_yaml.Datasets attribute), [1] (ibl_alignment_gui.utils.parse_yaml.Probe attribute), [1] pen (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] picks (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute), [1] pids (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) plot_all() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) plot_channels() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_empty() (ibl_alignment_gui.app.shank_view.ShankView method) plot_feature() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_features() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) plot_fit() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_histology() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_histology_cumulative() (ibl_alignment_gui.app.shank_view.ShankView method) plot_histology_ref() (ibl_alignment_gui.app.shank_controller.ShankController method) plot_idx (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) plot_image() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_keys (ibl_alignment_gui.plugins.range_controller.RangeController attribute) plot_line() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_name (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) plot_original_regions() (in module ibl_alignment_gui.plugins.channel_prediction) plot_panels() (ibl_alignment_gui.plugins.range_controller.RangeController method) plot_predicted_regions() (in module ibl_alignment_gui.plugins.channel_prediction) plot_probe() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView method) plot_region() (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView 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.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_scatter() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) plot_single_feature() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) plot_slice() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) PlotLoader (class in ibl_alignment_gui.loaders.plot_loader) plots_cbar (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView attribute) plots_feat (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView attribute) plots_hist (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView attribute) points (ibl_alignment_gui.app.shank_controller.ShankController property) populate_combobox() (ibl_alignment_gui.utils.qt.custom_widgets.SelectionWidget static method) populate_exclusive_tab() (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget method) populate_menu_tab() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) populate_non_exclusive_tab() (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget method) populate_selection_dropdown() (ibl_alignment_gui.app.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) popup_status (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager attribute) PopupWindow (class in ibl_alignment_gui.utils.qt.custom_widgets) 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_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_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_lf() (ibl_alignment_gui.loaders.plot_loader.PlotLoader method) ProbeData (class in ibl_alignment_gui.loaders.plot_loader) ProbeHandler (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), [1] processed_ephys (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute), [1]

Q

QCDialog (class in ibl_alignment_gui.plugins.qc_dialog)

QRangeSlider (class in ibl_alignment_gui.utils.qt.qrange_slider)

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), [1] raw_task (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute), [1] region_data (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) released (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute), [1] remove_actions() (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget static method) remove_grid_layout() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) remove_header() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) remove_items() (ibl_alignment_gui.app.shank_view.ShankView static method) remove_lut() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget method) remove_point() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) remove_points_from_display() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) remove_reference_line() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) remove_reference_lines_from_display() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method)

remove_tab_layout() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) replace_axis() (in module ibl_alignment_gui.utils.qt.adapted_axis) reset (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute), [1] reset() (ibl_alignment_gui.plugins.cluster_features.ClusterPopupManager method) reset_button (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) reset_default_levels() (in module ibl_alignment_gui.plugins.range_controller) 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.shank_controller.ShankController method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler method) reset_pressed() (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget method) reset_slice_axis() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) reset_view() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) resolve_path() (in module ibl_alignment_gui.utils.parse_yaml)

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) scale (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] scale_hist_data() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler method) (ibl_alignment_gui.handlers.shank_handler.ShankHandler 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) selected_idx (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) selected_pid (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) SelectionWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) set_axis() (ibl_alignment_gui.utils.qt.custom_widgets.ColorBar method) (in module ibl_alignment_gui.utils.qt.custom_widgets) set_checked() (ibl_alignment_gui.utils.qt.custom_widgets.CheckBoxGroup method) set_feature_title() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) set_fig_scale_title() (ibl_alignment_gui.app.shank_view.ShankView method) set_font() (in module ibl_alignment_gui.utils.qt.custom_widgets) set_header_style() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.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_labels() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) set_levels() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) (ibl_alignment_gui.utils.qt.custom_widgets.ColorBar method) (in module ibl_alignment_gui.plugins.range_controller) set_lut() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget method) set_lut_levels() (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget method) set_probe_lims() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) set_scale_title() (ibl_alignment_gui.app.shank_controller.ShankController method) set_selected_path() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) set_selection_dropdown() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) set_shank_tab() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) set_slice_tab() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) set_slider_intervals() (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget method) set_slider_values() (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget method) set_tabs() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) set_user_qc() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) set_xaxis_range() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method)

set_yaxis_lims() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) set_yaxis_range() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) setHigh() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) setLow() (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider method) setup() (ibl_alignment_gui.plugins.cluster_features.ClusterPopup 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) (ibl_alignment_gui.utils.qt.custom_widgets.PopupWindow method) (in module ibl_alignment_gui.plugins.additional_plots) (in module ibl_alignment_gui.plugins.channel_prediction) (in module ibl_alignment_gui.plugins.cluster_features) (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.utils.qt.custom_widgets.CheckBoxGroup method) setup_double_click() (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget method) setup_mouse_hover() (ibl_alignment_gui.utils.qt.custom_widgets.ConfigWidget method) shank_loop() (in module ibl_alignment_gui.utils.utils) ShankController (class in ibl_alignment_gui.app.shank_controller) ShankHandler (class in ibl_alignment_gui.handlers.shank_handler) ShankView (class in ibl_alignment_gui.app.shank_view) Signals (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) SingleConfigFeatureWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) SingleConfigWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) size (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] skip_missing() (in module ibl_alignment_gui.loaders.plot_loader) slice_keys (ibl_alignment_gui.handlers.probe_handler.ProbeHandler property) slice_lut (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget attribute) slice_plots (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) SliceLoader (class in ibl_alignment_gui.loaders.histology_loader) slider (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) slider_labels (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) slider_released() (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget method) slider_type (ibl_alignment_gui.utils.qt.custom_widgets.SliderWidget attribute) sliderMoved (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider attribute) sliderReleased (ibl_alignment_gui.utils.qt.qrange_slider.QRangeSlider attribute) SliderWidget (class in ibl_alignment_gui.utils.qt.custom_widgets) 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), [1] 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) step (ibl_alignment_gui.plugins.ephys_features.EphysFeatures attribute) (ibl_alignment_gui.plugins.ephys_features.EphysFeatureView attribute) symbol (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1]

T

tab_widget (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher attribute) tabs (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget attribute) task (ibl_alignment_gui.utils.parse_yaml.DatasetPaths attribute), [1] tif2nrrd() (in module ibl_alignment_gui.loaders.histology_loader) title (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] (ibl_alignment_gui.plugins.range_controller.RangeController attribute) toggle_action() (ibl_alignment_gui.utils.qt.custom_widgets.MenuWidget static method) toggle_channels() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) toggle_labels() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method)

toggle_layout() (ibl_alignment_gui.utils.qt.custom_widgets.GridTabSwitcher method) toggle_menu_option() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) toggle_tabs() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) total_idx (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.alignment_handler.CircularIndexTracker attribute) (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) track_lines (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler property) (ibl_alignment_gui.handlers.shank_handler.ShankHandler property) tracks (ibl_alignment_gui.handlers.alignment_handler.AlignmentHandler attribute) trigger_menu_option() (ibl_alignment_gui.app.app_view.AlignmentGUIView method)

U

update_feature_reference_line_and_point() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.shank_view.ShankView method) update_lut_levels() (ibl_alignment_gui.utils.qt.custom_widgets.LutWidget method) update_page_label() (ibl_alignment_gui.plugins.ephys_features.EphysFeatures method) update_track_reference_line_and_point() (ibl_alignment_gui.app.shank_controller.ShankController method) (ibl_alignment_gui.app.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.AlignmentUploaderLocal method) (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) upload_info() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) upload_prompt() (ibl_alignment_gui.app.app_view.AlignmentGUIView method) upload_qc() (ibl_alignment_gui.loaders.alignment_uploader.AlignmentUploaderOne method) UploadDialog (class in ibl_alignment_gui.plugins.upload_dialog)

V

view (ibl_alignment_gui.app.shank_controller.ShankController attribute) (ibl_alignment_gui.plugins.range_controller.RangeController attribute)

vlines (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1]

X

x (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] xaxis (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1] xrange (ibl_alignment_gui.loaders.plot_loader.ImageData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.LineData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ProbeData attribute), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1]

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_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), [1] (ibl_alignment_gui.loaders.plot_loader.ScatterData attribute), [1]

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