Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | R | S | T | U | V | W | X _ _abc_impl (neurotorchmz.core.logs.StdOutCatcher attribute) (neurotorchmz.core.task_system._TaskFunction attribute) _btn_remove_cick() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _btn_stage_click() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _callbacks (neurotorchmz.utils.synapse_detection.DetectionResult attribute) (neurotorchmz.utils.synapse_detection.ISynapse attribute) (neurotorchmz.utils.synapse_detection.ISynapseROI attribute) (neurotorchmz.utils.synapse_detection.ROIList attribute) _canvas1_resize() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) _coords (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI attribute) _format() (neurotorchmz.utils.synapse_detection.ISynapse method) _frame (neurotorchmz.utils.synapse_detection.ISynapseROI attribute) _FrameResize() (neurotorchmz.gui.tabWelcome.TabWelcome method) _FrameResizeEvent() (neurotorchmz.gui.tabWelcome.TabWelcome method) _id_count (neurotorchmz.core.task_system.Task attribute) _image_object (neurotorchmz.core.session.Session attribute) _image_path (neurotorchmz.core.session.Session attribute) _imageJ_ready() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) _insert_dict_into_tree() (neurotorchmz.gui.tab1.TabImage method) _int_var_update() (neurotorchmz.gui.components.general.Intstring_var method) _is_protocol (neurotorchmz.core.task_system._TaskFunction attribute) _is_valid_image_stack() (neurotorchmz.utils.image.ImageObject static method) _loading_error_callback() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) _location (neurotorchmz.utils.synapse_detection.ISynapseROI attribute) (neurotorchmz.utils.synapse_detection.MultiframeSynapse attribute) _mpl_ini (neurotorchmz.gui.window.Neurotorch_GUI attribute) _name (neurotorchmz.utils.synapse_detection.ISynapse attribute) _on_closing() (neurotorchmz.gui.window.Neurotorch_GUI method) _on_context_menu_add() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_context_menu_all_from_stage() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_context_menu_all_to_stage() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_context_menu_export() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_context_menu_remove() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_context_menu_reset_name() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_context_menu_toggle_stage() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_double_click() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_entry_changed() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_lower_timer_tick() (neurotorchmz.gui.components.general.Statusbar method) _on_right_click() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_select() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _on_timer_tick() (neurotorchmz.gui.components.general.Statusbar method) _open_image_error_callback() (neurotorchmz.gui.window.Neurotorch_GUI method) _pipe_thread() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) _polygon (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI attribute) _radius (neurotorchmz.utils.synapse_detection.CircularSynapseROI attribute) _region_props (neurotorchmz.utils.synapse_detection.ISynapseROI attribute) _roifinder_detection_result (neurotorchmz.core.session.Session attribute) _rois (neurotorchmz.utils.synapse_detection.ROIList attribute) _rois_callbacks (neurotorchmz.utils.synapse_detection.ROIList attribute) _signal_strength (neurotorchmz.utils.synapse_detection.ISynapseROI attribute) _snalysis_detection_result (neurotorchmz.core.session.Session attribute) _staged (neurotorchmz.utils.synapse_detection.ISynapse attribute) _string_var_update() (neurotorchmz.gui.components.general.Intstring_var method) _synapses (neurotorchmz.utils.synapse_detection.DetectionResult attribute) _synapses_callbacks (neurotorchmz.utils.synapse_detection.DetectionResult attribute) _sync_synapses_task() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _task_wrapper() (neurotorchmz.core.task_system.Task method) _TaskFunction (class in neurotorchmz.core.task_system) _tasks (neurotorchmz.core.task_system.Task attribute) _update_ISynapseROI() (neurotorchmz.gui.components.treeview.SynapseTreeview method) _update_lbl_minarea() (neurotorchmz.utils.synapse_detection_integration.HysteresisTh_Integration method) (neurotorchmz.utils.synapse_detection_integration.LocalMax_Integration method) (neurotorchmz.utils.synapse_detection_integration.Thresholding_Integration method) _update_loop() (neurotorchmz.gui.window.Neurotorch_GUI method) _window_thread (neurotorchmz.core.session.Session attribute) A active_image_object (neurotorchmz.core.session.Session property) (neurotorchmz.gui.window.Tab property) add_callback() (neurotorchmz.core.task_system.Task method) ALGORITHM (neurotorchmz.utils.signal_detection.SignalObject attribute) AlreadyLoadingError append() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) as_dict() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) ask_for_imagej_path() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) ask_for_installation() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) ask_for_start() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) ask_ram_warning() (neurotorchmz.gui.window.Neurotorch_GUI method) axis (neurotorchmz.utils.image.AxisImage property) AxisImage (class in neurotorchmz.utils.image) B baseline_delta() (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS static method) BoolOption (class in neurotorchmz.core.settings) btnDown_click() (neurotorchmz.gui.tab2.TabSignal method) BtnGithub() (neurotorchmz.gui.tabWelcome.TabWelcome method) BtnOpenDocs() (neurotorchmz.gui.tabWelcome.TabWelcome method) btnUp_click() (neurotorchmz.gui.tab2.TabSignal method) C canvas1_click() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) CircularSynapseROI (class in neurotorchmz.utils.synapse_detection) CLASS_DESC (neurotorchmz.utils.synapse_detection.CircularSynapseROI attribute) (neurotorchmz.utils.synapse_detection.ISynapseROI attribute) (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI attribute) clear() (neurotorchmz.utils.image.ImageObject method) (neurotorchmz.utils.signal_detection.SignalObject method) (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) clear_cache() (neurotorchmz.utils.image.ImageObject method) clear_image_plot() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) clear_peaks() (neurotorchmz.utils.signal_detection.SignalObject method) clear_synapses() (neurotorchmz.gui.components.treeview.SynapseTreeview method) clear_temp_files() (in module neurotorchmz.core.settings) clear_where() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) cluster() (neurotorchmz.utils.synapse_detection.SimpleCustering static method) (neurotorchmz.utils.synapse_detection.SynapseClusteringAlgorithm static method) comboImage_changed() (neurotorchmz.gui.tab3.TabROIFinder method) Config (class in neurotorchmz.core.settings) config (neurotorchmz.core.settings.Section attribute) (neurotorchmz.core.settings.UserSettings.IMAGEJ attribute) (neurotorchmz.core.settings.UserSettings.SIGNAL_DETECTION attribute) config_parser (neurotorchmz.core.settings.Config attribute) (neurotorchmz.core.settings.Option property) (neurotorchmz.core.settings.UserSettings attribute) config_path (neurotorchmz.core.settings.Config attribute) (neurotorchmz.core.settings.UserSettings attribute) coords (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI property) copy() (neurotorchmz.utils.image.AxisImage method) CREATED (neurotorchmz.core.task_system.TaskState attribute) current_input_description (neurotorchmz.gui.tab3.TabROIFinder property) current_input_image (neurotorchmz.gui.tab3.TabROIFinder property) (neurotorchmz.gui.tabAnalysis.TabAnalysis property) D debugging (in module neurotorchmz.core.logs) DEFAULT (neurotorchmz.utils.image.ImageView attribute) delta video: deserialize() (neurotorchmz.core.serialize.Serializable class method) (neurotorchmz.utils.image.ImageObject class method) DeserializeError detect() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) (neurotorchmz.utils.synapse_detection.HysteresisTh method) (neurotorchmz.utils.synapse_detection.IDetectionAlgorithm method) (neurotorchmz.utils.synapse_detection.LocalMax method) (neurotorchmz.utils.synapse_detection.Thresholding method) detect_auto_params() (neurotorchmz.utils.synapse_detection_integration.HysteresisTh_Integration method) (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration method) (neurotorchmz.utils.synapse_detection_integration.LocalMax_Integration method) (neurotorchmz.utils.synapse_detection_integration.Thresholding_Integration method) detection_result (neurotorchmz.gui.tab3.TabROIFinder property) (neurotorchmz.gui.tabAnalysis.TabAnalysis property) DetectionError DetectionResult (class in neurotorchmz.utils.synapse_detection) E editableFiels (neurotorchmz.gui.components.treeview.SynapseTreeview attribute) Edition (class in neurotorchmz.core.session) edition (neurotorchmz.core.session.Session attribute) EntryPopup (class in neurotorchmz.gui.components.general) (class in neurotorchmz.gui.components.treeview) ERROR (neurotorchmz.core.task_system.TaskState attribute) estimate_params() (neurotorchmz.utils.synapse_detection_integration.HysteresisTh_Integration method) (neurotorchmz.utils.synapse_detection_integration.LocalMax_Integration method) Event (class in neurotorchmz.core.events) export_img() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) (neurotorchmz.utils.image.ImageObject method) export_img_diff() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) (neurotorchmz.utils.image.ImageObject method) export_img_only_signal() (neurotorchmz.utils.signal_detection.SignalObject method) export_img_without_signal() (neurotorchmz.utils.signal_detection.SignalObject method) export_roifinder_traces() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) export_rois_from_roifinder() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) export_synapses() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) export_traces() (neurotorchmz.utils.synapse_detection.DetectionResult method) extend() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) extend_rois() (neurotorchmz.utils.synapse_detection.MultiframeSynapse method) F file_logging_handler (in module neurotorchmz.core.logs) filter_rois() (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration method) finished (neurotorchmz.core.task_system.Task property) FINISHED (neurotorchmz.core.task_system.TaskState attribute) FloatOption (class in neurotorchmz.core.settings) flush() (neurotorchmz.core.logs.StdOutCatcher method) frame (neurotorchmz.utils.synapse_detection.ISynapseROI property) FUNCTION_CLASS (neurotorchmz.utils.denoising.PRE_FUNCTIONS attribute) (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS attribute) (neurotorchmz.utils.denoising.XY_DIFF_FUNCTIONS attribute) FunctionType (class in neurotorchmz.utils.image) G gaussian_t_kernel() (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS static method) gaussian_xy_kernel() (neurotorchmz.utils.denoising.XY_DIFF_FUNCTIONS static method) gc_task_list() (neurotorchmz.core.task_system.Task static method) get() (neurotorchmz.core.settings.BoolOption method) (neurotorchmz.core.settings.FloatOption method) (neurotorchmz.core.settings.IntOption method) (neurotorchmz.core.settings.Option method) (neurotorchmz.core.settings.PathOption method) (neurotorchmz.core.settings.StringOption method) (neurotorchmz.gui.components.general.GridSetting method) get_active_tasks() (neurotorchmz.core.task_system.Task static method) get_baseline_delta() (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS static method) get_coordinates() (neurotorchmz.utils.synapse_detection.CircularSynapseROI method) (neurotorchmz.utils.synapse_detection.ISynapseROI method) (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI method) get_distance() (neurotorchmz.utils.synapse_detection.ISynapseROI static method) get_distance_between_rois() (neurotorchmz.utils.synapse_detection.ISynapseROI static method) get_free_ram_in_gb() (neurotorchmz.gui.components.general.Statusbar static method) get_functions_identifier() (neurotorchmz.utils.image.ImageObject method) get_gaussian_t_kernel() (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS static method) get_gaussian_xy_kernel() (neurotorchmz.utils.denoising.XY_DIFF_FUNCTIONS static method) get_image() (in module neurotorchmz.core.resources) get_module() (in module neurotorchmz.core.plugin_manager) get_options_frame() (neurotorchmz.utils.synapse_detection_integration.HysteresisTh_Integration method) (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration method) (neurotorchmz.utils.synapse_detection_integration.LocalMax_Integration method) (neurotorchmz.utils.synapse_detection_integration.Thresholding_Integration method) get_rawdata_overlay() (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration method) (neurotorchmz.utils.synapse_detection_integration.LocalMax_Integration method) (neurotorchmz.utils.synapse_detection_integration.Thresholding_Integration method) get_recently_ended_tasks() (neurotorchmz.core.task_system.Task static method) get_recently_failed_tasks() (neurotorchmz.core.task_system.Task static method) get_roi_description() (neurotorchmz.utils.synapse_detection.ISynapse method) (neurotorchmz.utils.synapse_detection.MultiframeSynapse method) (neurotorchmz.utils.synapse_detection.SingleframeSynapse method) get_selected_synapse() (neurotorchmz.gui.components.treeview.SynapseTreeview method) get_signal() (neurotorchmz.utils.signal_detection.ISignalDetectionAlgorithm method) (neurotorchmz.utils.signal_detection.SigDetect_DiffMax method) (neurotorchmz.utils.signal_detection.SigDetect_DiffStd method) get_signal_from_image() (neurotorchmz.utils.synapse_detection.ISynapseROI method) get_sliding_cumsum() (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS static method) get_string() (in module neurotorchmz.core.resources) get_synapse_by_row_id() (neurotorchmz.gui.components.treeview.SynapseTreeview method) get_tasks() (neurotorchmz.core.task_system.Task static method) get_view() (neurotorchmz.utils.signal_detection.SignalObject method) GridSetting (class in neurotorchmz.gui.components.general) H headless (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) hook() (neurotorchmz.core.events.Event class method) HOOKS (neurotorchmz.core.events.Event attribute) (neurotorchmz.core.session.SessionCreateEvent attribute) (neurotorchmz.gui.events.ImageObjectChangedEvent attribute) (neurotorchmz.gui.events.SynapseTreeviewContextMenuEvent attribute) (neurotorchmz.gui.events.WindowLoadedEvent attribute) (neurotorchmz.gui.events.WindowTKReadyEvent attribute) HysteresisTh (class in neurotorchmz.utils.synapse_detection) HysteresisTh_Integration (class in neurotorchmz.utils.synapse_detection_integration) I IDetectionAlgorithm (class in neurotorchmz.utils.synapse_detection) IDetectionAlgorithmIntegration (class in neurotorchmz.utils.synapse_detection_integration) ij (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) IJ_Plugin_Duplicator (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) ij_start_task (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) image (neurotorchmz.utils.image.AxisImage property) image_obj (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration attribute) image_prop (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration attribute) image_props (neurotorchmz.utils.image.AxisImage property) ImageChangedEvent (class in neurotorchmz.gui.window) imagej_path (neurotorchmz.core.settings.UserSettings.IMAGEJ attribute) ImageJHandler (class in neurotorchmz.plugins.pyimage_j.pyimagej) ImageObject (class in neurotorchmz.utils.image) ImageObjectChangedEvent (class in neurotorchmz.gui.events) ImageObjectError ImageProperties (class in neurotorchmz.utils.image) ImageShapeError ImageView (class in neurotorchmz.utils.image) img (neurotorchmz.utils.image.ImageObject property) (neurotorchmz.utils.image.ImageProperties property) Img_DetectionOverlay() (neurotorchmz.utils.synapse_detection_integration.HysteresisTh_Integration method) img_diff (neurotorchmz.utils.image.ImageObject property) img_diff_frame_props() (neurotorchmz.utils.image.ImageObject method) img_diff_functions (neurotorchmz.utils.image.ImageObject property) img_diff_only_signal_view() (neurotorchmz.utils.signal_detection.SignalObject method) img_diff_props (neurotorchmz.utils.image.ImageObject property) img_diff_props_only_signal (neurotorchmz.utils.signal_detection.SignalObject property) img_diff_props_without_signal (neurotorchmz.utils.signal_detection.SignalObject property) img_diff_raw (neurotorchmz.utils.image.ImageObject property) img_diff_view() (neurotorchmz.utils.image.ImageObject method) img_diff_without_signal_view() (neurotorchmz.utils.signal_detection.SignalObject method) img_frame_props() (neurotorchmz.utils.image.ImageObject method) img_functions (neurotorchmz.utils.image.ImageObject property) img_only_signal_view() (neurotorchmz.utils.signal_detection.SignalObject method) img_props (neurotorchmz.utils.image.ImageObject property) img_props_only_signal (neurotorchmz.utils.signal_detection.SignalObject property) img_props_without_signal (neurotorchmz.utils.signal_detection.SignalObject property) img_raw (neurotorchmz.utils.image.ImageObject property) img_signed (neurotorchmz.utils.image.ImageObject property) img_view() (neurotorchmz.utils.image.ImageObject method) img_without_signal_view() (neurotorchmz.utils.signal_detection.SignalObject method) import_image() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) import_rois() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) import_rois_into_roifinder() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) inactive (neurotorchmz.core.task_system.Task property) init() (neurotorchmz.gui.tab1.TabImage method) (neurotorchmz.gui.tab2.TabSignal method) (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) (neurotorchmz.gui.tabWelcome.TabWelcome method) (neurotorchmz.gui.window.Tab method) init_file_handler() (in module neurotorchmz.core.logs) install_trace_selector() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) IntOption (class in neurotorchmz.core.settings) Intstring_var (class in neurotorchmz.gui.components.general) invalidate_algorithm() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) invalidate_delta_plot() (neurotorchmz.gui.tabAnalysis.TabAnalysis method) invalidate_functions() (neurotorchmz.utils.image.ImageObject method) invalidate_image() (neurotorchmz.gui.tab2.TabSignal method) (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) invalidate_image_plot() (neurotorchmz.gui.tab2.TabSignal method) invalidate_peaks() (neurotorchmz.gui.tab2.TabSignal method) invalidate_ROIs() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) invalidate_selected_ROI() (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) invalidate_signal() (neurotorchmz.gui.tab2.TabSignal method) invalidate_stimulation() (neurotorchmz.gui.tabAnalysis.TabAnalysis method) invert() (neurotorchmz.utils.denoising.PRE_FUNCTIONS static method) invoke_tab_about_update() (neurotorchmz.gui.window.Neurotorch_GUI method) invoke_tab_update_event() (neurotorchmz.gui.window.Neurotorch_GUI method) invoke_update() (neurotorchmz.gui.window.Tab method) is_determinate() (neurotorchmz.core.task_system.Task method) is_trace_selector_running() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) ISignalDetectionAlgorithm (class in neurotorchmz.utils.signal_detection) ISynapse (class in neurotorchmz.utils.synapse_detection) ISynapseROI (class in neurotorchmz.utils.synapse_detection) J join() (neurotorchmz.core.task_system.Task method) K kill_trace_selector() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) L launch() (neurotorchmz.core.session.Session method) (neurotorchmz.gui.window.Neurotorch_GUI method) load_config() (neurotorchmz.core.settings.Config class method) load_pickle() (neurotorchmz.core.serialize.Serializable method) load_plugins_from_dir() (in module neurotorchmz.core.plugin_manager) load_settings() (neurotorchmz.utils.signal_detection.SignalObject class method) LocalMax (class in neurotorchmz.utils.synapse_detection) LocalMax_Integration (class in neurotorchmz.utils.synapse_detection_integration) location (neurotorchmz.utils.synapse_detection.ISynapse property) (neurotorchmz.utils.synapse_detection.ISynapseROI property) (neurotorchmz.utils.synapse_detection.MultiframeSynapse property) (neurotorchmz.utils.synapse_detection.SingleframeSynapse property) location_string (neurotorchmz.utils.synapse_detection.ISynapse property) (neurotorchmz.utils.synapse_detection.ISynapseROI property) location_x (neurotorchmz.utils.synapse_detection.ISynapse property) (neurotorchmz.utils.synapse_detection.ISynapseROI property) location_y (neurotorchmz.utils.synapse_detection.ISynapse property) (neurotorchmz.utils.synapse_detection.ISynapseROI property) log_exceptions_hook() (in module neurotorchmz.core.logs) logged_std_out (in module neurotorchmz.core.logs) logger (in module neurotorchmz.core.logs) lowerTimerSpeed (neurotorchmz.gui.components.general.Statusbar attribute) M max (neurotorchmz.utils.image.ImageProperties property) max_image (neurotorchmz.utils.image.AxisImage property) max_props (neurotorchmz.utils.image.AxisImage property) mean (neurotorchmz.utils.image.ImageProperties property) mean_image (neurotorchmz.utils.image.AxisImage property) mean_normed_image (neurotorchmz.utils.image.AxisImage property) mean_normed_props (neurotorchmz.utils.image.AxisImage property) mean_props (neurotorchmz.utils.image.AxisImage property) median (neurotorchmz.utils.image.ImageProperties property) median_image (neurotorchmz.utils.image.AxisImage property) median_props (neurotorchmz.utils.image.AxisImage property) menu_debug_enable_debugging_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_debug_load_peaks_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_debug_save_peaks_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_debug_test() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_export_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_file_close_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_file_open_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_image_clear_cache_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_image_diable_all_filters_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_install_click() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) menu_locate_installation_click() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) menu_neurotorch_about_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_neurotorch_logs_click() (neurotorchmz.gui.window.Neurotorch_GUI method) menu_plugins() (neurotorchmz.gui.events.WindowLoadedEvent method) menu_settings (neurotorchmz.gui.events.WindowLoadedEvent property) menu_start_imageJ_click() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) menu_test_installation_click() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) metadata (neurotorchmz.utils.image.ImageObject property) min (neurotorchmz.utils.image.ImageProperties property) min_image (neurotorchmz.utils.image.AxisImage property) min_props (neurotorchmz.utils.image.AxisImage property) minClipped (neurotorchmz.utils.image.ImageProperties property) module neurotorchmz neurotorchmz.core neurotorchmz.core.api neurotorchmz.core.events neurotorchmz.core.logs neurotorchmz.core.plugin_manager neurotorchmz.core.resources neurotorchmz.core.serialize neurotorchmz.core.session neurotorchmz.core.settings neurotorchmz.core.task_system neurotorchmz.gui neurotorchmz.gui.components neurotorchmz.gui.components.general neurotorchmz.gui.components.treeview neurotorchmz.gui.events neurotorchmz.gui.tab1 neurotorchmz.gui.tab2 neurotorchmz.gui.tab3 neurotorchmz.gui.tabAnalysis neurotorchmz.gui.tabWelcome neurotorchmz.gui.window neurotorchmz.plugins neurotorchmz.plugins.pyimage_j neurotorchmz.plugins.pyimage_j.pyimagej neurotorchmz.plugins.trace_selector neurotorchmz.plugins.trace_selector.trace_selector neurotorchmz.utils neurotorchmz.utils.denoising neurotorchmz.utils.image neurotorchmz.utils.signal_detection neurotorchmz.utils.synapse_detection neurotorchmz.utils.synapse_detection_integration MultiframeSynapse (class in neurotorchmz.utils.synapse_detection) N name (neurotorchmz.core.settings.Option attribute) (neurotorchmz.utils.image.AxisImage property) (neurotorchmz.utils.image.ImageObject property) (neurotorchmz.utils.synapse_detection.ISynapse property) name_without_extension (neurotorchmz.utils.image.ImageObject property) NEUROTORCH (neurotorchmz.core.session.Edition attribute) NEUROTORCH_DEBUG (neurotorchmz.core.session.Edition attribute) Neurotorch_GUI (class in neurotorchmz.gui.window) NEUROTORCH_LIGHT (neurotorchmz.core.session.Edition attribute) neurotorchmz module neurotorchmz.core module neurotorchmz.core.api module neurotorchmz.core.events module neurotorchmz.core.logs module neurotorchmz.core.plugin_manager module neurotorchmz.core.resources module neurotorchmz.core.serialize module neurotorchmz.core.session module neurotorchmz.core.settings module neurotorchmz.core.task_system module neurotorchmz.gui module neurotorchmz.gui.components module neurotorchmz.gui.components.general module neurotorchmz.gui.components.treeview module neurotorchmz.gui.events module neurotorchmz.gui.tab1 module neurotorchmz.gui.tab2 module neurotorchmz.gui.tab3 module neurotorchmz.gui.tabAnalysis module neurotorchmz.gui.tabWelcome module neurotorchmz.gui.window module neurotorchmz.plugins module neurotorchmz.plugins.pyimage_j module neurotorchmz.plugins.pyimage_j.pyimagej module neurotorchmz.plugins.trace_selector module neurotorchmz.plugins.trace_selector.trace_selector module neurotorchmz.utils module neurotorchmz.utils.denoising module neurotorchmz.utils.image module neurotorchmz.utils.signal_detection module neurotorchmz.utils.synapse_detection module neurotorchmz.utils.synapse_detection_integration module NoImageError notebook (neurotorchmz.gui.window.Tab attribute) notify() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ISynapse method) (neurotorchmz.utils.synapse_detection.ISynapseROI method) (neurotorchmz.utils.synapse_detection.ROIList method) notify_image_object_change() (neurotorchmz.core.session.Session method) O on_return() (neurotorchmz.gui.components.general.EntryPopup method) (neurotorchmz.gui.components.treeview.EntryPopup method) on_session_created() (in module neurotorchmz.plugins.pyimage_j.pyimagej) (in module neurotorchmz.plugins.trace_selector.trace_selector) on_synapse_tv_context_menu_create() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) on_tv_context_menu_created() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) on_window_loaded() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) open_file() (neurotorchmz.core.session.SessionAPI method) (neurotorchmz.utils.image.ImageObject method) open_roi_manager() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) Option (class in neurotorchmz.core.settings) OvalRoi (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) P pack() (neurotorchmz.gui.components.treeview.SynapseTreeview method) path (neurotorchmz.utils.image.ImageObject property) PathOption (class in neurotorchmz.core.settings) peak_width_left (neurotorchmz.core.settings.UserSettings.SIGNAL_DETECTION attribute) PEAK_WIDTH_LEFT (neurotorchmz.utils.signal_detection.SignalObject attribute) peak_width_right (neurotorchmz.core.settings.UserSettings.SIGNAL_DETECTION attribute) PEAK_WIDTH_RIGHT (neurotorchmz.utils.signal_detection.SignalObject attribute) peaks (neurotorchmz.utils.signal_detection.SignalObject property) PeaksChangedEvent (class in neurotorchmz.gui.window) pickle() (neurotorchmz.core.serialize.Serializable method) pipe_thread (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge attribute) place_auto() (neurotorchmz.gui.components.treeview.EntryPopup method) plot_3D_multiframe() (neurotorchmz.gui.tabAnalysis.TabAnalysis method) polygon (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI property) PolygonalSynapseROI (class in neurotorchmz.utils.synapse_detection) PolygonRoi (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) PRE_FUNCTION (neurotorchmz.utils.image.FunctionType attribute) PRE_FUNCTIONS (class in neurotorchmz.utils.denoising) precompute_image() (neurotorchmz.utils.image.ImageObject method) proc (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge attribute) progress (neurotorchmz.core.task_system.Task property) progress_text (neurotorchmz.gui.components.general.Statusbar property) prominence_factor (neurotorchmz.utils.signal_detection.SignalObject property) provides_rawPlot (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration attribute) R radius (neurotorchmz.utils.synapse_detection.CircularSynapseROI property) region_props (neurotorchmz.utils.synapse_detection.ISynapseROI property) register() (neurotorchmz.core.events.Event class method) register_callback() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ISynapse method) (neurotorchmz.utils.synapse_detection.ISynapseROI method) (neurotorchmz.utils.synapse_detection.ROIList method) reinitalize() (neurotorchmz.core.task_system.Task method) remove() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) remove_callback() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ISynapse method) (neurotorchmz.utils.synapse_detection.ISynapseROI method) (neurotorchmz.utils.synapse_detection.ROIList method) reset() (neurotorchmz.core.task_system.Task method) (neurotorchmz.utils.synapse_detection.HysteresisTh method) (neurotorchmz.utils.synapse_detection.IDetectionAlgorithm method) (neurotorchmz.utils.synapse_detection.LocalMax method) (neurotorchmz.utils.synapse_detection.Thresholding method) reset_progress() (neurotorchmz.core.task_system.Task method) RM (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) Roi (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) roifinder_detection_result (neurotorchmz.core.session.Session property) ROIList (class in neurotorchmz.utils.synapse_detection) RoiManager (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler attribute) root (neurotorchmz.core.session.Session property) (neurotorchmz.gui.window.Tab attribute) (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler property) running (neurotorchmz.core.task_system.Task property) RUNNING (neurotorchmz.core.task_system.TaskState attribute) runtime (neurotorchmz.core.task_system.Task property) S save() (neurotorchmz.core.settings.Option method) save_config() (neurotorchmz.core.settings.Config class method) ScrolledFrame (class in neurotorchmz.gui.components.general) Section (class in neurotorchmz.core.settings) section (neurotorchmz.core.settings.Option attribute) select() (neurotorchmz.gui.components.treeview.SynapseTreeview method) select_all() (neurotorchmz.gui.components.general.EntryPopup method) (neurotorchmz.gui.components.treeview.EntryPopup method) Serializable (class in neurotorchmz.core.serialize) serialize() (neurotorchmz.core.serialize.Serializable method) (neurotorchmz.utils.image.ImageObject method) SerializeError Session (class in neurotorchmz.core.session) session (neurotorchmz.gui.window.Tab attribute) SessionAPI (class in neurotorchmz.core.session) SessionCreateEvent (class in neurotorchmz.core.session) set() (neurotorchmz.core.settings.Option method) (neurotorchmz.gui.components.general.GridSetting method) set_active_image_object() (neurotorchmz.core.session.Session method) set_callback() (neurotorchmz.gui.components.general.Intstring_var method) set_error_callback() (neurotorchmz.core.task_system.Task method) set_finished() (neurotorchmz.core.task_system.Task method) set_frame() (neurotorchmz.utils.synapse_detection.ISynapseROI method) set_image_precompute() (neurotorchmz.utils.image.ImageObject method) set_img_diff_trigger() (neurotorchmz.gui.window.Neurotorch_GUI method) set_img_diff_xy_function() (neurotorchmz.gui.window.Neurotorch_GUI method) set_indeterminate() (neurotorchmz.core.task_system.Task method) set_location() (neurotorchmz.utils.synapse_detection.ISynapseROI method) (neurotorchmz.utils.synapse_detection.MultiframeSynapse method) set_message() (neurotorchmz.core.task_system.Task method) set_name() (neurotorchmz.utils.synapse_detection.ISynapse method) set_percentage_mode() (neurotorchmz.core.task_system.Task method) set_polygon() (neurotorchmz.utils.synapse_detection.PolygonalSynapseROI method) set_progress() (neurotorchmz.core.task_system.Task method) set_radius() (neurotorchmz.utils.synapse_detection.CircularSynapseROI method) set_range() (neurotorchmz.gui.components.general.GridSetting method) set_region_props() (neurotorchmz.utils.synapse_detection.ISynapseROI method) set_roi() (neurotorchmz.utils.synapse_detection.SingleframeSynapse method) set_rois() (neurotorchmz.utils.synapse_detection.MultiframeSynapse method) set_settings() (neurotorchmz.utils.signal_detection.SignalObject class method) set_signal_strength() (neurotorchmz.utils.synapse_detection.ISynapseROI method) set_step_mode() (neurotorchmz.core.task_system.Task method) set_step_progress() (neurotorchmz.core.task_system.Task method) set_string_var_bounds() (neurotorchmz.gui.components.general.Intstring_var method) set_visibility() (neurotorchmz.gui.components.general.GridSetting method) set_window_title() (neurotorchmz.gui.window.Neurotorch_GUI method) show_external_plot() (neurotorchmz.gui.tabAnalysis.TabAnalysis method) SigDetect_DiffMax (class in neurotorchmz.utils.signal_detection) SigDetect_DiffStd (class in neurotorchmz.utils.signal_detection) signal (neurotorchmz.utils.signal_detection.SignalObject property) signal_obj (neurotorchmz.utils.image.ImageObject property) signal_strength (neurotorchmz.utils.synapse_detection.ISynapseROI property) SignalChangedEvent (class in neurotorchmz.gui.window) SignalObject (class in neurotorchmz.utils.signal_detection) SimpleCustering (class in neurotorchmz.utils.synapse_detection) SingleframeSynapse (class in neurotorchmz.utils.synapse_detection) sliderFrame_changed() (neurotorchmz.gui.tabAnalysis.TabAnalysis method) sliderPeak_changed() (neurotorchmz.gui.tabAnalysis.TabAnalysis method) sliding_cumsum() (neurotorchmz.utils.denoising.TRIGGER_FUNCTIONS static method) sort_functions() (neurotorchmz.utils.image.ImageObject method) SPATIAL (neurotorchmz.utils.image.ImageView attribute) staged (neurotorchmz.utils.synapse_detection.ISynapse property) STANDBY (neurotorchmz.core.task_system.TaskState attribute) start() (in module neurotorchmz) (neurotorchmz.core.task_system.Task method) start_background() (in module neurotorchmz) start_debugging() (in module neurotorchmz.core.logs) start_imageJ() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) start_trace_selector() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) state (neurotorchmz.core.task_system.Task property) status_text (neurotorchmz.gui.components.general.Statusbar property) Statusbar (class in neurotorchmz.gui.components.general) std (neurotorchmz.utils.image.ImageProperties property) std_image (neurotorchmz.utils.image.AxisImage property) std_normed_image (neurotorchmz.utils.image.AxisImage property) std_normed_props (neurotorchmz.utils.image.AxisImage property) std_props (neurotorchmz.utils.image.AxisImage property) StdOutCatcher (class in neurotorchmz.core.logs) stream_logging_handler (in module neurotorchmz.core.logs) StringOption (class in neurotorchmz.core.settings) SUPPORTED_EXPORT_EXTENSIONS (neurotorchmz.utils.image.ImageObject attribute) synapse_analysis_detection_result (neurotorchmz.core.session.Session property) SynapseClusteringAlgorithm (class in neurotorchmz.utils.synapse_detection) SynapseTreeview (class in neurotorchmz.gui.components.treeview) SynapseTreeviewContextMenuEvent (class in neurotorchmz.gui.events) sync_synapses() (neurotorchmz.gui.components.treeview.SynapseTreeview method) T T (neurotorchmz.utils.image.FunctionType attribute) Tab (class in neurotorchmz.gui.window) tab_name (neurotorchmz.gui.window.Tab attribute) TabAnalysis (class in neurotorchmz.gui.tabAnalysis) TabAnalysis_InvalidateEvent (class in neurotorchmz.gui.tabAnalysis) TabImage (class in neurotorchmz.gui.tab1) TabImage_ViewChangedEvent (class in neurotorchmz.gui.tab1) TabROIFinder (class in neurotorchmz.gui.tab3) TabROIFinder_InvalidateEvent (class in neurotorchmz.gui.tab3) TabSignal (class in neurotorchmz.gui.tab2) TabSignal_AlgorithmChangedEvent (class in neurotorchmz.gui.tab2) TabSignal_RefindPeaksEvent (class in neurotorchmz.gui.tab2) TabUpdateEvent (class in neurotorchmz.gui.window) TabWelcome (class in neurotorchmz.gui.tabWelcome) Task (class in neurotorchmz.core.task_system) task_finished_text (neurotorchmz.gui.components.general.Statusbar property) TaskError TaskState (class in neurotorchmz.core.task_system) TEMPORAL (neurotorchmz.utils.image.ImageView attribute) test_for_java() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) test_for_maven() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) test_installation() (neurotorchmz.plugins.trace_selector.trace_selector.TraceSelectorBridge method) thread_exceptions_hook() (in module neurotorchmz.core.logs) Thresholding (class in neurotorchmz.utils.synapse_detection) Thresholding_Integration (class in neurotorchmz.utils.synapse_detection_integration) time_since_end (neurotorchmz.core.task_system.Task property) time_since_start (neurotorchmz.core.task_system.Task property) timerHighSpeed (neurotorchmz.gui.components.general.Statusbar attribute) timerLowSpeed (neurotorchmz.gui.components.general.Statusbar attribute) to_list() (neurotorchmz.utils.synapse_detection.DetectionResult method) (neurotorchmz.utils.synapse_detection.ROIList method) to_pandas() (neurotorchmz.utils.synapse_detection.DetectionResult method) TraceSelectorBridge (class in neurotorchmz.plugins.trace_selector.trace_selector) TRIGGER_FUNCTIONS (class in neurotorchmz.utils.denoising) U UnsupportedExtensionError UnsupportedImageError update() (neurotorchmz.utils.synapse_detection_integration.HysteresisTh_Integration method) (neurotorchmz.utils.synapse_detection_integration.IDetectionAlgorithmIntegration method) (neurotorchmz.utils.synapse_detection_integration.LocalMax_Integration method) update_menu() (neurotorchmz.gui.window.Neurotorch_GUI method) update_peak_width_left_setting() (neurotorchmz.gui.tab2.TabSignal method) update_tab() (neurotorchmz.gui.tab1.TabImage method) (neurotorchmz.gui.tab2.TabSignal method) (neurotorchmz.gui.tab3.TabROIFinder method) (neurotorchmz.gui.tabAnalysis.TabAnalysis method) (neurotorchmz.gui.window.Tab method) UpdateRoiFinderDetectionResultEvent (class in neurotorchmz.gui.window) UserSettings (class in neurotorchmz.core.settings) UserSettings.IMAGEJ (class in neurotorchmz.core.settings) UserSettings.SIGNAL_DETECTION (class in neurotorchmz.core.settings) uuid (neurotorchmz.utils.synapse_detection.ISynapse property) (neurotorchmz.utils.synapse_detection.ISynapseROI property) V validate_imagej_path() (neurotorchmz.plugins.pyimage_j.pyimagej.ImageJHandler method) W window (neurotorchmz.gui.window.Tab property) WindowLoadedEvent (class in neurotorchmz.gui.events) WindowTKReadyEvent (class in neurotorchmz.gui.events) writable() (neurotorchmz.core.logs.StdOutCatcher method) write() (neurotorchmz.core.logs.StdOutCatcher method) X XY (neurotorchmz.utils.image.FunctionType attribute) XY_DIFF_FUNCTIONS (class in neurotorchmz.utils.denoising)