Index

A

active (BaseSettingGroup attribute) (CheckRangeFloat attribute) (CheckRangeInt attribute) add() (Logger method) add_color_to_tracks() (PALMTracer method) add_extension() (in module palm_tracer.Tools.FileIO) add_file() (FileList method) add_setting_row() (in module palm_tracer.Tools.Ui) add_suffix() (in module palm_tracer.Tools.FileIO) add_test_info() (Monitoring method) align() (Palm method) AlignmentWidget (class in palm_tracer.UI.AlignmentWidget)

always_active() (BaseSettingGroup method) analyze() (FileMigrator method) apply_dataframe_type() (in module palm_tracer.Processing.Parsing) apply_drift() (in module palm_tracer.Processing.Drift) astigmatism3d_curve() (Grapher method) Astigmatism3DWidget (class in palm_tracer.UI.Astigmatism3DWidget) astigmatism_3d_calibration() (Palm method) astigmatism_3d_estimation() (Palm method) attach_to_form() (BaseSettingType method) auto_threshold() built-in function auto_threshold() (Palm method)

B

BasePlotlyWidget (class in palm_tracer.UI.BasePlotlyWidget) BaseSettingGroup (class in palm_tracer.Settings.Groups.BaseSettingGroup) BaseSettingType (class in palm_tracer.Settings.Types.BaseSettingType) Batch (class in palm_tracer.Settings.Groups.Batch) batch (Settings attribute) beads (PALMTracer attribute) (Settings attribute) BeadsExtraction (class in palm_tracer.Settings.Groups.BeadsExtraction) blank() (Grapher static method) blinking (Settings attribute) blinking_reconnection() (Palm method)

BlinkingReconnection (class in palm_tracer.Settings.Groups.BlinkingReconnection) blocked() (SignalWrapper method) box (BaseSettingType attribute) (CheckRangeFloat attribute) (CheckRangeInt attribute) browse_file() (BrowseFile method) BrowseFile (class in palm_tracer.Settings.Types.BrowseFile) built-in function auto_threshold() Button (class in palm_tracer.Settings.Types.Button) buttons (FileList attribute) (Filtering attribute)

C

Calibration (class in palm_tracer.Settings.Groups.Calibration) calibration (Settings attribute) check_max() (CheckRangeFloat method) (CheckRangeInt method) check_min() (CheckRangeFloat method) (CheckRangeInt method) CheckBox (class in palm_tracer.Settings.Types.CheckBox) CheckRangeFloat (class in palm_tracer.Settings.Types.CheckRangeFloat) CheckRangeInt (class in palm_tracer.Settings.Types.CheckRangeInt) clear_files() (FileList method) close() (Logger method)

closeEvent() (BasePlotlyWidget method) cloud() (Grapher method) column_migrator() (FileMigrator static method) Combo (class in palm_tracer.Settings.Types.Combo) connect() (BaseSettingGroup method) (BaseSettingType method) (Button method) (Settings method) (SignalWrapper method) create_viewer3d() (in module palm_tracer.UI.Viewer3DWidget) create_viewerhr() (in module palm_tracer.UI.ViewerHRWidget) current_text (Combo attribute)

D

dataframe_migrator() (FileMigrator method) deactivate_filters() (Filtering method) (FilteringL method) (FilteringT method) default (BaseSettingType attribute) (BrowseFile attribute) (CheckBox attribute) (CheckRangeFloat attribute) (CheckRangeInt attribute) (Combo attribute) (FileList attribute) (SpinFloat attribute) (SpinInt attribute)

df (PALMTracer attribute) disconnect() (BaseSettingGroup method) (BaseSettingType method) (Settings method) (SignalWrapper method) draw_line() (Renderer static method) draw_test_section() (Monitoring static method) Drift Drift correction drift_correction() (in module palm_tracer.Processing.Drift)

E

emit() (BaseSettingType method) (SignalWrapper method)

eventFilter() (KeyBlocker method) extract_beads() (in module palm_tracer.Processing.Drift) extract_suffix() (in module palm_tracer.Tools.FileIO)

F

file_handle (Logger attribute) FileList (class in palm_tracer.Settings.Types.FileList) FileMigrator (class in palm_tracer.Tools.FileMigrator) FileMigratorWidget (class in palm_tracer.UI.FileMigratorWidget) filename (Logger attribute) files (FileMigrator attribute) FILES_LINK (FileMigrator attribute) filter_localizations() (PALMTracer method) filter_tracks() (PALMTracer method)

filter_tracks_compute() (PALMTracer method) Filtering (class in palm_tracer.Settings.Groups.Filtering) filtering (Settings attribute) FilteringL (class in palm_tracer.Settings.Groups.FilteringL) FilteringT (class in palm_tracer.Settings.Groups.FilteringT) format_time() (in module palm_tracer.Tools.Ui) from_dict() (BaseSettingGroup class method) (BaseSettingType class method) (Settings class method)

G

Gallery (class in palm_tracer.Settings.Groups.Gallery) gallery (Settings attribute) Gaussian fitting GaussianFit (class in palm_tracer.Settings.Groups.GaussianFit) get_bins_number() (in module palm_tracer.Processing.Visualization) get_color_map_by_name() (Monitoring static method) get_drift() (in module palm_tracer.Processing.Drift) get_fit() (Localization method) get_fit_params() (Localization method) get_last_file() (in module palm_tracer.Tools.FileIO) get_list() (FileList method) get_localization_colors() (Renderer static method) get_localization_key() (PALMTracer method)

get_meta() (in module palm_tracer.Processing.Parsing) get_paths() (Batch method) get_selected() (FileList method) get_stacks() (Batch method) get_status() (PALMTracer method) get_timestamp_for_files() (in module palm_tracer.Tools.FileIO) get_tracks_colors() (Renderer static method) get_tracks_compute_key() (PALMTracer method) get_tracks_key() (PALMTracer method) get_y_range() (Monitoring static method) Grapher (class in palm_tracer.Processing.Grapher) GraphViewerWidget (class in palm_tracer.UI.GraphViewerWidget) grayscale_to_color() (in module palm_tracer.Tools.FileIO)

H

hide() (BaseSettingGroup method) (BaseSettingType method) (CheckRangeFloat method) (CheckRangeInt method)

High-resolution image histogram() (Grapher method)

I

init_layout() (in module palm_tracer.Tools.Ui) initialize() (BaseSettingGroup method) (BaseSettingType method) (BrowseFile method) (Button method) (CheckBox method) (CheckRangeFloat method) (CheckRangeInt method) (Combo method) (FileList method) (SpinFloat method) (SpinInt method)

initialize_ui() (BaseSettingGroup method) (Filtering method) (Localization method) (VisualizationHR method) input_folder (FileMigrator attribute) interval (Monitoring attribute) is_dll_valid() (PALMTracer method) is_valid() (BaseSettingGroup static method) (Palm method) items (Combo attribute) (FileList attribute)

K

KeyBlocker (class in palm_tracer.UI.KeyBlocker)

KEYS_TO_FILE (PALMTracer attribute)

L

label (BaseSettingGroup attribute) (BaseSettingType attribute) (Batch attribute) (BeadsExtraction attribute) (BlinkingReconnection attribute) (Calibration attribute) (Filtering attribute) (FilteringL attribute) (FilteringT attribute) (Gallery attribute) (GaussianFit attribute) (Localization attribute) (SplineFit attribute) (Tracking attribute) (TracksCompute attribute) (VisualizationGraph attribute) (VisualizationHR attribute)

label_widget (BaseSettingType attribute) layout (BaseSettingType attribute) limits (CheckRangeFloat attribute) (CheckRangeInt attribute) (SpinFloat attribute) (SpinInt attribute) Link (class in palm_tracer.Tools.FileMigrator) load() (PALMTracer method) load_csv() (Viewer3DWidget method) load_dll() (in module palm_tracer.Tools.FileIO) Localization (class in palm_tracer.Settings.Groups.Localization) localization (Settings attribute) localization() (Palm method) localizations (PALMTracer attribute) localizations() (Renderer method) log10_dataframe() (in module palm_tracer.Processing.Parsing) Logger (class in palm_tracer.Tools.Logger)

M

make_exclusive_btn_group() (in module palm_tracer.Tools.Ui) make_file_info_group() (in module palm_tracer.Tools.Ui) make_form() (in module palm_tracer.Tools.Ui) make_gallery() (in module palm_tracer.Processing.Gallery) make_group() (in module palm_tracer.Tools.Ui) make_horizontal_separator() (in module palm_tracer.Tools.Ui) make_info_grid() (in module palm_tracer.Tools.Ui) make_meta() (FileMigrator method) make_path_label() (in module palm_tracer.Tools.Ui) make_spin() (in module palm_tracer.Tools.Ui) make_tab() (in module palm_tracer.Tools.Ui) make_vertical_separator() (in module palm_tracer.Tools.Ui) max_allocation_bytes() (Palm static method) meta (FileMigrator attribute) migrate() (FileMigrator method) migrate_astigmatism_3d_model() (FileMigrator method) migrate_localization() (FileMigrator method) migrate_tracks() (FileMigrator method) migrate_tracks_fit() (FileMigrator method)

migrate_tracks_instant_diffusion() (FileMigrator method) migrate_tracks_msd() (FileMigrator method) model_projection_validity() (in module palm_tracer.Processing.Astigmatism3D) model_validity() (in module palm_tracer.Processing.Astigmatism3D) module palm_tracer.Processing.Astigmatism3D palm_tracer.Processing.Drift palm_tracer.Processing.Gallery palm_tracer.Processing.Parsing palm_tracer.Processing.Visualization palm_tracer.Tools.FileIO palm_tracer.Tools.FileMigrator palm_tracer.Tools.Ui palm_tracer.UI.AlignmentWidget palm_tracer.UI.Astigmatism3DWidget palm_tracer.UI.FileMigratorWidget palm_tracer.UI.Viewer3DWidget palm_tracer.UI.ViewerHRWidget monitor() (Monitoring method) Monitoring (class in palm_tracer.Tools.Monitoring)

N

n_entries (Monitoring attribute)

new (Link attribute) normalize_data() (in module palm_tracer.Processing.Visualization)

O

old (Link attribute) open() (FileMigrator method) (Logger method) open_alignment() (in module palm_tracer.UI.AlignmentWidget) open_astigmatism3d() (in module palm_tracer.UI.Astigmatism3DWidget) open_calibration_mat() (in module palm_tracer.Tools.FileIO) open_json() (in module palm_tracer.Tools.FileIO)

open_migrator() (in module palm_tracer.UI.FileMigratorWidget) open_old_file() (FileMigrator static method) open_old_irregular_file() (FileMigrator static method) open_tif() (in module palm_tracer.Tools.FileIO) open_viewer3d() (in module palm_tracer.UI.Viewer3DWidget) open_viewerhr() (in module palm_tracer.UI.ViewerHRWidget) output_folder (FileMigrator attribute)

P

Palm (class in palm_tracer.Processing.Palm) palm (PALMTracer attribute) palm_tracer.Processing.Astigmatism3D module palm_tracer.Processing.Drift module palm_tracer.Processing.Gallery module palm_tracer.Processing.Parsing module palm_tracer.Processing.Visualization module palm_tracer.Tools.FileIO module palm_tracer.Tools.FileMigrator module palm_tracer.Tools.Ui module palm_tracer.UI.AlignmentWidget module palm_tracer.UI.Astigmatism3DWidget module palm_tracer.UI.FileMigratorWidget module

palm_tracer.UI.Viewer3DWidget module palm_tracer.UI.ViewerHRWidget module PALMTracer (class in palm_tracer.PALMTracer) PALMTracerWidget (class in palm_tracer.UI.PALMTracerWidget) parse_irregular_array() (in module palm_tracer.Processing.Parsing) parse_localization_for_tracking() (in module palm_tracer.Processing.Parsing) parse_result() (in module palm_tracer.Processing.Parsing) path (PALMTracer attribute) Pipeline PLOT_DIV_ID (BasePlotlyWidget attribute) plot_histogram() (in module palm_tracer.Processing.Visualization) plot_plane_heatmap() (in module palm_tracer.Processing.Visualization) plot_plane_violin() (in module palm_tracer.Processing.Visualization) PLOTLY_JS_PATH (BasePlotlyWidget attribute) PLOTLY_JS_URL (BasePlotlyWidget attribute) precision (CheckRangeFloat attribute) (SpinFloat attribute) print_error() (in module palm_tracer.Tools.Ui) print_success() (in module palm_tracer.Tools.Ui) print_warning() (in module palm_tracer.Tools.Ui) process() (PALMTracer method) PSF (Point Spread Function)

R

rearrange_dataframe_columns() (in module palm_tracer.Processing.Parsing) remove_beads() (in module palm_tracer.Processing.Drift) remove_file() (FileList method) remove_header() (BaseSettingGroup method) remove_multi_loc() (in module palm_tracer.Processing.Astigmatism3D) render_hr_image() (in module palm_tracer.Processing.Visualization) render_roi() (in module palm_tracer.Processing.Visualization) render_tracks_image() (in module palm_tracer.Processing.Visualization) Renderer (class in palm_tracer.Processing.Renderer) reset() (BaseSettingGroup method) (BaseSettingType method) (Button method) (CheckRangeFloat method) (CheckRangeInt method) (FileList method) (Settings method)

reset_filtered() (PALMTracer method) reset_result() (PALMTracer method) RESOURCE_DIR (BasePlotlyWidget attribute) ROI (Region Of Interest)

S

save() (Monitoring method) save_filtered() (PALMTracer method) save_json() (in module palm_tracer.Tools.FileIO) save_png() (in module palm_tracer.Tools.FileIO) save_tif() (in module palm_tracer.Tools.FileIO) scatter() (Grapher method) set_size() (Renderer method) set_spin_width() (in module palm_tracer.Tools.Ui) setting_list (BaseSettingGroup attribute) (Batch attribute) (BeadsExtraction attribute) (BlinkingReconnection attribute) (Calibration attribute) (Filtering attribute) (FilteringL attribute) (FilteringT attribute) (Gallery attribute) (GaussianFit attribute) (Localization attribute) (SplineFit attribute) (Tracking attribute) (TracksCompute attribute) (VisualizationGraph attribute) (VisualizationHR attribute)

settings (BaseSettingGroup attribute) Settings (class in palm_tracer.Settings.Settings) settings (PALMTracer attribute) settings_names (BaseSettingGroup attribute) show() (BaseSettingGroup method) (BaseSettingType method) (CheckRangeFloat method) (CheckRangeInt method) sigma_model() (in module palm_tracer.Processing.Astigmatism3D) signal_blocked() (BaseSettingGroup method) (BaseSettingType method) (Settings method) SignalWrapper (class in palm_tracer.Settings.Types.SignalWrapper) SNR (Signal-to-Noise Ratio) SpinFloat (class in palm_tracer.Settings.Types.SpinFloat) SpinInt (class in palm_tracer.Settings.Types.SpinInt) SplineFit (class in palm_tracer.Settings.Groups.SplineFit) stack (PALMTracer attribute) start() (Monitoring method) step (SpinFloat attribute) (SpinInt attribute) stop() (Monitoring method) suffix (FileMigrator attribute) (PALMTracer attribute) sync_spin() (in module palm_tracer.Tools.Ui)

T

Threshold to_compact_dict() (BaseSettingGroup method) (BaseSettingType method) (FileList method) (Settings method) to_dict() (BaseSettingGroup method) (BaseSettingType method) (BrowseFile method) (Button method) (CheckBox method) (CheckRangeFloat method) (CheckRangeInt method) (Combo method) (FileList method) (Settings method) (SpinFloat method) (SpinInt method) toggle_active() (BaseSettingGroup method) (CheckRangeFloat method) (CheckRangeInt method)

toggle_fit_mode() (Localization method) toggle_type() (VisualizationHR method) tooltip (BaseSettingType attribute) tostring() (BaseSettingGroup method) (Monitoring method) (Settings method) Tracking (class in palm_tracer.Settings.Groups.Tracking) tracking (Settings attribute) tracking() (Palm method) tracks (PALMTracer attribute) tracks() (Renderer method) tracks_compute (PALMTracer attribute) (Settings attribute) tracks_compute() (Palm method) TracksCompute (class in palm_tracer.Settings.Groups.TracksCompute)

U

update_box() (Combo method) (FileList method) update_filtered() (PALMTracer method) update_from_compact_dict() (BaseSettingGroup method) (BaseSettingType method) (FileList method) (Settings method) update_from_dict() (BaseSettingGroup method) (BaseSettingType method) (BrowseFile method) (Button method) (CheckBox method) (CheckRangeFloat method) (CheckRangeInt method) (Combo method) (FileList method) (Settings method) (SpinFloat method) (SpinInt method)

update_layer() (Viewer3DWidget method) update_limits() (CheckRangeFloat method) (CheckRangeInt method) (Filtering method) update_meta() (FileMigrator method) update_path_label() (in module palm_tracer.Tools.Ui) update_spin_limits() (in module palm_tracer.Tools.Ui)

V

value (BaseSettingGroup attribute) (BaseSettingType attribute) (BrowseFile attribute) (CheckBox attribute) (CheckRangeFloat attribute) (CheckRangeInt attribute) (Combo attribute) (FileList attribute) (SpinFloat attribute) (SpinInt attribute)

Viewer3DWidget (class in palm_tracer.UI.Viewer3DWidget) ViewerHRWidget (class in palm_tracer.UI.ViewerHRWidget) visualization (PALMTracer attribute) visualization_graph (Settings attribute) visualization_hr (Settings attribute) VisualizationGraph (class in palm_tracer.Settings.Groups.VisualizationGraph) VisualizationHR (class in palm_tracer.Settings.Groups.VisualizationHR)

W

Watershed

wavelett() (Palm method) widget (BaseSettingGroup attribute)

Z

z_from_planes() (in module palm_tracer.Processing.Astigmatism3D)

z_from_step() (in module palm_tracer.Processing.Astigmatism3D)