Index

_

__init__() (AnalysisMethodsUI method) (BaseDataClass method) (BaseUIClass method) (CentralManager method) (ChannelAssignmentDialog method) (CondensateAnalysisUI method) (DataFrameModel method) (FibrilAnalysisUI method) (FileIOClass method) (GeneralAnalysisUI method) (LayerDataframeSelectionDialog method) (MeasurementDialog method) (MenuManager method) (obcaDialog method) (ObjectColocAnalysisUI method) (PixelColocAnalysisUI method) (PlottingWidget method) (pwcaDialog method) (ToolboxFunctionsUI method)

_data (DataFrameModel attribute)

A

active_data_class (CentralManager attribute) add_column_to_df() (BaseDataClass method) add_image_with_default_colormap() (in module pycat.ui.ui_utils) add_text_label() (BaseUIClass method) analysis_data (FileIOClass attribute) analysis_methods_ui (CentralManager attribute) AnalysisMethodsUI (class in pycat.ui.ui_modules)

append_to_df() (BaseDataClass method) apply_bilateral_filter() (in module pycat.toolbox.image_processing_tools) apply_laplace_of_gauss_enhancement() (in module pycat.toolbox.image_processing_tools) apply_laplace_of_gauss_filter() (in module pycat.toolbox.image_processing_tools) apply_rescale_intensity() (in module pycat.toolbox.image_processing_tools) apply_watershed_labeling() (in module pycat.toolbox.segmentation_tools) assign_channels_in_dialog() (FileIOClass method) autocorrelation_analysis() (in module pycat.toolbox.correlation_func_analysis_tools)

B

background_inpainting_func() (in module pycat.toolbox.image_processing_tools) base_file_name (FileIOClass attribute)

BaseDataClass (class in pycat.data.data_modules) BaseUIClass (class in pycat.ui.ui_modules) binary_morph_operation() (in module pycat.toolbox.label_and_mask_tools)

C

calculate_autocorrelation() (in module pycat.toolbox.correlation_func_analysis_tools) calculate_centroid_distance() (in module pycat.toolbox.obj_based_coloc_analysis_tools) calculate_glcm_features() (in module pycat.toolbox.feature_analysis_tools) calculate_image_entropy() (in module pycat.toolbox.feature_analysis_tools) calculate_image_features() (in module pycat.toolbox.feature_analysis_tools) calculate_image_kurtosis() (in module pycat.toolbox.feature_analysis_tools) calculate_indices_and_plot_limits() (in module pycat.toolbox.correlation_func_analysis_tools) calculate_lbp_features() (in module pycat.toolbox.feature_analysis_tools) calculate_length() (BaseDataClass method) calculate_r_squared() (in module pycat.utils.math_utils) categorize_pairings() (in module pycat.toolbox.obj_based_coloc_analysis_tools) ccf_analysis() (in module pycat.toolbox.correlation_func_analysis_tools) cell_analysis_func() (in module pycat.toolbox.feature_analysis_tools) cell_mask_stretching() (in module pycat.toolbox.segmentation_tools) cellpose_segmentation() (in module pycat.toolbox.segmentation_tools) central_manager (AnalysisMethodsUI attribute) (CondensateAnalysisUI attribute) (FibrilAnalysisUI attribute) (GeneralAnalysisUI attribute) (MenuManager attribute) (ObjectColocAnalysisUI attribute) (PixelColocAnalysisUI attribute) (PlottingWidget attribute) (ToolboxFunctionsUI attribute) CentralManager (class in pycat.central_manager)

channel_name_inputs (ChannelAssignmentDialog attribute) ChannelAssignmentDialog (class in pycat.file_io.file_io) check_contrast_func() (in module pycat.utils.general_utils) checkboxes (MeasurementDialog attribute) (obcaDialog attribute) (pwcaDialog attribute) clear_dock() (BaseUIClass method) columnCount() (DataFrameModel method) compute_rolling_ball_background() (in module pycat.toolbox.image_processing_tools) condensate_layout (CondensateAnalysisUI attribute) CondensateAnalysisUI (class in pycat.ui.ui_modules) copy_table_content() (in module pycat.ui.ui_utils) costes_linear_model() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) costes_thresholding() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) create_2d_gaussian_kernel() (in module pycat.utils.math_utils) create_hist_options() (PlottingWidget method) create_layer_dropdown() (BaseUIClass method) create_line_options() (PlottingWidget method) create_overlay_image() (in module pycat.utils.general_utils) create_table_view() (in module pycat.ui.ui_utils) create_violin_options() (PlottingWidget method) crop_bounding_box() (in module pycat.utils.general_utils) cross_correlation_matrix() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) custom_binary_closing() (in module pycat.toolbox.label_and_mask_tools) custom_binary_opening() (in module pycat.toolbox.label_and_mask_tools) cytofluorogram_plot() (in module pycat.toolbox.pixel_wise_corr_analysis_tools)

D

data() (DataFrameModel method) data_class_instance (PlottingWidget attribute) data_repository (BaseDataClass attribute) DataFrameModel (class in pycat.ui.ui_utils) dataframes (PlottingWidget attribute) deblur_by_pixel_reassignment() (in module pycat.toolbox.image_processing_tools)

deselect_all() (MeasurementDialog method) (obcaDialog method) (pwcaDialog method) determine_file_format_and_process_data() (FileIOClass method) df_combo (PlottingWidget attribute) dtype_conversion_func() (in module pycat.utils.general_utils)

E

extend_mask_to_edges() (in module pycat.toolbox.label_and_mask_tools)

F

felzenszwalb_segmentation_and_merging() (in module pycat.toolbox.segmentation_tools) fibril_layout (FibrilAnalysisUI attribute) FibrilAnalysisUI (class in pycat.ui.ui_modules) file_io (CentralManager attribute) FileIOClass (class in pycat.file_io.file_io)

filePath (FileIOClass attribute) fit_gaussian_1d() (in module pycat.toolbox.correlation_func_analysis_tools) fit_gaussian_1d_acf() (in module pycat.toolbox.correlation_func_analysis_tools) fit_gaussian_2d() (in module pycat.toolbox.correlation_func_analysis_tools) fz_segmentation_and_binarization() (in module pycat.toolbox.segmentation_tools)

G

gabor_filter_func() (in module pycat.toolbox.image_processing_tools) gaussian_1d() (in module pycat.toolbox.correlation_func_analysis_tools) gaussian_1d_offset() (in module pycat.toolbox.correlation_func_analysis_tools) gaussian_2d() (in module pycat.toolbox.correlation_func_analysis_tools) general_layout (GeneralAnalysisUI attribute) GeneralAnalysisUI (class in pycat.ui.ui_modules) generate_cross_structuring_element() (in module pycat.toolbox.label_and_mask_tools)

get_all_variables() (BaseDataClass method) get_data() (BaseDataClass method) get_dataframes() (BaseDataClass method) get_default_intensity_range() (in module pycat.utils.general_utils) get_selected_methods() (obcaDialog method) (pwcaDialog method) get_selected_props() (MeasurementDialog method) get_selections() (LayerDataframeSelectionDialog method)

H

headerData() (DataFrameModel method)

I

initUI() (ChannelAssignmentDialog method)

invert_image() (in module pycat.toolbox.image_processing_tools)

J

jaccard_index_calculation() (in module pycat.toolbox.obj_based_coloc_analysis_tools)

K

kendall_tau_calculation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools)

L

LayerDataframeSelectionDialog (class in pycat.file_io.file_io) layout (PlottingWidget attribute) li_ica_histogram() (in module pycat.toolbox.pixel_wise_corr_analysis_tools)

li_ica_plot() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) li_intensity_correlation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) load_into_viewer() (FileIOClass method) local_thresholding_func() (in module pycat.toolbox.segmentation_tools)

M

main() (in module pycat.run_pycat) make_lambda() (MenuManager method) manders_coloc() (in module pycat.toolbox.obj_based_coloc_analysis_tools) manders_k1_calculation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) manders_k2_calculation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) manders_m1_calculation() (in module pycat.toolbox.obj_based_coloc_analysis_tools) manders_m2_calculation() (in module pycat.toolbox.obj_based_coloc_analysis_tools) manders_overlap() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) measure_region_props() (in module pycat.toolbox.label_and_mask_tools) MeasurementDialog (class in pycat.toolbox.label_and_mask_tools) menu_manager (CentralManager attribute) MenuManager (class in pycat.ui.ui_modules) merge_mean_color() (in module pycat.toolbox.segmentation_tools) module pycat.central_manager pycat.data pycat.data.data_modules pycat.file_io pycat.file_io.file_io pycat.run_pycat pycat.toolbox pycat.toolbox.correlation_func_analysis_tools pycat.toolbox.data_viz_tools pycat.toolbox.feature_analysis_tools pycat.toolbox.image_processing_tools pycat.toolbox.label_and_mask_tools pycat.toolbox.layer_tools pycat.toolbox.obj_based_coloc_analysis_tools pycat.toolbox.pixel_wise_corr_analysis_tools pycat.toolbox.segmentation_tools pycat.ui pycat.ui.ui_modules pycat.ui.ui_utils pycat.utils pycat.utils.general_utils pycat.utils.math_utils

O

obcaDialog (class in pycat.toolbox.obj_based_coloc_analysis_tools) object_based_colocalization_analysis() (in module pycat.toolbox.obj_based_coloc_analysis_tools) object_based_distance_analysis() (in module pycat.toolbox.obj_based_coloc_analysis_tools) object_coloc_layout (ObjectColocAnalysisUI attribute) ObjectColocAnalysisUI (class in pycat.ui.ui_modules)

on_dataframe_changed() (PlottingWidget method) on_general_button_clicked() (BaseUIClass method) open_2d_image() (FileIOClass method) open_2d_mask() (FileIOClass method) opencv_contour_func() (in module pycat.toolbox.label_and_mask_tools) opencv_watershed_func() (in module pycat.toolbox.segmentation_tools)

P

peak_and_edge_enhancement_func() (in module pycat.toolbox.image_processing_tools) pearsons_correlation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) perform_costes_test() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) pixel_coloc_layout (PixelColocAnalysisUI attribute) pixel_wise_correlation_analysis() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) PixelColocAnalysisUI (class in pycat.ui.ui_modules) plot_1d_auto_correlation() (in module pycat.toolbox.correlation_func_analysis_tools) plot_1d_results() (in module pycat.toolbox.correlation_func_analysis_tools) plot_2d_autocorrelation() (in module pycat.toolbox.correlation_func_analysis_tools) plot_2d_results() (in module pycat.toolbox.correlation_func_analysis_tools) plot_acf_image() (in module pycat.toolbox.correlation_func_analysis_tools) plot_button (PlottingWidget attribute) plot_data() (PlottingWidget method) PlottingWidget (class in pycat.toolbox.data_viz_tools) pre_process_image() (in module pycat.toolbox.image_processing_tools) prepare_1d_result_dfs() (in module pycat.toolbox.correlation_func_analysis_tools) prepare_2d_result_dfs() (in module pycat.toolbox.correlation_func_analysis_tools) process_ccf() (in module pycat.toolbox.correlation_func_analysis_tools) process_multiple_pairs() (in module pycat.toolbox.obj_based_coloc_analysis_tools) process_obca_methods() (in module pycat.toolbox.obj_based_coloc_analysis_tools) process_pwcca_methods() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) process_single_pairs() (in module pycat.toolbox.obj_based_coloc_analysis_tools) puncta_analysis_func() (in module pycat.toolbox.feature_analysis_tools) puncta_refinement_filtering_func() (in module pycat.toolbox.segmentation_tools) puncta_refinement_func() (in module pycat.toolbox.segmentation_tools) pwcaDialog (class in pycat.toolbox.pixel_wise_corr_analysis_tools) pycat.central_manager module pycat.data module pycat.data.data_modules module pycat.file_io module pycat.file_io.file_io module

pycat.run_pycat module pycat.toolbox module pycat.toolbox.correlation_func_analysis_tools module pycat.toolbox.data_viz_tools module pycat.toolbox.feature_analysis_tools module pycat.toolbox.image_processing_tools module pycat.toolbox.label_and_mask_tools module pycat.toolbox.layer_tools module pycat.toolbox.obj_based_coloc_analysis_tools module pycat.toolbox.pixel_wise_corr_analysis_tools module pycat.toolbox.segmentation_tools module pycat.ui module pycat.ui.ui_modules module pycat.ui.ui_utils module pycat.utils module pycat.utils.general_utils module pycat.utils.math_utils module

R

rb_gaussian_background_removal() (in module pycat.toolbox.image_processing_tools) rb_gaussian_bg_removal_with_edge_enhancement() (in module pycat.toolbox.image_processing_tools) refine_labels_with_contours() (in module pycat.toolbox.segmentation_tools) refresh_viewer_with_new_data() (in module pycat.ui.ui_utils) remove_outliers_iqr() (in module pycat.utils.math_utils) reset_values() (BaseDataClass method) rowCount() (DataFrameModel method) run_advanced_two_layer_merge() (in module pycat.toolbox.layer_tools) run_apply_bilateral_filter() (in module pycat.toolbox.image_processing_tools) run_apply_laplace_of_gauss_filter() (in module pycat.toolbox.image_processing_tools) run_apply_rescale_intensity() (in module pycat.toolbox.image_processing_tools) run_autocorrelation_analysis() (in module pycat.toolbox.correlation_func_analysis_tools) run_binary_morph_operation() (in module pycat.toolbox.label_and_mask_tools) run_ccf_analysis() (in module pycat.toolbox.correlation_func_analysis_tools) run_cell_analysis_func() (in module pycat.toolbox.feature_analysis_tools) run_cellpose_segmentation() (in module pycat.toolbox.segmentation_tools) run_clahe() (in module pycat.toolbox.image_processing_tools) run_convert_labels_to_mask() (in module pycat.toolbox.label_and_mask_tools) run_dpr() (in module pycat.toolbox.image_processing_tools) run_enhanced_rb_gaussian_bg_removal() (in module pycat.toolbox.image_processing_tools) run_fz_segmentation_and_merging() (in module pycat.toolbox.segmentation_tools)

run_invert_image() (in module pycat.toolbox.image_processing_tools) run_label_binary_mask() (in module pycat.toolbox.label_and_mask_tools) run_local_thresholding() (in module pycat.toolbox.segmentation_tools) run_manders_coloc() (in module pycat.toolbox.obj_based_coloc_analysis_tools) run_measure_binary_mask() (in module pycat.toolbox.label_and_mask_tools) run_measure_region_props() (in module pycat.toolbox.label_and_mask_tools) run_morphological_gaussian_filter() (in module pycat.toolbox.image_processing_tools) run_obca() (in module pycat.toolbox.obj_based_coloc_analysis_tools) run_peak_and_edge_enhancement() (in module pycat.toolbox.image_processing_tools) run_pre_process_image() (in module pycat.toolbox.image_processing_tools) run_puncta_analysis_func() (in module pycat.toolbox.feature_analysis_tools) run_pwcca() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) run_pycat_func() (in module pycat.run_pycat) run_rb_gaussian_background_removal() (in module pycat.toolbox.image_processing_tools) run_segment_subcellular_objects() (in module pycat.toolbox.segmentation_tools) run_simple_multi_merge() (in module pycat.toolbox.layer_tools) run_train_and_apply_rf_classifier() (in module pycat.toolbox.segmentation_tools) run_update_labels() (in module pycat.toolbox.label_and_mask_tools) run_upscaling_func() (in module pycat.toolbox.image_processing_tools) run_wavelet_noise_subtraction() (in module pycat.toolbox.image_processing_tools) run_wbns() (in module pycat.toolbox.image_processing_tools)

S

save_and_clear_all() (FileIOClass method) save_table_as_csv() (in module pycat.ui.ui_utils) scramble_blocks() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) scramble_pixels() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) scramble_pixels_within_mask() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) segment_subcellular_objects() (in module pycat.toolbox.segmentation_tools) select_all() (MeasurementDialog method) (obcaDialog method) (pwcaDialog method) selected_dataframes (LayerDataframeSelectionDialog attribute) selected_layers (LayerDataframeSelectionDialog attribute) set_active_data_class() (CentralManager method)

set_data() (BaseDataClass method) setup_ui() (CondensateAnalysisUI method) (FibrilAnalysisUI method) (GeneralAnalysisUI method) (ObjectColocAnalysisUI method) (PixelColocAnalysisUI method) show_dataframes_dialog() (in module pycat.ui.ui_utils) smooth_array() (in module pycat.toolbox.correlation_func_analysis_tools) sorensen_dice_coefficient_calculation() (in module pycat.toolbox.obj_based_coloc_analysis_tools) spearman_r_calculation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools) split_touching_objects() (in module pycat.toolbox.label_and_mask_tools) subtract_background() (in module pycat.toolbox.image_processing_tools)

T

table_context_menu() (in module pycat.ui.ui_utils) textboxes (MeasurementDialog attribute) toggle_scroll_area() (MeasurementDialog method)

toolbox_functions_ui (CentralManager attribute) ToolboxFunctionsUI (class in pycat.ui.ui_modules) train_and_apply_rf_classifier() (in module pycat.toolbox.segmentation_tools)

U

update_dataframes() (PlottingWidget method) update_df() (BaseDataClass method) update_dropdown_items() (BaseUIClass method) update_metadata() (BaseDataClass method)

update_plot_options_dropdowns() (PlottingWidget method) update_tool() (BaseUIClass method) update_ui() (PlottingWidget method) upscale_image_interp() (in module pycat.toolbox.image_processing_tools)

V

viewer (AnalysisMethodsUI attribute) (BaseUIClass attribute) (CentralManager attribute) (CondensateAnalysisUI attribute) (FibrilAnalysisUI attribute) (FileIOClass attribute) (GeneralAnalysisUI attribute) (MenuManager attribute) (ObjectColocAnalysisUI attribute) (PixelColocAnalysisUI attribute)

W

wavelet_bg_and_noise_calculation() (in module pycat.toolbox.image_processing_tools)

wbns_func() (in module pycat.toolbox.image_processing_tools) weighted_tau_calculation() (in module pycat.toolbox.pixel_wise_corr_analysis_tools)