Core Modules
preprocess_generate_masks()
generate_cellpose_masks()
generate_screen_graphs()
process_non_tif_non_2D_images()
CombineLoaders
CombineLoaders.train_loaders
CombineLoaders.loader_iters
CombineLoaders.__iter__()
CombineLoaders.__next__()
CombinedDataset
CombinedDataset.datasets
CombinedDataset.lengths
CombinedDataset.total_length
CombinedDataset.shuffle
CombinedDataset.__getitem__()
CombinedDataset.__len__()
NoClassDataset
NoClassDataset.data_dir
NoClassDataset.transform
NoClassDataset.shuffle
NoClassDataset.load_to_memory
NoClassDataset.filenames
NoClassDataset.load_image()
NoClassDataset.__len__()
NoClassDataset.shuffle_dataset()
NoClassDataset.__getitem__()
spacrDataset
spacrDataset.data_dir
spacrDataset.classes
spacrDataset.transform
spacrDataset.shuffle
spacrDataset.pin_memory
spacrDataset.filenames
spacrDataset.labels
spacrDataset.load_image()
spacrDataset.__len__()
spacrDataset.shuffle_dataset()
spacrDataset.get_plate()
spacrDataset.__getitem__()
spacrDataLoader
spacrDataLoader.preload_batches
spacrDataLoader.batch_queue
spacrDataLoader.process
spacrDataLoader.current_batch_index
spacrDataLoader.pin_memory
spacrDataLoader.__iter__()
spacrDataLoader.__next__()
spacrDataLoader.cleanup()
spacrDataLoader.__del__()
TarImageDataset
TarImageDataset.members
TarImageDataset.tar_path
TarImageDataset.transform
TarImageDataset.__len__()
TarImageDataset.__getitem__()
load_images_from_paths()
concatenate_and_normalize()
delete_empty_subdirectories()
preprocess_img_data()
read_plot_model_stats()
convert_numpy_to_tiff()
generate_cellpose_train_test()
parse_gz_files()
generate_dataset()
generate_loaders()
generate_training_dataset()
training_dataset_from_annotation()
training_dataset_from_annotation_metadata()
generate_dataset_from_lists()
convert_separate_files_to_yokogawa()
convert_to_yokogawa()
apply_augmentation()
process_instruction()
prepare_cellpose_dataset()
spacr_path
filepaths_to_database()
activation_maps_to_database()
activation_correlations_to_database()
calculate_activation_correlations()
load_settings()
save_settings()
print_progress()
reset_mp()
is_multiprocessing_process()
close_file_descriptors()
close_multiprocessing_processes()
check_mask_folder()
smooth_hull_lines()
mask_object_count()
is_list_of_lists()
normalize_to_dtype()
annotate_conditions()
Cache
Cache.cache
Cache.max_size
Cache.get()
Cache.put()
ScaledDotProductAttention_v1
ScaledDotProductAttention_v1.d_k
ScaledDotProductAttention_v1.forward()
SelfAttention_v1
SelfAttention_v1.W_q
SelfAttention_v1.W_k
SelfAttention_v1.W_v
SelfAttention_v1.attention
SelfAttention_v1.forward()
ScaledDotProductAttention
ScaledDotProductAttention.d_k
ScaledDotProductAttention.forward()
SelfAttention
SelfAttention.W_q
SelfAttention.W_k
SelfAttention.W_v
SelfAttention.attention
SelfAttention.forward()
EarlyFusion
EarlyFusion.conv1
EarlyFusion.forward()
SpatialAttention
SpatialAttention.conv1
SpatialAttention.sigmoid
SpatialAttention.forward()
MultiScaleBlockWithAttention
MultiScaleBlockWithAttention.dilated_conv1
MultiScaleBlockWithAttention.spatial_attention
MultiScaleBlockWithAttention.custom_forward()
MultiScaleBlockWithAttention.forward()
CustomCellClassifier
CustomCellClassifier.early_fusion
CustomCellClassifier.multi_scale_block_1
CustomCellClassifier.fc1
CustomCellClassifier.use_checkpoint
CustomCellClassifier.custom_forward()
CustomCellClassifier.forward()
TorchModel
TorchModel.model_name
TorchModel.use_checkpoint
TorchModel.base_model
TorchModel.num_ftrs
TorchModel.apply_dropout_rate()
TorchModel.init_base_model()
TorchModel.get_weight_choice()
TorchModel.get_num_ftrs()
TorchModel.init_spacr_classifier()
TorchModel.forward()
FocalLossWithLogits
FocalLossWithLogits.alpha
FocalLossWithLogits.gamma
FocalLossWithLogits.forward()
ResNet
ResNet.initialize_base()
ResNet.forward()
split_my_dataset()
classification_metrics()
compute_irm_penalty()
choose_model()
calculate_loss()
pick_best_model()
get_paths_from_db()
save_file_lists()
augment_single_image()
augment_images()
augment_classes()
annotate_predictions()
initiate_counter()
add_images_to_tar()
generate_fraction_map()
fishers_odds()
model_metrics()
check_multicollinearity()
lasso_reg()
MLR()
get_files_from_dir()
create_circular_mask()
apply_mask()
invert_image()
resize_images_and_labels()
resize_labels_back()
calculate_iou()
match_masks()
compute_average_precision()
pad_to_same_shape()
compute_ap_over_iou_thresholds()
compute_segmentation_ap()
jaccard_index()
dice_coefficient()
extract_boundaries()
boundary_f1_score()
merge_touching_objects()
remove_intensity_objects()
SelectChannels
SelectChannels.channels
SelectChannels.__call__()
preprocess_image_v1()
SaliencyMapGenerator
SaliencyMapGenerator.model
SaliencyMapGenerator.compute_saliency_maps()
SaliencyMapGenerator.compute_saliency_and_predictions()
SaliencyMapGenerator.plot_activation_grid()
SaliencyMapGenerator.percentile_normalize()
GradCAMGenerator
GradCAMGenerator.model
GradCAMGenerator.target_layer
GradCAMGenerator.cam_type
GradCAMGenerator.gradients
GradCAMGenerator.activations
GradCAMGenerator.target_layer_module
GradCAMGenerator.hook_layers()
GradCAMGenerator.get_layer()
GradCAMGenerator.compute_gradcam_maps()
GradCAMGenerator.compute_gradcam_and_predictions()
GradCAMGenerator.plot_activation_grid()
GradCAMGenerator.percentile_normalize()
preprocess_image()
class_visualization()
get_submodules()
GradCAM
GradCAM.model
GradCAM.target_layers
GradCAM.cuda
GradCAM.forward()
GradCAM.__call__()
show_cam_on_image()
recommend_target_layers()
IntegratedGradients
IntegratedGradients.model
IntegratedGradients.generate_integrated_gradients()
get_db_paths()
get_sequencing_paths()
load_image_paths()
merge_dataframes()
remove_highly_correlated_columns_v1()
filter_columns()
reduction_and_clustering()
remove_noise()
plot_embedding()
generate_colors()
assign_colors()
setup_plot()
plot_clusters()
plot_umap_images()
plot_images_by_cluster()
plot_image()
remove_canvas()
plot_clusters_grid()
plot_grid()
generate_path_list_from_db()
correct_paths()
delete_folder()
measure_test_mode()
preprocess_data()
remove_low_variance_columns()
remove_highly_correlated_columns()
filter_dataframe_features()
check_overlap()
find_non_overlapping_position()
search_reduction_and_clustering()
load_image()
extract_features()
check_normality()
random_forest_feature_importance()
perform_statistical_tests()
combine_results()
cluster_feature_analysis()
process_mask_file_adjust_cell()
adjust_cell_masks()
adjust_cell_masks_v1()
process_masks()
merge_regression_res_with_metadata()
process_vision_results()
get_ml_results_paths()
augment_image()
augment_dataset()
convert_and_relabel_masks()
correct_masks()
count_reads_in_fastq()
get_cuda_version()
all_elements_match()
prepare_batch_for_segmentation()
check_index()
map_condition()
download_models()
generate_cytoplasm_mask()
add_column_to_database()
fill_holes_in_mask()
correct_metadata_column_names()
control_filelist()
rename_columns_in_db()
group_feature_class()
delete_intermedeate_files()
filter_and_save_csv()
extract_tar_bz2_files()
calculate_shortest_distance()
format_path_for_system()
normalize_src_path()
generate_image_path_map()
copy_images_to_consolidated()
correct_metadata()
remove_outliers_by_group()
set_default_plot_merge_settings()
set_default_settings_preprocess_generate_masks()
set_default_plot_data_from_db()
set_default_settings_preprocess_img_data()
set_default_umap_image_settings()
get_measure_crop_settings()
set_default_analyze_screen()
set_default_train_test_model()
set_generate_training_dataset_defaults()
deep_spacr_defaults()
get_train_test_model_settings()
get_analyze_recruitment_default_settings()
get_default_test_cellpose_model_settings()
get_default_apply_cellpose_model_settings()
default_settings_analyze_percent_positive()
get_analyze_reads_default_settings()
get_map_barcodes_default_settings()
get_train_cellpose_default_settings()
set_generate_dataset_defaults()
get_perform_regression_default_settings()
get_check_cellpose_models_default_settings()
get_identify_masks_finetune_default_settings()
q
expected_types
categories
category_keys
check_settings()
generate_fields()
descriptions
set_annotate_default_settings()
set_default_generate_barecode_mapping()
get_default_generate_activation_map_settings()
get_analyze_plaque_settings()
set_graph_importance_defaults()
set_interperate_vision_model_defaults()
set_analyze_endodyogeny_defaults()
set_analyze_class_proportion_defaults()
get_plot_data_from_csv_default_settings()
choose_p_adjust_method()
perform_normality_tests()
perform_levene_test()
perform_posthoc_tests()
chi_pairwise()
Image Analysis
get_components()
save_and_add_image_to_grid()
img_list_to_grid()
measure_crop()
process_meassure_crop_results()
generate_cellpose_train_set()
get_object_counts()
plot_image_mask_overlay()
plot_cellpose4_output()
plot_masks()
generate_mask_random_cmap()
random_cmap()
plot_images_and_arrays()
plot_arrays()
plot_arrays_v1()
plot_merged()
generate_plate_heatmap()
plot_plates()
print_mask_and_flows()
plot_resize()
normalize_and_visualize()
visualize_masks()
visualize_cellpose_masks()
plot_comparison_results()
plot_object_outlines()
volcano_plot()
plot_histogram()
plot_lorenz_curves()
plot_permutation()
plot_feature_importance()
read_and_plot__vision_results()
jitterplot_by_annotation()
create_grouped_plot()
spacrGraph
spacrGraph.df
spacrGraph.grouping_column
spacrGraph.order
spacrGraph.data_column
spacrGraph.graph_type
spacrGraph.summary_func
spacrGraph.colors
spacrGraph.output_dir
spacrGraph.save
spacrGraph.error_bar_type
spacrGraph.remove_outliers
spacrGraph.theme
spacrGraph.representation
spacrGraph.paired
spacrGraph.all_to_all
spacrGraph.compare_group
spacrGraph.y_lim
spacrGraph.graph_name
spacrGraph.log_x
spacrGraph.log_y
spacrGraph.results_df
spacrGraph.sns_palette
spacrGraph.fig
spacrGraph.results_name
spacrGraph.raw_df
spacrGraph.preprocess_data()
spacrGraph.remove_outliers_from_plot()
spacrGraph.perform_normality_tests()
spacrGraph.perform_levene_test()
spacrGraph.perform_statistical_tests()
spacrGraph.perform_posthoc_tests()
spacrGraph.create_plot()
spacrGraph.get_results()
spacrGraph.get_figure()
plot_data_from_db()
plot_data_from_csv()
plot_region()
plot_image_grid()
overlay_masks_on_images()
graph_importance()
plot_proportion_stacked_bars()
create_venn_diagram()
parse_cellpose4_output()
identify_masks_finetune()
generate_masks_from_imgs()
check_cellpose_models()
save_results_and_figure()
compare_mask()
compare_cellpose_masks()
Classification
QuasiBinomial
QuasiBinomial.dispersion
QuasiBinomial.variance()
calculate_p_values()
perform_mixed_model()
create_volcano_filename()
scale_variables()
select_glm_family()
prepare_formula()
fit_mixed_model()
check_and_clean_data()
minimum_cell_simulation()
process_model_coefficients()
check_distribution()
pick_glm_family_and_link()
regression_model()
regression()
save_summary_to_file()
perform_regression()
process_reads()
apply_transformation()
clean_controls()
process_scores()
generate_ml_scores()
ml_analysis()
shap_analysis()
find_optimal_threshold()
interperate_vision_model()
apply_model()
apply_model_to_tar()
evaluate_model_performance()
test_model_core()
test_model_performance()
train_test_model()
train_model()
generate_activation_map()
visualize_classes()
visualize_integrated_gradients()
SmoothGrad
SmoothGrad.model
SmoothGrad.n_samples
SmoothGrad.stdev_spread
SmoothGrad.compute_smooth_grad()
visualize_smooth_grad()
deep_spacr()
model_knowledge_transfer()
model_fusion()
annotate_filter_vision()
GUI Components
MainApp
MainApp.color_settings
MainApp.main_buttons
MainApp.additional_buttons
MainApp.main_gui_apps
MainApp.additional_gui_apps
MainApp.selected_app
MainApp.create_widgets()
MainApp.create_startup_screen()
MainApp.update_description()
MainApp.show_description()
MainApp.clear_description()
MainApp.load_app()
MainApp.clear_frame()
gui_app()
console_output
parent_frame
vars_dict
canvas
canvas_widget
scrollable_frame
progress_label
fig_queue
figures
figure_index
progress_bar
usage_bars
index_control
thread_control
toggle_settings()
display_figure()
clear_unused_figures()
show_previous_figure()
show_next_figure()
process_fig_queue()
update_figure()
setup_plot_section()
set_globals()
import_settings()
setup_settings_panel()
setup_console()
setup_button_section()
setup_usage_panel()
initiate_abort()
check_src_folders_files()
start_process()
process_console_queue()
main_thread_update_function()
cleanup_previous_instance()
initiate_root()
fig
restart_gui_app()
create_menu_bar()
set_element_size()
set_dark_style()
spacrFont
spacrFont.font_name
spacrFont.font_style
spacrFont.font_size
spacrFont.font_path
spacrFont.get_font_path()
spacrFont.load_font()
spacrFont.get_font()
spacrContainer
spacrContainer.orient
spacrContainer.bg
spacrContainer.sash_thickness
spacrContainer.panes
spacrContainer.sashes
spacrContainer.add()
spacrContainer.create_sash()
spacrContainer.reposition_panes()
spacrContainer.on_configure()
spacrContainer.on_enter_sash()
spacrContainer.on_leave_sash()
spacrContainer.start_resize()
spacrContainer.perform_resize()
spacrEntry
spacrEntry.bg_color
spacrEntry.active_color
spacrEntry.fg_color
spacrEntry.outline
spacrEntry.font_family
spacrEntry.font_size
spacrEntry.font_loader
spacrEntry.canvas_height
spacrEntry.canvas
spacrEntry.draw_rounded_rectangle()
spacrEntry.on_focus_in()
spacrEntry.on_focus_out()
spacrCheck
spacrCheck.bg_color
spacrCheck.active_color
spacrCheck.fg_color
spacrCheck.inactive_color
spacrCheck.variable
spacrCheck.canvas_width
spacrCheck.canvas_height
spacrCheck.canvas
spacrCheck.draw_rounded_square()
spacrCheck.update_check()
spacrCheck.toggle_variable()
spacrCombo
spacrCombo.bg_color
spacrCombo.active_color
spacrCombo.fg_color
spacrCombo.inactive_color
spacrCombo.font_family
spacrCombo.font_size
spacrCombo.font_loader
spacrCombo.values
spacrCombo.canvas_width
spacrCombo.canvas_height
spacrCombo.canvas
spacrCombo.var
spacrCombo.selected_value
spacrCombo.dropdown_menu
spacrCombo.draw_rounded_rectangle()
spacrCombo.on_click()
spacrCombo.open_dropdown()
spacrCombo.close_dropdown()
spacrCombo.on_select()
spacrCombo.set()
spacrDropdownMenu
spacrDropdownMenu.variable
spacrDropdownMenu.options
spacrDropdownMenu.command
spacrDropdownMenu.text
spacrDropdownMenu.size
spacrDropdownMenu.font_size
spacrDropdownMenu.font_loader
spacrDropdownMenu.button_width
spacrDropdownMenu.canvas_width
spacrDropdownMenu.canvas_height
spacrDropdownMenu.canvas
spacrDropdownMenu.inactive_color
spacrDropdownMenu.active_color
spacrDropdownMenu.fg_color
spacrDropdownMenu.bg_color
spacrDropdownMenu.button_bg
spacrDropdownMenu.button_text
spacrDropdownMenu.menu
spacrDropdownMenu.create_rounded_rectangle()
spacrDropdownMenu.on_enter()
spacrDropdownMenu.on_leave()
spacrDropdownMenu.on_click()
spacrDropdownMenu.post_menu()
spacrDropdownMenu.on_select()
spacrDropdownMenu.update_styles()
spacrCheckbutton
spacrCheckbutton.text
spacrCheckbutton.variable
spacrCheckbutton.command
spacrProgressBar
spacrProgressBar.fg_color
spacrProgressBar.bg_color
spacrProgressBar.active_color
spacrProgressBar.inactive_color
spacrProgressBar.font_size
spacrProgressBar.font_loader
spacrProgressBar.style
spacrProgressBar.label
spacrProgressBar.operation_type
spacrProgressBar.additional_info
spacrProgressBar.set_label_position()
spacrProgressBar.update_label()
spacrSlider
spacrSlider.specified_length
spacrSlider.knob_radius
spacrSlider.thickness
spacrSlider.knob_position
spacrSlider.slider_line
spacrSlider.knob
spacrSlider.position
spacrSlider.offset
spacrSlider.from_
spacrSlider.to
spacrSlider.value
spacrSlider.show_index
spacrSlider.command
spacrSlider.fg_color
spacrSlider.bg_color
spacrSlider.active_color
spacrSlider.inactive_color
spacrSlider.canvas
spacrSlider.length
spacrSlider.resize_slider()
spacrSlider.value_to_position()
spacrSlider.position_to_value()
spacrSlider.draw_slider()
spacrSlider.move_knob()
spacrSlider.activate_knob()
spacrSlider.release_knob()
spacrSlider.set_to()
spacrSlider.get()
spacrSlider.set()
spacrSlider.jump_to_click()
spacrSlider.update_slider_from_entry()
spacrScrollbarStyle()
spacrFrame
spacrFrame.scrollable_frame
spacrFrame.inactive_color
spacrFrame.active_color
spacrFrame.fg_color
spacrFrame.rounded_rectangle()
spacrLabel
spacrLabel.text
spacrLabel.align
spacrLabel.style_out
spacrLabel.font_style
spacrLabel.font_size
spacrLabel.font_family
spacrLabel.font_loader
spacrLabel.canvas
spacrLabel.style
spacrLabel.set_text()
spacrButton
spacrButton.text
spacrButton.command
spacrButton.icon_name
spacrButton.size
spacrButton.show_text
spacrButton.outline
spacrButton.animation
spacrButton.font_size
spacrButton.font_loader
spacrButton.canvas
spacrButton.inactive_color
spacrButton.bg_color
spacrButton.active_color
spacrButton.fg_color
spacrButton.is_zoomed_in
spacrButton.load_icon()
spacrButton.get_icon_path()
spacrButton.on_enter()
spacrButton.on_leave()
spacrButton.on_click()
spacrButton.create_rounded_rectangle()
spacrButton.update_description()
spacrButton.clear_description()
spacrButton.animate_zoom()
spacrButton.zoom_icon()
spacrSwitch
spacrSwitch.text
spacrSwitch.variable
spacrSwitch.command
spacrSwitch.canvas
spacrSwitch.switch_bg
spacrSwitch.switch
spacrSwitch.label
spacrSwitch.toggle()
spacrSwitch.update_switch()
spacrSwitch.animate_switch()
spacrSwitch.animate_movement()
spacrSwitch.get()
spacrSwitch.set()
spacrSwitch.create_rounded_rectangle()
spacrToolTip
spacrToolTip.widget
spacrToolTip.text
spacrToolTip.tooltip_window
spacrToolTip.show_tooltip()
spacrToolTip.hide_tooltip()
standardize_figure()
modify_figure_properties()
save_figure_as_format()
modify_figure()
generate_dna_matrix()
initialize_cuda()
set_high_priority()
set_cpu_affinity()
proceed_with_app()
load_app()
parse_list()
create_input_field()
process_stdout_stderr()
WriteToQueue
WriteToQueue.q
WriteToQueue.write()
WriteToQueue.flush()
cancel_after_tasks()
load_next_app()
convert_settings_dict_for_gui()
spacrFigShow()
function_gui_wrapper()
run_function_gui()
hide_all_settings()
setup_frame()
download_hug_dataset()
download_dataset()
ensure_after_tasks()
display_gif_in_plot_frame()
display_media_in_plot_frame()
print_widget_structure()
get_screen_dimensions()
convert_to_number()
Sequencing & Submodules
map_sequences_to_names()
save_df_to_hdf5()
save_unique_combinations_to_csv()
save_qc_df_to_csv()
extract_sequence_and_quality()
create_consensus()
get_consensus_base()
reverse_complement()
process_chunk()
saver_process()
paired_read_chunked_processing()
single_read_chunked_processing()
generate_barecode_mapping()
barecodes_reverse_complement()
graph_sequencing_stats()
custom_volcano_plot()
go_term_enrichment_by_column()
plot_gene_phenotypes()
plot_gene_heatmaps()
generate_score_heatmap()
CellposeLazyDataset
CellposeLazyDataset.normalize
CellposeLazyDataset.percentiles
CellposeLazyDataset.target_size
CellposeLazyDataset.augment
CellposeLazyDataset.__len__()
CellposeLazyDataset.apply_augmentation()
CellposeLazyDataset.__getitem__()
train_cellpose()
test_cellpose_model()
apply_cellpose_model()
plot_cellpose_batch()
analyze_percent_positive()
analyze_recruitment()
analyze_plaques()
count_phenotypes()
compare_reads_to_scores()
analyze_endodyogeny()
analyze_class_proportion()
post_regression_analysis()
This page contains auto-generated API reference documentation [1].