spacr
- spacr package
- Submodules
- spacr.app_annotate module
- spacr.app_classify module
- spacr.app_make_masks module
- spacr.app_mask module
- spacr.app_measure module
- spacr.app_sequencing module
- spacr.app_umap module
- spacr.core module
all_elements_match()
analyze_data_reg()
analyze_plaques()
analyze_recruitment()
annotate_results()
apply_model()
apply_model_to_tar()
check_cellpose_models()
check_index()
compare_cellpose_masks()
compare_mask()
find_optimal_threshold()
generate_cellpose_masks()
generate_dataset()
generate_dataset_from_lists()
generate_image_umap()
generate_loaders()
generate_masks_from_imgs()
generate_ml_scores()
generate_training_data_file_list()
generate_training_dataset()
identify_masks_finetune()
jitterplot_by_annotation()
join_measurments_and_annotation()
map_condition()
merge_pred_mes()
ml_analysis()
prepare_batch_for_cellpose()
preprocess_generate_masks()
process_reads()
reducer_hyperparameter_search()
regression_analasys()
save_results_and_figure()
shap_analysis()
train_cellpose()
training_dataset_from_annotation()
- spacr.deep_spacr module
- spacr.graph_learning module
Decoder
Encoder
GraphTransformer
analyze_associations()
apply_model()
construct_well_graph()
create_graphs_for_wells()
extract_metadata_from_path()
generate_synthetic_grna_data()
load_images()
load_mnist_data()
normalize_sequencing_data()
preprocess_image()
process_sequencing_df()
train()
train_graph_transformer()
- spacr.gui module
- spacr.gui_core module
clear_unused_figures()
display_figure()
import_settings()
initiate_abort()
initiate_root()
main_thread_update_function()
process_console_queue()
process_fig_queue()
set_globals()
setup_button_section()
setup_console()
setup_plot_section()
setup_progress_frame()
setup_settings_panel()
setup_usage_panel()
show_next_figure()
show_previous_figure()
start_process()
toggle_settings()
- spacr.gui_elements module
AnnotateApp
AnnotateApp.add_colored_border()
AnnotateApp.calculate_grid_dimensions()
AnnotateApp.filter_channels()
AnnotateApp.get_on_image_click()
AnnotateApp.load_images()
AnnotateApp.load_single_image()
AnnotateApp.next_page()
AnnotateApp.normalize_image()
AnnotateApp.prefilter_paths_annotations()
AnnotateApp.previous_page()
AnnotateApp.shutdown()
AnnotateApp.update_database_worker()
AnnotateApp.update_gui_text()
AnnotateApp.update_html()
ModifyMaskApp
ModifyMaskApp.apply_brush()
ModifyMaskApp.apply_brush_release()
ModifyMaskApp.apply_dividing_line()
ModifyMaskApp.apply_magic_wand()
ModifyMaskApp.apply_normalization()
ModifyMaskApp.apply_zoom_on_enter()
ModifyMaskApp.canvas_to_image()
ModifyMaskApp.clear_objects()
ModifyMaskApp.display_image()
ModifyMaskApp.display_zoomed_image()
ModifyMaskApp.draw()
ModifyMaskApp.draw_on_zoomed_mask()
ModifyMaskApp.erase_brush()
ModifyMaskApp.erase_brush_release()
ModifyMaskApp.erase_object()
ModifyMaskApp.fill_objects()
ModifyMaskApp.finish_dividing_line()
ModifyMaskApp.finish_drawing()
ModifyMaskApp.finish_drawing_if_active()
ModifyMaskApp.get_scaling_factors()
ModifyMaskApp.image_to_canvas()
ModifyMaskApp.initialize_flags()
ModifyMaskApp.invert_mask()
ModifyMaskApp.load_first_image()
ModifyMaskApp.load_image_and_mask()
ModifyMaskApp.magic_wand_normal()
ModifyMaskApp.magic_wand_zoomed()
ModifyMaskApp.next_image()
ModifyMaskApp.normalize_image()
ModifyMaskApp.overlay_mask_on_image()
ModifyMaskApp.previous_image()
ModifyMaskApp.relabel_objects()
ModifyMaskApp.remove_small_objects()
ModifyMaskApp.resize_arrays()
ModifyMaskApp.save_mask()
ModifyMaskApp.set_zoom_rectangle_end()
ModifyMaskApp.set_zoom_rectangle_start()
ModifyMaskApp.setup_canvas()
ModifyMaskApp.setup_function_toolbar()
ModifyMaskApp.setup_mode_toolbar()
ModifyMaskApp.setup_navigation_toolbar()
ModifyMaskApp.setup_zoom_toolbar()
ModifyMaskApp.start_dividing_line()
ModifyMaskApp.toggle_brush_mode()
ModifyMaskApp.toggle_dividing_line_mode()
ModifyMaskApp.toggle_draw_mode()
ModifyMaskApp.toggle_erase_mode()
ModifyMaskApp.toggle_magic_wand_mode()
ModifyMaskApp.toggle_zoom_mode()
ModifyMaskApp.update_display()
ModifyMaskApp.update_dividing_line_preview()
ModifyMaskApp.update_mouse_info()
ModifyMaskApp.update_original_mask()
ModifyMaskApp.update_original_mask_from_zoom()
ModifyMaskApp.update_zoom_box()
ModifyMaskApp.use_magic_wand()
create_menu_bar()
modify_figure()
modify_figure_properties()
save_figure_as_format()
set_dark_style()
set_element_size()
spacrButton
spacrCheck
spacrCheckbutton
spacrCombo
spacrContainer
spacrDropdownMenu
spacrEntry
spacrFont
spacrFrame
spacrLabel
spacrProgressBar
spacrScrollbarStyle()
spacrSwitch
spacrToolTip
standardize_figure()
- spacr.gui_utils module
WriteToQueue
annotate()
annotate_app()
annotate_with_image_refs()
cancel_after_tasks()
convert_settings_dict_for_gui()
create_input_field()
download_dataset()
download_hug_dataset()
ensure_after_tasks()
function_gui_wrapper()
generate_annotate_fields()
hide_all_settings()
initialize_cuda()
load_app()
load_next_app()
parse_list()
proceed_with_app()
process_stdout_stderr()
run_annotate_app()
run_function_gui()
set_cpu_affinity()
set_high_priority()
setup_frame()
spacrFigShow()
- spacr.io module
- spacr.logger module
- spacr.measure module
- spacr.plot module
generate_mask_random_cmap()
generate_plate_heatmap()
normalize_and_visualize()
plot_arrays()
plot_comparison_results()
plot_feature_importance()
plot_histogram()
plot_image_mask_overlay()
plot_images_and_arrays()
plot_lorenz_curves()
plot_masks()
plot_merged()
plot_object_outlines()
plot_permutation()
plot_plates()
plot_resize()
print_mask_and_flows()
random_cmap()
read_and_plot__vision_results()
visualize_cellpose_masks()
visualize_masks()
volcano_plot()
- spacr.sequencing module
apply_transformation()
calculate_p_values()
check_normality()
clean_controls()
complement()
consensus_sequence()
consensus_sequence_v1()
count_mismatches()
equalize_lengths()
extract_barcodes_from_fastq()
extract_barcodes_from_fastq_v1()
extract_barecodes()
file_len()
find_grna()
generate_barecode_mapping()
generate_fraction_map()
generate_plate_heatmap()
get_read_data()
get_sequence_data()
get_top_two_matches()
grna_plate_heatmap()
map_unmapped_grnas()
parse_gz_files()
perform_mixed_model()
perform_regression()
plot_data()
plot_plates()
pos_dict()
precess_reads()
process_barecodes()
process_chunk_for_consensus()
process_chunk_for_mapping()
process_scores()
regression()
regression_model()
remove_outliers()
reverse_complement()
save_to_hdf()
split_fastq()
test_error()
translate_barecodes()
truncate_read()
vert_horiz()
- spacr.settings module
check_settings()
deep_spacr_defaults()
generate_fields()
get_analyze_reads_default_settings()
get_analyze_recruitment_default_settings()
get_check_cellpose_models_default_settings()
get_identify_masks_finetune_default_settings()
get_map_barcodes_default_settings()
get_measure_crop_settings()
get_perform_regression_default_settings()
get_train_cellpose_default_settings()
set_annotate_default_settings()
set_default_analyze_screen()
set_default_generate_barecode_mapping()
set_default_plot_merge_settings()
set_default_settings_preprocess_generate_masks()
set_default_settings_preprocess_img_data()
set_default_train_test_model()
set_default_umap_image_settings()
set_generate_training_dataset_defaults()
- spacr.sim module
append_database()
calculate_permutation_importance()
cell_level_roc_auc()
classifier()
classifier_v2()
compute_precision_recall()
compute_roc_auc()
create_database()
dist_gen()
generate_floats()
generate_gene_list()
generate_gene_weights()
generate_integers()
generate_paramiters()
generate_plate_map()
generate_power_law_distribution()
generate_shap_summary_plot()
generate_well_score()
get_optimum_threshold()
gini()
gini_coefficient()
gini_gene_well()
normalize_array()
plot_confusion_matrix()
plot_correlation_matrix()
plot_feature_importance()
plot_histogram()
plot_partial_dependences()
plot_roc_pr()
plot_simulations()
power_law_dist_gen()
read_simulations_table()
regression_roc_auc()
remove_columns_with_single_value()
remove_constant_columns()
run_and_save()
run_experiment()
run_multiple_simulations()
run_simulation()
save_data()
save_plot()
save_shap_plot()
sequence_plates()
update_scores_and_get_cm()
validate_and_adjust_beta_params()
vis_dists()
visualize_all()
- spacr.sim_app module
- spacr.timelapse module
- spacr.utils module
Cache
CustomCellClassifier
EarlyFusion
FocalLossWithLogits
GradCAM
IntegratedGradients
MLR()
MultiScaleBlockWithAttention
ResNet
SaliencyMapGenerator
ScaledDotProductAttention
SelectChannels
SelfAttention
SpatialAttention
TorchModel
add_images_to_tar()
adjust_cell_masks()
annotate_conditions()
annotate_predictions()
apply_mask()
assign_colors()
augment_classes()
augment_dataset()
augment_image()
augment_images()
augment_single_image()
boundary_f1_score()
calculate_iou()
calculate_loss()
check_mask_folder()
check_multicollinearity()
check_normality()
check_overlap()
choose_model()
class_visualization()
classification_metrics()
close_file_descriptors()
close_multiprocessing_processes()
cluster_feature_analysis()
combine_results()
compute_ap_over_iou_thresholds()
compute_average_precision()
compute_irm_penalty()
compute_segmentation_ap()
convert_and_relabel_masks()
correct_masks()
correct_paths()
count_reads_in_fastq()
create_circular_mask()
delete_folder()
dice_coefficient()
extract_boundaries()
extract_features()
filter_columns()
filter_dataframe_features()
find_non_overlapping_position()
fishers_odds()
generate_colors()
generate_dependent_variable()
generate_fraction_map()
get_db_paths()
get_files_from_dir()
get_ml_results_paths()
get_paths_from_db()
get_sequencing_paths()
get_submodules()
initiate_counter()
invert_image()
is_list_of_lists()
is_multiprocessing_process()
jaccard_index()
lasso_reg()
load_image()
load_image_paths()
mask_object_count()
match_masks()
measure_test_mode()
merge_dataframes()
merge_regression_res_with_metadata()
merge_touching_objects()
model_metrics()
normalize_to_dtype()
pad_to_same_shape()
perform_statistical_tests()
pick_best_model()
plot_clusters()
plot_clusters_grid()
plot_embedding()
plot_grid()
plot_image()
plot_images_by_cluster()
plot_umap_images()
preprocess_data()
preprocess_image()
print_progress()
process_masks()
process_vision_results()
random_forest_feature_importance()
recommend_target_layers()
reduction_and_clustering()
remove_canvas()
remove_highly_correlated_columns()
remove_intensity_objects()
remove_low_variance_columns()
remove_noise()
reset_mp()
resize_images_and_labels()
resize_labels_back()
save_file_lists()
save_settings()
search_reduction_and_clustering()
setup_plot()
show_cam_on_image()
smooth_hull_lines()
split_my_dataset()
- spacr.version module
- Module contents