spacr
0.2.65
Contents:
spacr
spacr
Index
Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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Z
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__iter__() (spacr.io.CombineLoaders method)
__next__() (spacr.io.CombineLoaders method)
A
add() (spacr.gui_elements.spacrContainer method)
add_colored_border() (spacr.gui_elements.AnnotateApp method)
add_images_to_tar() (in module spacr.utils)
adjust_cell_masks() (in module spacr.utils)
all_elements_match() (in module spacr.core)
analyze_associations() (in module spacr.graph_learning)
analyze_calcium_oscillations() (in module spacr.timelapse)
analyze_data_reg() (in module spacr.core)
analyze_plaques() (in module spacr.core)
analyze_recruitment() (in module spacr.core)
animate_movement() (spacr.gui_elements.spacrSwitch method)
animate_switch() (spacr.gui_elements.spacrSwitch method)
animate_zoom() (spacr.gui_elements.spacrButton method)
annotate() (in module spacr.gui_utils)
annotate_app() (in module spacr.gui_utils)
annotate_conditions() (in module spacr.utils)
annotate_predictions() (in module spacr.utils)
annotate_results() (in module spacr.core)
annotate_with_image_refs() (in module spacr.gui_utils)
AnnotateApp (class in spacr.gui_elements)
append_database() (in module spacr.sim)
apply_brush() (spacr.gui_elements.ModifyMaskApp method)
apply_brush_release() (spacr.gui_elements.ModifyMaskApp method)
apply_dividing_line() (spacr.gui_elements.ModifyMaskApp method)
apply_dropout_rate() (spacr.utils.TorchModel method)
apply_magic_wand() (spacr.gui_elements.ModifyMaskApp method)
apply_mask() (in module spacr.utils)
apply_model() (in module spacr.core)
(in module spacr.graph_learning)
apply_model_to_tar() (in module spacr.core)
apply_normalization() (spacr.gui_elements.ModifyMaskApp method)
apply_transformation() (in module spacr.sequencing)
apply_zoom_on_enter() (spacr.gui_elements.ModifyMaskApp method)
assign_colors() (in module spacr.utils)
augment_classes() (in module spacr.utils)
augment_dataset() (in module spacr.utils)
augment_image() (in module spacr.utils)
augment_images() (in module spacr.utils)
augment_single_image() (in module spacr.utils)
B
boundary_f1_score() (in module spacr.utils)
C
Cache (class in spacr.utils)
cache (spacr.utils.Cache attribute)
calculate_grid_dimensions() (spacr.gui_elements.AnnotateApp method)
calculate_iou() (in module spacr.utils)
calculate_loss() (in module spacr.utils)
calculate_p_values() (in module spacr.sequencing)
calculate_permutation_importance() (in module spacr.sim)
cancel_after_tasks() (in module spacr.gui_utils)
canvas_to_image() (spacr.gui_elements.ModifyMaskApp method)
cell_level_roc_auc() (in module spacr.sim)
check_cellpose_models() (in module spacr.core)
check_index() (in module spacr.core)
check_mask_folder() (in module spacr.utils)
check_multicollinearity() (in module spacr.utils)
check_normality() (in module spacr.sequencing)
(in module spacr.utils)
check_overlap() (in module spacr.utils)
check_settings() (in module spacr.settings)
choose_model() (in module spacr.utils)
class_visualization() (in module spacr.utils)
classification_metrics() (in module spacr.utils)
classifier() (in module spacr.sim)
classifier_v2() (in module spacr.sim)
clean_controls() (in module spacr.sequencing)
cleanup() (spacr.io.spacrDataLoader method)
clear_description() (spacr.gui.MainApp method)
(spacr.gui_elements.spacrButton method)
clear_frame() (spacr.gui.MainApp method)
clear_objects() (spacr.gui_elements.ModifyMaskApp method)
clear_unused_figures() (in module spacr.gui_core)
close_dropdown() (spacr.gui_elements.spacrCombo method)
close_file_descriptors() (in module spacr.utils)
close_multiprocessing_processes() (in module spacr.utils)
cluster_feature_analysis() (in module spacr.utils)
combine_results() (in module spacr.utils)
CombinedDataset (class in spacr.io)
CombineLoaders (class in spacr.io)
compare_cellpose_masks() (in module spacr.core)
compare_mask() (in module spacr.core)
complement() (in module spacr.sequencing)
compute_ap_over_iou_thresholds() (in module spacr.utils)
compute_average_precision() (in module spacr.utils)
compute_irm_penalty() (in module spacr.utils)
compute_precision_recall() (in module spacr.sim)
compute_roc_auc() (in module spacr.sim)
compute_saliency_maps() (spacr.utils.SaliencyMapGenerator method)
compute_segmentation_ap() (in module spacr.utils)
compute_smooth_grad() (spacr.deep_spacr.SmoothGrad method)
concatenate_and_normalize() (in module spacr.io)
consensus_sequence() (in module spacr.sequencing)
consensus_sequence_v1() (in module spacr.sequencing)
construct_well_graph() (in module spacr.graph_learning)
convert_and_relabel_masks() (in module spacr.utils)
convert_numpy_to_tiff() (in module spacr.io)
convert_settings_dict_for_gui() (in module spacr.gui_utils)
correct_masks() (in module spacr.utils)
correct_paths() (in module spacr.utils)
count_mismatches() (in module spacr.sequencing)
count_reads_in_fastq() (in module spacr.utils)
create_circular_mask() (in module spacr.utils)
create_database() (in module spacr.sim)
create_graphs_for_wells() (in module spacr.graph_learning)
create_input_field() (in module spacr.gui_utils)
create_menu_bar() (in module spacr.gui_elements)
create_rounded_rectangle() (spacr.gui_elements.spacrButton method)
(spacr.gui_elements.spacrDropdownMenu method)
(spacr.gui_elements.spacrSwitch method)
create_sash() (spacr.gui_elements.spacrContainer method)
create_startup_screen() (spacr.gui.MainApp method)
create_widgets() (spacr.gui.MainApp method)
custom_forward() (spacr.utils.CustomCellClassifier method)
(spacr.utils.MultiScaleBlockWithAttention method)
CustomCellClassifier (class in spacr.utils)
D
Decoder (class in spacr.graph_learning)
deep_spacr() (in module spacr.deep_spacr)
deep_spacr_defaults() (in module spacr.settings)
delete_empty_subdirectories() (in module spacr.io)
delete_folder() (in module spacr.utils)
dice_coefficient() (in module spacr.utils)
display_figure() (in module spacr.gui_core)
display_image() (spacr.gui_elements.ModifyMaskApp method)
display_zoomed_image() (spacr.gui_elements.ModifyMaskApp method)
dist_gen() (in module spacr.sim)
download_dataset() (in module spacr.gui_utils)
download_hug_dataset() (in module spacr.gui_utils)
draw() (spacr.gui_elements.ModifyMaskApp method)
draw_on_zoomed_mask() (spacr.gui_elements.ModifyMaskApp method)
draw_rounded_rectangle() (spacr.gui_elements.spacrCombo method)
(spacr.gui_elements.spacrEntry method)
draw_rounded_square() (spacr.gui_elements.spacrCheck method)
E
EarlyFusion (class in spacr.utils)
Encoder (class in spacr.graph_learning)
ensure_after_tasks() (in module spacr.gui_utils)
equalize_lengths() (in module spacr.sequencing)
erase_brush() (spacr.gui_elements.ModifyMaskApp method)
erase_brush_release() (spacr.gui_elements.ModifyMaskApp method)
erase_object() (spacr.gui_elements.ModifyMaskApp method)
evaluate_model_performance() (in module spacr.deep_spacr)
exponential_decay() (in module spacr.timelapse)
extract_barcodes_from_fastq() (in module spacr.sequencing)
extract_barcodes_from_fastq_v1() (in module spacr.sequencing)
extract_barecodes() (in module spacr.sequencing)
extract_boundaries() (in module spacr.utils)
extract_features() (in module spacr.utils)
extract_metadata_from_path() (in module spacr.graph_learning)
F
file_len() (in module spacr.sequencing)
filepaths_to_database() (in module spacr.measure)
fill_objects() (spacr.gui_elements.ModifyMaskApp method)
filter_channels() (spacr.gui_elements.AnnotateApp method)
filter_columns() (in module spacr.utils)
filter_dataframe_features() (in module spacr.utils)
find_grna() (in module spacr.sequencing)
find_non_overlapping_position() (in module spacr.utils)
find_optimal_threshold() (in module spacr.core)
finish_dividing_line() (spacr.gui_elements.ModifyMaskApp method)
finish_drawing() (spacr.gui_elements.ModifyMaskApp method)
finish_drawing_if_active() (spacr.gui_elements.ModifyMaskApp method)
fishers_odds() (in module spacr.utils)
flush() (spacr.gui_utils.WriteToQueue method)
FocalLossWithLogits (class in spacr.utils)
forward() (spacr.graph_learning.Decoder method)
(spacr.graph_learning.Encoder method)
(spacr.graph_learning.GraphTransformer method)
(spacr.utils.CustomCellClassifier method)
(spacr.utils.EarlyFusion method)
(spacr.utils.FocalLossWithLogits method)
(spacr.utils.GradCAM method)
(spacr.utils.MultiScaleBlockWithAttention method)
(spacr.utils.ResNet method)
(spacr.utils.ScaledDotProductAttention method)
(spacr.utils.SelfAttention method)
(spacr.utils.SpatialAttention method)
(spacr.utils.TorchModel method)
function_gui_wrapper() (in module spacr.gui_utils)
G
generate_annotate_fields() (in module spacr.gui_utils)
generate_barecode_mapping() (in module spacr.sequencing)
generate_cellpose_masks() (in module spacr.core)
generate_cellpose_train_set() (in module spacr.measure)
generate_cellpose_train_test() (in module spacr.io)
generate_colors() (in module spacr.utils)
generate_dataset() (in module spacr.core)
generate_dataset_from_lists() (in module spacr.core)
generate_dependent_variable() (in module spacr.utils)
generate_fields() (in module spacr.settings)
generate_floats() (in module spacr.sim)
generate_fraction_map() (in module spacr.sequencing)
(in module spacr.utils)
generate_gene_list() (in module spacr.sim)
generate_gene_weights() (in module spacr.sim)
generate_image_umap() (in module spacr.core)
generate_integers() (in module spacr.sim)
generate_integrated_gradients() (spacr.utils.IntegratedGradients method)
generate_loaders() (in module spacr.core)
generate_mask_random_cmap() (in module spacr.plot)
generate_masks_from_imgs() (in module spacr.core)
generate_ml_scores() (in module spacr.core)
generate_paramiters() (in module spacr.sim)
generate_plate_heatmap() (in module spacr.plot)
(in module spacr.sequencing)
generate_plate_map() (in module spacr.sim)
generate_power_law_distribution() (in module spacr.sim)
generate_shap_summary_plot() (in module spacr.sim)
generate_synthetic_grna_data() (in module spacr.graph_learning)
generate_training_data_file_list() (in module spacr.core)
generate_training_dataset() (in module spacr.core)
generate_well_score() (in module spacr.sim)
get() (spacr.gui_elements.spacrSwitch method)
(spacr.utils.Cache method)
get_analyze_reads_default_settings() (in module spacr.settings)
get_analyze_recruitment_default_settings() (in module spacr.settings)
get_check_cellpose_models_default_settings() (in module spacr.settings)
get_components() (in module spacr.measure)
get_db_paths() (in module spacr.utils)
get_files_from_dir() (in module spacr.utils)
get_font() (spacr.gui_elements.spacrFont method)
get_font_path() (spacr.gui_elements.spacrFont method)
get_icon_path() (spacr.gui_elements.spacrButton method)
get_identify_masks_finetune_default_settings() (in module spacr.settings)
get_map_barcodes_default_settings() (in module spacr.settings)
get_measure_crop_settings() (in module spacr.settings)
get_ml_results_paths() (in module spacr.utils)
get_num_ftrs() (spacr.utils.TorchModel method)
get_object_counts() (in module spacr.measure)
get_on_image_click() (spacr.gui_elements.AnnotateApp method)
get_optimum_threshold() (in module spacr.sim)
get_paths_from_db() (in module spacr.utils)
get_perform_regression_default_settings() (in module spacr.settings)
get_plate() (spacr.io.spacrDataset method)
get_read_data() (in module spacr.sequencing)
get_scaling_factors() (spacr.gui_elements.ModifyMaskApp method)
get_sequence_data() (in module spacr.sequencing)
get_sequencing_paths() (in module spacr.utils)
get_submodules() (in module spacr.utils)
get_top_two_matches() (in module spacr.sequencing)
get_train_cellpose_default_settings() (in module spacr.settings)
get_weight_choice() (spacr.utils.TorchModel method)
gini() (in module spacr.sim)
gini_coefficient() (in module spacr.sim)
gini_gene_well() (in module spacr.sim)
GradCAM (class in spacr.utils)
GraphTransformer (class in spacr.graph_learning)
grna_plate_heatmap() (in module spacr.sequencing)
gui_app() (in module spacr.gui)
H
hide_all_settings() (in module spacr.gui_utils)
hide_tooltip() (spacr.gui_elements.spacrToolTip method)
I
identify_masks_finetune() (in module spacr.core)
image_to_canvas() (spacr.gui_elements.ModifyMaskApp method)
img_list_to_grid() (in module spacr.measure)
import_settings() (in module spacr.gui_core)
infected_vs_noninfected() (in module spacr.timelapse)
init_base_model() (spacr.utils.TorchModel method)
init_spacr_classifier() (spacr.utils.TorchModel method)
initialize_base() (spacr.utils.ResNet method)
initialize_cuda() (in module spacr.gui_utils)
initialize_flags() (spacr.gui_elements.ModifyMaskApp method)
initiate_abort() (in module spacr.gui_core)
initiate_annotation_app() (in module spacr.app_annotate)
initiate_counter() (in module spacr.utils)
initiate_make_mask_app() (in module spacr.app_make_masks)
initiate_root() (in module spacr.gui_core)
IntegratedGradients (class in spacr.utils)
invert_image() (in module spacr.utils)
invert_mask() (spacr.gui_elements.ModifyMaskApp method)
is_list_of_lists() (in module spacr.utils)
is_multiprocessing_process() (in module spacr.utils)
J
jaccard_index() (in module spacr.utils)
jitterplot_by_annotation() (in module spacr.core)
join_measurments_and_annotation() (in module spacr.core)
L
lasso_reg() (in module spacr.utils)
load_app() (in module spacr.gui_utils)
(spacr.gui.MainApp method)
load_first_image() (spacr.gui_elements.ModifyMaskApp method)
load_font() (spacr.gui_elements.spacrFont method)
load_icon() (spacr.gui_elements.spacrButton method)
load_image() (in module spacr.utils)
(spacr.io.NoClassDataset method)
(spacr.io.spacrDataset method)
load_image_and_mask() (spacr.gui_elements.ModifyMaskApp method)
load_image_paths() (in module spacr.utils)
load_images() (in module spacr.graph_learning)
(spacr.gui_elements.AnnotateApp method)
load_mnist_data() (in module spacr.graph_learning)
load_next_app() (in module spacr.gui_utils)
load_single_image() (spacr.gui_elements.AnnotateApp method)
loader_iters (spacr.io.CombineLoaders attribute)
log_function_call() (in module spacr.logger)
M
magic_wand_normal() (spacr.gui_elements.ModifyMaskApp method)
magic_wand_zoomed() (spacr.gui_elements.ModifyMaskApp method)
main_thread_update_function() (in module spacr.gui_core)
MainApp (class in spacr.gui)
map_condition() (in module spacr.core)
map_unmapped_grnas() (in module spacr.sequencing)
mask_object_count() (in module spacr.utils)
match_masks() (in module spacr.utils)
max_size (spacr.utils.Cache attribute)
measure_crop() (in module spacr.measure)
measure_test_mode() (in module spacr.utils)
merge_dataframes() (in module spacr.utils)
merge_pred_mes() (in module spacr.core)
merge_regression_res_with_metadata() (in module spacr.utils)
merge_touching_objects() (in module spacr.utils)
ml_analysis() (in module spacr.core)
MLR() (in module spacr.utils)
model_metrics() (in module spacr.utils)
modify_figure() (in module spacr.gui_elements)
modify_figure_properties() (in module spacr.gui_elements)
ModifyMaskApp (class in spacr.gui_elements)
module
spacr
spacr.app_annotate
spacr.app_classify
spacr.app_make_masks
spacr.app_mask
spacr.app_measure
spacr.app_sequencing
spacr.app_umap
spacr.core
spacr.deep_spacr
spacr.graph_learning
spacr.gui
spacr.gui_core
spacr.gui_elements
spacr.gui_utils
spacr.io
spacr.logger
spacr.measure
spacr.plot
spacr.sequencing
spacr.settings
spacr.sim
spacr.sim_app
spacr.timelapse
spacr.utils
spacr.version
MultiScaleBlockWithAttention (class in spacr.utils)
N
next_image() (spacr.gui_elements.ModifyMaskApp method)
next_page() (spacr.gui_elements.AnnotateApp method)
NoClassDataset (class in spacr.io)
normalize_and_visualize() (in module spacr.plot)
normalize_array() (in module spacr.sim)
normalize_image() (spacr.gui_elements.AnnotateApp static method)
(spacr.gui_elements.ModifyMaskApp method)
normalize_sequencing_data() (in module spacr.graph_learning)
normalize_to_dtype() (in module spacr.utils)
O
on_click() (spacr.gui_elements.spacrButton method)
(spacr.gui_elements.spacrCombo method)
(spacr.gui_elements.spacrDropdownMenu method)
on_configure() (spacr.gui_elements.spacrContainer method)
on_enter() (spacr.gui_elements.spacrButton method)
(spacr.gui_elements.spacrDropdownMenu method)
on_enter_sash() (spacr.gui_elements.spacrContainer method)
on_focus_in() (spacr.gui_elements.spacrEntry method)
on_focus_out() (spacr.gui_elements.spacrEntry method)
on_leave() (spacr.gui_elements.spacrButton method)
(spacr.gui_elements.spacrDropdownMenu method)
on_leave_sash() (spacr.gui_elements.spacrContainer method)
on_select() (spacr.gui_elements.spacrCombo method)
(spacr.gui_elements.spacrDropdownMenu method)
open_dropdown() (spacr.gui_elements.spacrCombo method)
overlay_mask_on_image() (spacr.gui_elements.ModifyMaskApp method)
P
pad_to_same_shape() (in module spacr.utils)
parse_gz_files() (in module spacr.sequencing)
parse_list() (in module spacr.gui_utils)
perform_mixed_model() (in module spacr.sequencing)
perform_regression() (in module spacr.sequencing)
perform_resize() (spacr.gui_elements.spacrContainer method)
perform_statistical_tests() (in module spacr.utils)
pick_best_model() (in module spacr.utils)
plot_arrays() (in module spacr.plot)
plot_clusters() (in module spacr.utils)
plot_clusters_grid() (in module spacr.utils)
plot_comparison_results() (in module spacr.plot)
plot_confusion_matrix() (in module spacr.sim)
plot_correlation_matrix() (in module spacr.sim)
plot_data() (in module spacr.sequencing)
(in module spacr.timelapse)
plot_embedding() (in module spacr.utils)
plot_feature_importance() (in module spacr.plot)
(in module spacr.sim)
plot_grid() (in module spacr.utils)
plot_histogram() (in module spacr.plot)
(in module spacr.sim)
plot_image() (in module spacr.utils)
plot_image_mask_overlay() (in module spacr.plot)
plot_images_and_arrays() (in module spacr.plot)
plot_images_by_cluster() (in module spacr.utils)
plot_lorenz_curves() (in module spacr.plot)
plot_masks() (in module spacr.plot)
plot_merged() (in module spacr.plot)
plot_object_outlines() (in module spacr.plot)
plot_partial_dependences() (in module spacr.sim)
plot_permutation() (in module spacr.plot)
plot_plates() (in module spacr.plot)
(in module spacr.sequencing)
plot_resize() (in module spacr.plot)
plot_roc_pr() (in module spacr.sim)
plot_saliency_maps() (spacr.utils.SaliencyMapGenerator method)
plot_simulations() (in module spacr.sim)
plot_umap_images() (in module spacr.utils)
pos_dict() (in module spacr.sequencing)
post_menu() (spacr.gui_elements.spacrDropdownMenu method)
power_law_dist_gen() (in module spacr.sim)
precess_reads() (in module spacr.sequencing)
prefilter_paths_annotations() (spacr.gui_elements.AnnotateApp method)
prepare_batch_for_cellpose() (in module spacr.core)
preprocess_data() (in module spacr.utils)
preprocess_generate_masks() (in module spacr.core)
preprocess_image() (in module spacr.graph_learning)
(in module spacr.utils)
preprocess_img_data() (in module spacr.io)
preprocess_pathogen_data() (in module spacr.timelapse)
previous_image() (spacr.gui_elements.ModifyMaskApp method)
previous_page() (spacr.gui_elements.AnnotateApp method)
print_mask_and_flows() (in module spacr.plot)
print_progress() (in module spacr.utils)
proceed_with_app() (in module spacr.gui_utils)
process_barecodes() (in module spacr.sequencing)
process_chunk_for_consensus() (in module spacr.sequencing)
process_chunk_for_mapping() (in module spacr.sequencing)
process_console_queue() (in module spacr.gui_core)
process_fig_queue() (in module spacr.gui_core)
process_masks() (in module spacr.utils)
process_meassure_crop_results() (in module spacr.measure)
process_reads() (in module spacr.core)
process_scores() (in module spacr.sequencing)
process_sequencing_df() (in module spacr.graph_learning)
process_stdout_stderr() (in module spacr.gui_utils)
process_vision_results() (in module spacr.utils)
put() (spacr.utils.Cache method)
R
random_cmap() (in module spacr.plot)
random_forest_feature_importance() (in module spacr.utils)
read_and_plot__vision_results() (in module spacr.plot)
read_plot_model_stats() (in module spacr.io)
read_simulations_table() (in module spacr.sim)
recommend_target_layers() (in module spacr.utils)
reducer_hyperparameter_search() (in module spacr.core)
reduction_and_clustering() (in module spacr.utils)
regression() (in module spacr.sequencing)
regression_analasys() (in module spacr.core)
regression_model() (in module spacr.sequencing)
regression_roc_auc() (in module spacr.sim)
relabel_objects() (spacr.gui_elements.ModifyMaskApp method)
remove_canvas() (in module spacr.utils)
remove_columns_with_single_value() (in module spacr.sim)
remove_constant_columns() (in module spacr.sim)
remove_highly_correlated_columns() (in module spacr.utils)
remove_intensity_objects() (in module spacr.utils)
remove_low_variance_columns() (in module spacr.utils)
remove_noise() (in module spacr.utils)
remove_outliers() (in module spacr.sequencing)
remove_small_objects() (spacr.gui_elements.ModifyMaskApp method)
reposition_panes() (spacr.gui_elements.spacrContainer method)
reset_mp() (in module spacr.utils)
resize_arrays() (spacr.gui_elements.ModifyMaskApp method)
resize_images_and_labels() (in module spacr.utils)
resize_labels_back() (in module spacr.utils)
ResNet (class in spacr.utils)
reverse_complement() (in module spacr.sequencing)
rounded_rectangle() (spacr.gui_elements.spacrFrame method)
run_and_save() (in module spacr.sim)
run_annotate_app() (in module spacr.gui_utils)
run_experiment() (in module spacr.sim)
run_function_gui() (in module spacr.gui_utils)
run_multiple_simulations() (in module spacr.sim)
run_simulation() (in module spacr.sim)
S
SaliencyMapGenerator (class in spacr.utils)
save_and_add_image_to_grid() (in module spacr.measure)
save_data() (in module spacr.sim)
save_figure() (in module spacr.timelapse)
save_figure_as_format() (in module spacr.gui_elements)
save_file_lists() (in module spacr.utils)
save_mask() (spacr.gui_elements.ModifyMaskApp method)
save_plot() (in module spacr.sim)
save_results_and_figure() (in module spacr.core)
save_results_dataframe() (in module spacr.timelapse)
save_settings() (in module spacr.utils)
save_shap_plot() (in module spacr.sim)
save_to_hdf() (in module spacr.sequencing)
ScaledDotProductAttention (class in spacr.utils)
search_reduction_and_clustering() (in module spacr.utils)
SelectChannels (class in spacr.utils)
SelfAttention (class in spacr.utils)
sequence_plates() (in module spacr.sim)
set() (spacr.gui_elements.spacrCombo method)
(spacr.gui_elements.spacrSwitch method)
set_annotate_default_settings() (in module spacr.settings)
set_cpu_affinity() (in module spacr.gui_utils)
set_dark_style() (in module spacr.gui_elements)
set_default_analyze_screen() (in module spacr.settings)
set_default_generate_barecode_mapping() (in module spacr.settings)
set_default_plot_merge_settings() (in module spacr.settings)
set_default_settings_preprocess_generate_masks() (in module spacr.settings)
set_default_settings_preprocess_img_data() (in module spacr.settings)
set_default_train_test_model() (in module spacr.settings)
set_default_umap_image_settings() (in module spacr.settings)
set_element_size() (in module spacr.gui_elements)
set_generate_training_dataset_defaults() (in module spacr.settings)
set_globals() (in module spacr.gui_core)
set_high_priority() (in module spacr.gui_utils)
set_label_position() (spacr.gui_elements.spacrProgressBar method)
set_text() (spacr.gui_elements.spacrLabel method)
set_zoom_rectangle_end() (spacr.gui_elements.ModifyMaskApp method)
set_zoom_rectangle_start() (spacr.gui_elements.ModifyMaskApp method)
setup_button_section() (in module spacr.gui_core)
setup_canvas() (spacr.gui_elements.ModifyMaskApp method)
setup_console() (in module spacr.gui_core)
setup_frame() (in module spacr.gui_utils)
setup_function_toolbar() (spacr.gui_elements.ModifyMaskApp method)
setup_mode_toolbar() (spacr.gui_elements.ModifyMaskApp method)
setup_navigation_toolbar() (spacr.gui_elements.ModifyMaskApp method)
setup_plot() (in module spacr.utils)
setup_plot_section() (in module spacr.gui_core)
setup_progress_frame() (in module spacr.gui_core)
setup_settings_panel() (in module spacr.gui_core)
setup_usage_panel() (in module spacr.gui_core)
setup_zoom_toolbar() (spacr.gui_elements.ModifyMaskApp method)
shap_analysis() (in module spacr.core)
show_cam_on_image() (in module spacr.utils)
show_description() (spacr.gui.MainApp method)
show_next_figure() (in module spacr.gui_core)
show_previous_figure() (in module spacr.gui_core)
show_tooltip() (spacr.gui_elements.spacrToolTip method)
shuffle_dataset() (spacr.io.NoClassDataset method)
(spacr.io.spacrDataset method)
shutdown() (spacr.gui_elements.AnnotateApp method)
smooth_hull_lines() (in module spacr.utils)
SmoothGrad (class in spacr.deep_spacr)
spacr
module
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
spacr.deep_spacr
module
spacr.graph_learning
module
spacr.gui
module
spacr.gui_core
module
spacr.gui_elements
module
spacr.gui_utils
module
spacr.io
module
spacr.logger
module
spacr.measure
module
spacr.plot
module
spacr.sequencing
module
spacr.settings
module
spacr.sim
module
spacr.sim_app
module
spacr.timelapse
module
spacr.utils
module
spacr.version
module
spacrButton (class in spacr.gui_elements)
spacrCheck (class in spacr.gui_elements)
spacrCheckbutton (class in spacr.gui_elements)
spacrCombo (class in spacr.gui_elements)
spacrContainer (class in spacr.gui_elements)
spacrDataLoader (class in spacr.io)
spacrDataset (class in spacr.io)
spacrDropdownMenu (class in spacr.gui_elements)
spacrEntry (class in spacr.gui_elements)
spacrFigShow() (in module spacr.gui_utils)
spacrFont (class in spacr.gui_elements)
spacrFrame (class in spacr.gui_elements)
spacrLabel (class in spacr.gui_elements)
spacrProgressBar (class in spacr.gui_elements)
spacrScrollbarStyle() (in module spacr.gui_elements)
spacrSwitch (class in spacr.gui_elements)
spacrToolTip (class in spacr.gui_elements)
SpatialAttention (class in spacr.utils)
split_fastq() (in module spacr.sequencing)
split_my_dataset() (in module spacr.utils)
standardize_figure() (in module spacr.gui_elements)
start_annotate_app() (in module spacr.app_annotate)
start_classify_app() (in module spacr.app_classify)
start_dividing_line() (spacr.gui_elements.ModifyMaskApp method)
start_make_mask_app() (in module spacr.app_make_masks)
start_mask_app() (in module spacr.app_mask)
start_measure_app() (in module spacr.app_measure)
start_process() (in module spacr.gui_core)
start_resize() (spacr.gui_elements.spacrContainer method)
start_seq_app() (in module spacr.app_sequencing)
start_umap_app() (in module spacr.app_umap)
summarize_per_well() (in module spacr.timelapse)
summarize_per_well_inf_non_inf() (in module spacr.timelapse)
T
TarImageDataset (class in spacr.io)
test_error() (in module spacr.sequencing)
test_model_core() (in module spacr.deep_spacr)
test_model_performance() (in module spacr.deep_spacr)
toggle() (spacr.gui_elements.spacrSwitch method)
toggle_brush_mode() (spacr.gui_elements.ModifyMaskApp method)
toggle_dividing_line_mode() (spacr.gui_elements.ModifyMaskApp method)
toggle_draw_mode() (spacr.gui_elements.ModifyMaskApp method)
toggle_erase_mode() (spacr.gui_elements.ModifyMaskApp method)
toggle_magic_wand_mode() (spacr.gui_elements.ModifyMaskApp method)
toggle_settings() (in module spacr.gui_core)
toggle_variable() (spacr.gui_elements.spacrCheck method)
toggle_zoom_mode() (spacr.gui_elements.ModifyMaskApp method)
TorchModel (class in spacr.utils)
train() (in module spacr.graph_learning)
train_cellpose() (in module spacr.core)
train_graph_transformer() (in module spacr.graph_learning)
train_loaders (spacr.io.CombineLoaders attribute)
train_model() (in module spacr.deep_spacr)
train_test_model() (in module spacr.deep_spacr)
training_dataset_from_annotation() (in module spacr.core)
translate_barecodes() (in module spacr.sequencing)
truncate_read() (in module spacr.sequencing)
U
update_check() (spacr.gui_elements.spacrCheck method)
update_database_worker() (spacr.gui_elements.AnnotateApp method)
update_description() (spacr.gui.MainApp method)
(spacr.gui_elements.spacrButton method)
update_display() (spacr.gui_elements.ModifyMaskApp method)
update_dividing_line_preview() (spacr.gui_elements.ModifyMaskApp method)
update_gui_text() (spacr.gui_elements.AnnotateApp method)
update_html() (spacr.gui_elements.AnnotateApp static method)
update_label() (spacr.gui_elements.spacrProgressBar method)
update_mouse_info() (spacr.gui_elements.ModifyMaskApp method)
update_original_mask() (spacr.gui_elements.ModifyMaskApp method)
update_original_mask_from_zoom() (spacr.gui_elements.ModifyMaskApp method)
update_scores_and_get_cm() (in module spacr.sim)
update_styles() (spacr.gui_elements.spacrDropdownMenu method)
update_switch() (spacr.gui_elements.spacrSwitch method)
update_zoom_box() (spacr.gui_elements.ModifyMaskApp method)
use_magic_wand() (spacr.gui_elements.ModifyMaskApp method)
V
validate_and_adjust_beta_params() (in module spacr.sim)
vert_horiz() (in module spacr.sequencing)
vis_dists() (in module spacr.sim)
visualize_all() (in module spacr.sim)
visualize_cellpose_masks() (in module spacr.plot)
visualize_classes() (in module spacr.deep_spacr)
visualize_grad_cam() (in module spacr.deep_spacr)
visualize_integrated_gradients() (in module spacr.deep_spacr)
visualize_masks() (in module spacr.plot)
visualize_saliency_map() (in module spacr.deep_spacr)
visualize_smooth_grad() (in module spacr.deep_spacr)
volcano_plot() (in module spacr.plot)
W
write() (spacr.gui_utils.WriteToQueue method)
WriteToQueue (class in spacr.gui_utils)
Z
zoom_icon() (spacr.gui_elements.spacrButton method)