Index

A

add_dir_to_experiment_filemap() (in module towbintools.foundation.file_handling) adjust_tensor_dimensions() (in module towbintools.deep_learning.utils.util) aggregate_interpolated_series() (in module towbintools.data_analysis.time_series) align_images_orientation_ssim() (in module towbintools.foundation.image_handling)

AttentionBlock1D (class in towbintools.deep_learning.architectures.archs) AttentionUnet1D (class in towbintools.deep_learning.architectures.archs) augment_contrast() (in module towbintools.foundation.image_handling) augment_contrast_zstack() (in module towbintools.foundation.zstack)

B

BCELossWithIgnore (class in towbintools.deep_learning.utils.loss) boxplot() (in module towbintools.plotting.boxplots) boxplot_larval_stage() (in module towbintools.plotting.boxplots)

build_conditions() (in module towbintools.plotting.plotting_structure) build_legend() (in module towbintools.plotting.utils_plotting) build_plotting_struct() (in module towbintools.plotting.plotting_structure)

C

check_if_stack() (in module towbintools.foundation.image_handling) check_if_time_series() (in module towbintools.foundation.image_handling) check_if_zstack() (in module towbintools.foundation.image_handling) ClassificationDataset (class in towbintools.deep_learning.utils.dataset) ClassificationModel (class in towbintools.deep_learning.architectures.models) classify_image() (in module towbintools.classification.classification_tools) classify_labels() (in module towbintools.classification.classification_tools) classify_labels_and_convert_to_dataframe() (in module towbintools.classification.classification_tools) classify_labels_and_convert_to_dataframe_features_dict() (in module towbintools.classification.classification_tools) classify_labels_and_convert_to_mask() (in module towbintools.classification.classification_tools) classify_labels_and_convert_to_mask_features_dict() (in module towbintools.classification.classification_tools) classify_labels_features_dict() (in module towbintools.classification.classification_tools) classify_plane() (in module towbintools.classification.classification_tools) collate_fn() (towbintools.deep_learning.utils.dataset.KeypointDetection1DPredictionDataset method) (towbintools.deep_learning.utils.dataset.KeypointDetection1DTrainingDataset method) (towbintools.deep_learning.utils.dataset.QualityControlDataset method) (towbintools.deep_learning.utils.dataset.QualityControlPredictionDataset method) (towbintools.deep_learning.utils.dataset.SegmentationDataset method) (towbintools.deep_learning.utils.dataset.SegmentationPredictionDataset method) combine_experiments() (in module towbintools.plotting.plotting_structure) combine_series() (in module towbintools.plotting.utils_data_processing) compute_background_fluorescence() (in module towbintools.quantification.quantification_tools) compute_base_label_features() (in module towbintools.foundation.worm_features) compute_bending_energy() (in module towbintools.foundation.worm_features) compute_bending_energy_mask() (in module towbintools.foundation.worm_features) compute_deviation_from_each_model_at_ecdysis() (in module towbintools.plotting.proportions) compute_deviation_from_model_at_ecdysis() (in module towbintools.plotting.proportions) compute_deviation_from_model_development_percentage() (in module towbintools.plotting.proportions) compute_exponential_series_at_time_classified() (in module towbintools.data_analysis.time_series) compute_features_of_label() (in module towbintools.classification.classification_tools) compute_features_of_plane() (in module towbintools.classification.classification_tools) compute_fluorescence_in_mask() (in module towbintools.quantification.quantification_tools) compute_growth_rate() (in module towbintools.plotting.utils_data_processing) compute_growth_rate_classified() (in module towbintools.data_analysis.growth_rate) compute_growth_rate_exponential() (in module towbintools.data_analysis.growth_rate) compute_growth_rate_linear() (in module towbintools.data_analysis.growth_rate) compute_growth_rate_per_larval_stage() (in module towbintools.data_analysis.growth_rate) compute_haralick_features() (in module towbintools.foundation.worm_features)

compute_image_features() (in module towbintools.foundation.worm_features) compute_instantaneous_growth_rate() (in module towbintools.data_analysis.growth_rate) compute_instantaneous_growth_rate_classified() (in module towbintools.data_analysis.growth_rate) compute_larval_stage_duration() (in module towbintools.data_analysis.growth_rate) compute_mask_area() (in module towbintools.foundation.worm_features) compute_mask_average_width() (in module towbintools.foundation.worm_features) compute_mask_length() (in module towbintools.foundation.worm_features) compute_mask_morphological_features() (in module towbintools.foundation.worm_features) compute_mask_type_features() (in module towbintools.foundation.worm_features) compute_mask_volume() (in module towbintools.foundation.worm_features) compute_max_width() (in module towbintools.foundation.worm_features) compute_mid_width() (in module towbintools.foundation.worm_features) compute_patch_features() (in module towbintools.foundation.worm_features) compute_qc_features() (in module towbintools.classification.qc_tools) compute_series_at_time_classified() (in module towbintools.data_analysis.time_series) compute_width_profile() (in module towbintools.foundation.worm_features) configure_optimizers() (towbintools.deep_learning.architectures.models.ClassificationModel method) (towbintools.deep_learning.architectures.models.KeypointDetection1DModel method) (towbintools.deep_learning.architectures.models.SegmentationModel method) connect_endpoints() (in module towbintools.foundation.binary_image) convert_classification_to_dataframe() (in module towbintools.classification.classification_tools) convert_classification_to_mask() (in module towbintools.classification.classification_tools) correct_series_with_classification() (in module towbintools.data_analysis.time_series) create_classification_dataloaders() (in module towbintools.deep_learning.utils.dataset) create_classification_model() (in module towbintools.deep_learning.deep_learning_tools) create_classification_training_dataframes() (in module towbintools.deep_learning.utils.dataset) create_keypoint_detection_model() (in module towbintools.deep_learning.deep_learning_tools) create_lightweight_checkpoint() (in module towbintools.deep_learning.utils.util) create_segmentation_dataloaders() (in module towbintools.deep_learning.utils.dataset) create_segmentation_dataloaders_from_filemap() (in module towbintools.deep_learning.utils.dataset) create_segmentation_model() (in module towbintools.deep_learning.deep_learning_tools) create_segmentation_training_dataframes() (in module towbintools.deep_learning.utils.dataset) create_segmentation_training_dataframes_and_dataloaders() (in module towbintools.deep_learning.utils.dataset) crop_images_to_same_dim() (in module towbintools.foundation.image_handling) crop_series_to_length() (in module towbintools.data_analysis.time_series) crop_to_dim() (in module towbintools.foundation.image_handling) crop_to_dim_equally() (in module towbintools.foundation.image_handling) CustomFlip (class in towbintools.deep_learning.utils.augmentation) CustomRotate90 (class in towbintools.deep_learning.utils.augmentation)

D

detrend_rescaled_series_population_mean() (in module towbintools.plotting.utils_data_processing)

divide_batch() (in module towbintools.deep_learning.utils.util) double_threshold_segmentation() (in module towbintools.segmentation.segmentation_tools)

E

edge_based_segmentation() (in module towbintools.segmentation.segmentation_tools) EnforceNChannels (class in towbintools.deep_learning.utils.augmentation)

exclude_arrests_from_series_at_ecdysis() (in module towbintools.plotting.utils_data_processing) extract_midline() (in module towbintools.straightening.straightening_tools) extract_time_point() (in module towbintools.foundation.file_handling)

F

feltz_miller_asymptotic_cv_test() (in module towbintools.plotting.boxplots) fill_bright_holes() (in module towbintools.foundation.binary_image) fill_empty_timepoints() (in module towbintools.foundation.file_handling) filter_non_worm_data() (in module towbintools.plotting.images) filter_series_with_classification() (in module towbintools.data_analysis.time_series) find_best_plane() (in module towbintools.foundation.zstack) find_best_string_match() (in module towbintools.foundation.utils) find_end_molts() (in module towbintools.foundation.detect_molts) find_endpoints() (in module towbintools.foundation.binary_image) find_hatch_time() (in module towbintools.foundation.detect_molts) find_mid_molts() (in module towbintools.foundation.detect_molts) find_molts() (in module towbintools.foundation.detect_molts) FocalTverskyLoss (class in towbintools.deep_learning.utils.loss)

forward() (towbintools.deep_learning.architectures.archs.AttentionBlock1D method) (towbintools.deep_learning.architectures.archs.AttentionUnet1D method) (towbintools.deep_learning.architectures.archs.Unet1D method) (towbintools.deep_learning.architectures.archs.UnetPlusPlus1D method) (towbintools.deep_learning.architectures.archs.VGGBlock1D method) (towbintools.deep_learning.architectures.models.ClassificationModel method) (towbintools.deep_learning.architectures.models.KeypointDetection1DModel method) (towbintools.deep_learning.architectures.models.SegmentationModel method) (towbintools.deep_learning.utils.loss.BCELossWithIgnore method) (towbintools.deep_learning.utils.loss.FocalTverskyLoss method) (towbintools.deep_learning.utils.loss.MultiClassFocalLoss method) (towbintools.deep_learning.utils.loss.PeakWeightedMSELoss method) from_img() (towbintools.straightening.straightening_tools.Warper class method) from_pickle() (towbintools.straightening.straightening_tools.Warper class method)

G

get_acquisition_date() (in module towbintools.foundation.image_handling) get_all_skimage_regionprops() (in module towbintools.classification.qc_tools) get_all_timepoints_from_dir() (in module towbintools.foundation.file_handling) get_available_mask_features() (in module towbintools.foundation.worm_features) get_available_regionprops() (in module towbintools.foundation.worm_features) get_biggest_object() (in module towbintools.foundation.binary_image) get_closest_lower_multiple() (in module towbintools.deep_learning.utils.util) get_closest_upper_multiple() (in module towbintools.deep_learning.utils.util) get_colors() (in module towbintools.plotting.utils_plotting) get_condition_filemaps_images() (in module towbintools.plotting.images) get_context() (in module towbintools.foundation.worm_features) get_context_features() (in module towbintools.foundation.worm_features) get_deviation_from_model() (in module towbintools.plotting.proportions) get_dir_filemap() (in module towbintools.foundation.file_handling)

get_experiment_dir_filemap() (in module towbintools.foundation.file_handling) get_features_to_compute_at_molt() (in module towbintools.foundation.worm_features) get_image_paths_of_time_point() (in module towbintools.plotting.images) get_image_size_metadata() (in module towbintools.foundation.image_handling) get_images_ecdysis() (in module towbintools.plotting.images) get_indices_from_percentages() (in module towbintools.plotting.images) get_input_channels_from_checkpoint() (in module towbintools.deep_learning.utils.util) get_mean_and_std() (in module towbintools.deep_learning.utils.augmentation) get_prediction_augmentation() (in module towbintools.deep_learning.utils.augmentation) get_prediction_augmentation_from_model() (in module towbintools.deep_learning.utils.augmentation) get_qc_training_augmentation() (in module towbintools.deep_learning.utils.augmentation) get_segmentation_function() (in module towbintools.segmentation.segmentation_tools) get_shape_from_tiff() (in module towbintools.foundation.image_handling) get_training_augmentation() (in module towbintools.deep_learning.utils.augmentation) get_unique_shapes_from_tiffs() (in module towbintools.deep_learning.utils.dataset)

I

inf_helper() (in module towbintools.foundation.utils) intensity_kurtosis() (in module towbintools.foundation.worm_features) intensity_skew() (in module towbintools.foundation.worm_features) intensity_std() (in module towbintools.foundation.worm_features) interpolate_entire_development() (in module towbintools.data_analysis.time_series)

interpolate_infs() (in module towbintools.foundation.utils) interpolate_larval_stage() (in module towbintools.data_analysis.time_series) interpolate_nans() (in module towbintools.foundation.utils) interpolate_nans_infs() (in module towbintools.foundation.utils) interpolate_peaks() (in module towbintools.foundation.detect_molts)

K

KeypointDetection1DModel (class in towbintools.deep_learning.architectures.models)

KeypointDetection1DPredictionDataset (class in towbintools.deep_learning.utils.dataset) KeypointDetection1DTrainingDataset (class in towbintools.deep_learning.utils.dataset)

L

LAPM() (in module towbintools.foundation.image_quality) LAPV() (in module towbintools.foundation.image_quality)

load_keypoint_detection_model_from_checkpoint() (in module towbintools.deep_learning.deep_learning_tools) load_segmentation_model_from_checkpoint() (in module towbintools.deep_learning.deep_learning_tools) log_tb_images() (towbintools.deep_learning.architectures.models.ClassificationModel method)

M

MLOG() (in module towbintools.foundation.image_quality) module towbintools.classification.classification_tools towbintools.classification.qc_tools towbintools.data_analysis.growth_rate towbintools.data_analysis.time_series towbintools.deep_learning.architectures.archs towbintools.deep_learning.architectures.models towbintools.deep_learning.deep_learning_tools towbintools.deep_learning.utils.augmentation towbintools.deep_learning.utils.dataset towbintools.deep_learning.utils.loss towbintools.deep_learning.utils.util towbintools.foundation.binary_image towbintools.foundation.detect_molts towbintools.foundation.file_handling towbintools.foundation.image_handling towbintools.foundation.image_quality towbintools.foundation.utils towbintools.foundation.worm_features towbintools.foundation.zstack towbintools.plotting.boxplots towbintools.plotting.curves towbintools.plotting.heterogeneity towbintools.plotting.images towbintools.plotting.plotting_structure towbintools.plotting.proportions towbintools.plotting.utils_data_processing towbintools.plotting.utils_plotting towbintools.quantification.quantification_tools towbintools.segmentation.segmentation_tools towbintools.straightening.straightening_tools

mslr_test() (in module towbintools.plotting.boxplots) MultiClassFocalLoss (class in towbintools.deep_learning.utils.loss)

N

nan_helper() (in module towbintools.foundation.utils) normalize_image() (in module towbintools.foundation.image_handling) normalize_zstack() (in module towbintools.foundation.zstack) normalized_variance_measure() (in module towbintools.foundation.image_quality)

NormalizeDataRange (class in towbintools.deep_learning.utils.augmentation) NormalizeMeanStd (class in towbintools.deep_learning.utils.augmentation) NormalizePercentile (class in towbintools.deep_learning.utils.augmentation) NotImplementedError

P

pad_images_to_same_dim() (in module towbintools.foundation.image_handling) pad_series_to_length() (in module towbintools.data_analysis.time_series) pad_to_dim() (in module towbintools.foundation.image_handling) pad_to_dim_equally() (in module towbintools.foundation.image_handling) PeakWeightedMSELoss (class in towbintools.deep_learning.utils.loss) plot_aggregated_series() (in module towbintools.plotting.curves) plot_continuous_deviation_from_model() (in module towbintools.plotting.proportions) plot_correlation() (in module towbintools.plotting.proportions) plot_correlation_at_ecdysis() (in module towbintools.plotting.proportions) plot_cv_at_ecdysis() (in module towbintools.plotting.heterogeneity)

plot_cv_development_percentage() (in module towbintools.plotting.heterogeneity) plot_cv_rescaled_data() (in module towbintools.plotting.heterogeneity) plot_deviation_from_model_at_ecdysis() (in module towbintools.plotting.proportions) plot_deviation_from_model_development_percentage() (in module towbintools.plotting.proportions) plot_growth_curves_individuals() (in module towbintools.plotting.curves) plot_model_comparison_at_ecdysis() (in module towbintools.plotting.proportions) plot_normalized_proportions_at_ecdysis() (in module towbintools.plotting.proportions) plot_std_at_ecdysis() (in module towbintools.plotting.heterogeneity) predict_step() (towbintools.deep_learning.architectures.models.KeypointDetection1DModel method) (towbintools.deep_learning.architectures.models.SegmentationModel method)

Q

QualityControlDataset (class in towbintools.deep_learning.utils.dataset)

QualityControlPredictionDataset (class in towbintools.deep_learning.utils.dataset)

R

random_crop_series_to_length() (in module towbintools.data_analysis.time_series) randomize() (towbintools.deep_learning.utils.augmentation.CustomFlip method) (towbintools.deep_learning.utils.augmentation.CustomRotate90 method) read_filemap() (in module towbintools.foundation.file_handling) read_tiff_file() (in module towbintools.foundation.image_handling) remove_ignored_molts() (in module towbintools.plotting.plotting_structure) remove_unwanted_info() (in module towbintools.plotting.plotting_structure)

rename_keys_and_adjust_dimensions() (in module towbintools.deep_learning.utils.util) rescale() (in module towbintools.plotting.utils_data_processing) rescale_and_aggregate() (in module towbintools.data_analysis.time_series) rescale_series() (in module towbintools.data_analysis.time_series) rescale_without_flattening() (in module towbintools.plotting.utils_data_processing) rescaled_3D_img() (towbintools.straightening.straightening_tools.Warper method) resize() (in module towbintools.deep_learning.utils.dataset) resize_series_to_length() (in module towbintools.data_analysis.time_series)

S

save_figure() (in module towbintools.plotting.utils_plotting) segment_image() (in module towbintools.segmentation.segmentation_tools) SegmentationDataset (class in towbintools.deep_learning.utils.dataset) SegmentationModel (class in towbintools.deep_learning.architectures.models) SegmentationPredictionDataset (class in towbintools.deep_learning.utils.dataset) separate_column_by_point() (in module towbintools.plotting.plotting_structure)

set_scale() (in module towbintools.plotting.utils_plotting) smooth_and_rescale_series() (in module towbintools.plotting.utils_data_processing) smooth_series() (in module towbintools.data_analysis.time_series) (in module towbintools.plotting.utils_data_processing) smooth_series_classified() (in module towbintools.data_analysis.time_series) split_dataset() (in module towbintools.deep_learning.utils.dataset) StackPredictionDataset (class in towbintools.deep_learning.utils.dataset)

T

TENG() (in module towbintools.foundation.image_quality) TENG_VARIANCE() (in module towbintools.foundation.image_quality) threshold_segmentation() (in module towbintools.segmentation.segmentation_tools) TiledSegmentationDataset (class in towbintools.deep_learning.utils.dataset) to_pickle() (towbintools.straightening.straightening_tools.Warper method) towbintools.classification.classification_tools module towbintools.classification.qc_tools module towbintools.data_analysis.growth_rate module towbintools.data_analysis.time_series module towbintools.deep_learning.architectures.archs module towbintools.deep_learning.architectures.models module towbintools.deep_learning.deep_learning_tools module towbintools.deep_learning.utils.augmentation module towbintools.deep_learning.utils.dataset module towbintools.deep_learning.utils.loss module towbintools.deep_learning.utils.util module towbintools.foundation.binary_image module towbintools.foundation.detect_molts module towbintools.foundation.file_handling module towbintools.foundation.image_handling module

towbintools.foundation.image_quality module towbintools.foundation.utils module towbintools.foundation.worm_features module towbintools.foundation.zstack module towbintools.plotting.boxplots module towbintools.plotting.curves module towbintools.plotting.heterogeneity module towbintools.plotting.images module towbintools.plotting.plotting_structure module towbintools.plotting.proportions module towbintools.plotting.utils_data_processing module towbintools.plotting.utils_plotting module towbintools.quantification.quantification_tools module towbintools.segmentation.segmentation_tools module towbintools.straightening.straightening_tools module training_step() (towbintools.deep_learning.architectures.models.ClassificationModel method) (towbintools.deep_learning.architectures.models.KeypointDetection1DModel method) (towbintools.deep_learning.architectures.models.SegmentationModel method) transform_series() (in module towbintools.plotting.utils_data_processing)

U

Unet1D (class in towbintools.deep_learning.architectures.archs)

UnetPlusPlus1D (class in towbintools.deep_learning.architectures.archs)

V

validate_mask() (in module towbintools.straightening.straightening_tools) validation_step() (towbintools.deep_learning.architectures.models.ClassificationModel method) (towbintools.deep_learning.architectures.models.KeypointDetection1DModel method) (towbintools.deep_learning.architectures.models.SegmentationModel method)

VGGBlock1D (class in towbintools.deep_learning.architectures.archs) violinplot() (in module towbintools.plotting.boxplots) violinplot_larval_stage() (in module towbintools.plotting.boxplots)

W

warp_2D_img() (towbintools.straightening.straightening_tools.Warper method) warp_3D_img() (towbintools.straightening.straightening_tools.Warper method)

Warper (class in towbintools.straightening.straightening_tools) write_filemap() (in module towbintools.foundation.file_handling)