Index

A

add_fits_spots_dataframe() (in module transcription_pipeline.spot_analysis.fitting) add_fits_spots_dataframe_parallel() (in module transcription_pipeline.spot_analysis.fitting) add_neighborhood_intensity_spot_dataframe() (in module transcription_pipeline.spot_analysis.fitting)

add_neighborhood_intensity_spot_dataframe_parallel() (in module transcription_pipeline.spot_analysis.fitting) add_velocity() (in module transcription_pipeline.tracking.track_features) all_equal() (in module transcription_pipeline.preprocessing.import_data) assign_nuclear_cycle() (in module transcription_pipeline.tracking.track_features)

B

binarize_frame() (in module transcription_pipeline.nuclear_analysis.segmentation) binarize_movie() (in module transcription_pipeline.nuclear_analysis.segmentation)

binarize_movie_parallel() (in module transcription_pipeline.nuclear_analysis.segmentation) bootstrap_intensity() (in module transcription_pipeline.spot_analysis.fitting)

C

check_metadata() (in module transcription_pipeline.preprocessing.import_data) choose_nuclear_analysis_parameters() (in module transcription_pipeline.nuclear_pipeline) choose_spot_analysis_parameters() (in module transcription_pipeline.spot_pipeline) collate_frame_metadata() (in module transcription_pipeline.preprocessing.import_data) collate_global_metadata() (in module transcription_pipeline.preprocessing.import_data) collate_metadata() (in module transcription_pipeline.preprocessing.import_data)

compile_successive_differences() (in module transcription_pipeline.spot_analysis.track_filtering) compile_traces() (in module transcription_pipeline.spot_analysis.compile_data) consolidate_traces() (in module transcription_pipeline.spot_analysis.compile_data) construct_lineage() (in module transcription_pipeline.tracking.detect_mitosis) construct_stitch_dataframe() (in module transcription_pipeline.tracking.stitch_tracks) corr_traces() (in module transcription_pipeline.spot_analysis.fluctuation_correlation) create_blocks() (in module transcription_pipeline.spot_analysis.fitting)

D

DataImport (class in transcription_pipeline.preprocessing_pipeline) denoise_frame() (in module transcription_pipeline.nuclear_analysis.segmentation) denoise_movie() (in module transcription_pipeline.nuclear_analysis.segmentation)

denoise_movie_parallel() (in module transcription_pipeline.nuclear_analysis.segmentation) detect_and_gather_spots() (in module transcription_pipeline.spot_analysis.detection) detect_spots() (in module transcription_pipeline.spot_analysis.detection) determine_nuclear_cycle_frames() (in module transcription_pipeline.tracking.track_features)

E

ellipsoid() (in module transcription_pipeline.utils.neighborhood_manipulation) expand_labels_movie() (in module transcription_pipeline.utils.label_manipulation) expand_labels_movie_parallel() (in module transcription_pipeline.utils.label_manipulation) extract_global_metadata() (in module transcription_pipeline.preprocessing.import_data) extract_neighborhood() (in module transcription_pipeline.utils.neighborhood_manipulation)

extract_renormalized_frame() (in module transcription_pipeline.preprocessing.process_metadata) extract_spot_mask() (in module transcription_pipeline.spot_analysis.fitting) extract_spot_shell() (in module transcription_pipeline.spot_analysis.fitting) extract_spot_traces() (transcription_pipeline.spot_pipeline.Spot method) extract_time() (in module transcription_pipeline.preprocessing.process_metadata)

F

filter_multiple_spots() (in module transcription_pipeline.spot_analysis.track_filtering) filter_spots_by_sigma() (in module transcription_pipeline.spot_analysis.track_filtering) filter_spots_by_tracks() (in module transcription_pipeline.spot_analysis.track_filtering)

fit_gaussian_3d_sym_xy() (in module transcription_pipeline.spot_analysis.fitting) FullEmbryoImport (class in transcription_pipeline.preprocessing_pipeline) futures_to_zarr() (in module transcription_pipeline.utils.parallel_computing)

G

gaussian3d_sym_xy() (in module transcription_pipeline.spot_analysis.fitting)

generate_gaussian_3d_sym_xy() (in module transcription_pipeline.spot_analysis.fitting) generate_trace_plot_list() (in module transcription_pipeline.utils.plottable)

H

histogram() (in module transcription_pipeline.utils.image_histogram)

I

import_dataset() (in module transcription_pipeline.preprocessing.import_data) import_full_embryo() (in module transcription_pipeline.preprocessing.import_data) import_save_dataset() (in module transcription_pipeline.preprocessing.import_data) inject_neighborhood() (in module transcription_pipeline.utils.neighborhood_manipulation)

intensity_error_from_fit_row() (in module transcription_pipeline.spot_analysis.fitting) intensity_from_fit_row() (in module transcription_pipeline.spot_analysis.fitting) intensity_stdev() (in module transcription_pipeline.nuclear_pipeline) iterative_peak_local_max() (in module transcription_pipeline.nuclear_analysis.segmentation)

L

link_df() (in module transcription_pipeline.tracking.track_features)

log_likelihood_step() (in module transcription_pipeline.spot_analysis.smMS2_calibration)

M

make_spot_mask() (in module transcription_pipeline.spot_analysis.detection) mark_frame() (in module transcription_pipeline.nuclear_analysis.segmentation) mark_movie() (in module transcription_pipeline.nuclear_analysis.segmentation) mark_movie_parallel() (in module transcription_pipeline.nuclear_analysis.segmentation) mean_corr_traces() (in module transcription_pipeline.spot_analysis.fluctuation_correlation) module transcription_pipeline transcription_pipeline.nuclear_analysis transcription_pipeline.nuclear_analysis.segmentation transcription_pipeline.nuclear_pipeline transcription_pipeline.preprocessing transcription_pipeline.preprocessing.import_data transcription_pipeline.preprocessing.process_metadata transcription_pipeline.preprocessing_pipeline transcription_pipeline.spot_analysis transcription_pipeline.spot_analysis.compile_data transcription_pipeline.spot_analysis.detection transcription_pipeline.spot_analysis.fitting transcription_pipeline.spot_analysis.fluctuation_correlation transcription_pipeline.spot_analysis.refine_traces transcription_pipeline.spot_analysis.smMS2_calibration transcription_pipeline.spot_analysis.track_filtering transcription_pipeline.spot_pipeline transcription_pipeline.tracking transcription_pipeline.tracking.detect_mitosis transcription_pipeline.tracking.stitch_tracks transcription_pipeline.tracking.track_features transcription_pipeline.utils transcription_pipeline.utils.image_histogram transcription_pipeline.utils.label_manipulation transcription_pipeline.utils.neighborhood_manipulation transcription_pipeline.utils.parallel_computing transcription_pipeline.utils.plottable

N

normalized_variation_intensity() (in module transcription_pipeline.spot_analysis.track_filtering)

Nuclear (class in transcription_pipeline.nuclear_pipeline) number_of_frames() (in module transcription_pipeline.utils.parallel_computing)

P

parallelize() (in module transcription_pipeline.utils.parallel_computing)

parse_parallelize_kwargs() (in module transcription_pipeline.utils.parallel_computing)

R

read() (transcription_pipeline.preprocessing_pipeline.DataImport method) (transcription_pipeline.preprocessing_pipeline.FullEmbryoImport method) read_results() (transcription_pipeline.nuclear_pipeline.Nuclear method) (transcription_pipeline.spot_pipeline.Spot method) read_trackpy_status() (in module transcription_pipeline.tracking.track_features)

refine_compile_traces() (in module transcription_pipeline.spot_analysis.refine_traces) refine_trace() (in module transcription_pipeline.spot_analysis.refine_traces) remove_duplicates() (in module transcription_pipeline.tracking.stitch_tracks) reorder_labels() (in module transcription_pipeline.tracking.track_features) reorder_labels_parallel() (in module transcription_pipeline.tracking.track_features)

S

save() (transcription_pipeline.preprocessing_pipeline.DataImport method) (transcription_pipeline.preprocessing_pipeline.FullEmbryoImport method) save_results() (transcription_pipeline.nuclear_pipeline.Nuclear method) (transcription_pipeline.spot_pipeline.Spot method) segment_frame() (in module transcription_pipeline.nuclear_analysis.segmentation) segment_movie() (in module transcription_pipeline.nuclear_analysis.segmentation)

segment_movie_parallel() (in module transcription_pipeline.nuclear_analysis.segmentation) segmentation_df() (in module transcription_pipeline.tracking.track_features) simple_bootstrap_intensity() (in module transcription_pipeline.spot_analysis.fitting) Spot (class in transcription_pipeline.spot_pipeline) stitch_tracks() (in module transcription_pipeline.tracking.stitch_tracks) successive_differences_quartile() (in module transcription_pipeline.spot_analysis.track_filtering)

T

tqdm_trackpy() (in module transcription_pipeline.tracking.track_features) track_and_filter_spots() (in module transcription_pipeline.spot_analysis.track_filtering) track_nuclei() (transcription_pipeline.nuclear_pipeline.Nuclear method) track_spots() (in module transcription_pipeline.spot_analysis.track_filtering) tracks_start() (in module transcription_pipeline.tracking.detect_mitosis) tracks_to_napari() (in module transcription_pipeline.tracking.detect_mitosis) transcription_pipeline module transcription_pipeline.nuclear_analysis module transcription_pipeline.nuclear_analysis.segmentation module transcription_pipeline.nuclear_pipeline module transcription_pipeline.preprocessing module transcription_pipeline.preprocessing.import_data module transcription_pipeline.preprocessing.process_metadata module transcription_pipeline.preprocessing_pipeline module transcription_pipeline.spot_analysis module transcription_pipeline.spot_analysis.compile_data module transcription_pipeline.spot_analysis.detection module transcription_pipeline.spot_analysis.fitting module

transcription_pipeline.spot_analysis.fluctuation_correlation module transcription_pipeline.spot_analysis.refine_traces module transcription_pipeline.spot_analysis.smMS2_calibration module transcription_pipeline.spot_analysis.track_filtering module transcription_pipeline.spot_pipeline module transcription_pipeline.tracking module transcription_pipeline.tracking.detect_mitosis module transcription_pipeline.tracking.stitch_tracks module transcription_pipeline.tracking.track_features module transcription_pipeline.utils module transcription_pipeline.utils.image_histogram module transcription_pipeline.utils.label_manipulation module transcription_pipeline.utils.neighborhood_manipulation module transcription_pipeline.utils.parallel_computing module transcription_pipeline.utils.plottable module transfer_nuclear_labels() (in module transcription_pipeline.spot_analysis.track_filtering)

V

vectorized_log_likelihood_step() (in module transcription_pipeline.spot_analysis.smMS2_calibration)

Z

z_cross_correlation_shift() (in module transcription_pipeline.preprocessing.import_data)

zarr_to_futures() (in module transcription_pipeline.utils.parallel_computing)