Index

A

apply_offset_mask() (ctrappy.image.Image method)

B

BeadDetector (class in ctrappy.tracking)

C

colocalize() (ctrappy.tracking.Colocalizer method) Colocalizer (class in ctrappy.tracking) convert_to_kbp() (ctrappy.scan.Experiment method) convert_to_kbp_autocorrelation() (ctrappy.scan.Experiment method) count_steps() (ctrappy.scan.Track method) count_traces() (ctrappy.scan.Experiment method) ctrappy.diffusion module ctrappy.file module ctrappy.gui_cpa_figs module

ctrappy.gui_figures module ctrappy.image module ctrappy.scan module ctrappy.stepfinder module ctrappy.tracking module

D

detect() (ctrappy.tracking.BeadDetector method) (ctrappy.tracking.Detector method)

Detector (class in ctrappy.tracking) double_step_func() (in module ctrappy.tracking) download_link() (in module ctrappy.file)

E

Experiment (class in ctrappy.scan)

export() (ctrappy.image.Image method) export_video() (ctrappy.image.Image method)

F

fermi_dirac() (in module ctrappy.tracking) filter_by_color() (ctrappy.scan.Experiment method) filter_by_loc_interval_kbp() (ctrappy.scan.Experiment method) filter_by_loc_kbp() (ctrappy.scan.Experiment method) filter_by_starting_frame() (ctrappy.scan.Experiment method) filter_by_stoichiometry() (ctrappy.scan.Experiment method)

filter_by_total_count() (ctrappy.scan.Experiment method) filter_experiment() (in module ctrappy.scan) find_steps() (in module ctrappy.stepfinder) fit_diffusion() (in module ctrappy.diffusion) fit_func() (in module ctrappy.diffusion) fit_gauss2d() (in module ctrappy.tracking) frame() (ctrappy.image.Image method)

G

gaussian() (in module ctrappy.tracking) gaussian2d() (in module ctrappy.tracking) get_anom_diff_fit_log() (in module ctrappy.gui_cpa_figs) get_avg_quantity_from_h5file() (in module ctrappy.file) get_bleaching_traces() (in module ctrappy.gui_figures) get_diffusion() (in module ctrappy.gui_figures) get_diffusion_coefficient() (in module ctrappy.diffusion) get_diffusion_hist() (in module ctrappy.gui_figures) get_diffusion_hist_bootstrap() (in module ctrappy.gui_figures) get_full_quantity_from_h5file() (in module ctrappy.file) get_lifetime() (in module ctrappy.gui_figures) get_loc_interval() (ctrappy.scan.Trace method) get_location_histogram() (in module ctrappy.gui_figures) get_location_traces() (in module ctrappy.gui_figures)

get_msd() (in module ctrappy.diffusion) get_p_min() (in module ctrappy.diffusion) get_processivity() (in module ctrappy.gui_figures) get_scan_force_distance_data() (in module ctrappy.file) get_scan_metadata() (in module ctrappy.file) get_splits() (ctrappy.scan.Experiment method) get_spots() (in module ctrappy.image) get_spots_per_DNA() (in module ctrappy.gui_figures) get_starting_loc() (ctrappy.scan.Trace method) (ctrappy.scan.Track method) get_step_calibration() (in module ctrappy.scan) get_step_sizes() (in module ctrappy.gui_figures) get_stoichiometry() (in module ctrappy.gui_figures) get_summary_table() (ctrappy.scan.Experiment method) get_velocity() (in module ctrappy.gui_cpa_figs)

I

Image (class in ctrappy.image)

L

lap_matrix() (ctrappy.tracking.Tracker method)

lap_matrix_segments() (ctrappy.tracking.Tracker method)

M

module ctrappy.diffusion ctrappy.file ctrappy.gui_cpa_figs ctrappy.gui_figures ctrappy.image ctrappy.scan ctrappy.stepfinder ctrappy.tracking

P

plot() (ctrappy.image.Image method) plot_anom_diff_fit_log() (in module ctrappy.gui_cpa_figs) plot_bead_detection() (in module ctrappy.gui_figures) plot_bleaching_traces() (in module ctrappy.gui_figures) plot_diffusion_hist() (in module ctrappy.gui_figures) plot_diffusion_hist_bootstrap() (in module ctrappy.gui_figures) plot_fdcurves() (in module ctrappy.gui_figures) plot_force_over_time() (in module ctrappy.gui_figures)

plot_lifetime() (in module ctrappy.gui_figures) plot_location_histogram() (in module ctrappy.gui_figures) plot_location_traces() (in module ctrappy.gui_figures) plot_processivity() (in module ctrappy.gui_figures) plot_scan_spots() (in module ctrappy.gui_figures) plot_spots_per_DNA() (in module ctrappy.gui_figures) plot_step_sizes() (in module ctrappy.gui_figures) plot_stoichiometry() (in module ctrappy.gui_figures) plot_velocity() (in module ctrappy.gui_cpa_figs)

R

read_biotiff() (in module ctrappy.file) read_config() (in module ctrappy.file) read_h5file() (in module ctrappy.file)

read_yaml() (in module ctrappy.file) rerun_colocalization() (in module ctrappy.scan) run_calibration_step_count() (ctrappy.scan.Trace method)

S

Scan (class in ctrappy.scan)

set_laser_colors() (in module ctrappy.scan) set_t() (ctrappy.scan.Experiment method)

T

to_dataframe() (ctrappy.scan.Experiment method) to_tiff() (ctrappy.image.Image method) total_count() (ctrappy.scan.Trace method) total_spot_count() (ctrappy.scan.Scan method)

Trace (class in ctrappy.scan) Track (class in ctrappy.scan) track() (ctrappy.tracking.Tracker method) track_spots() (in module ctrappy.image) Tracker (class in ctrappy.tracking)