Index

_

__call__() (Model method) (PassiveCalibrationModel method) __getitem__() (CorrelatedStack method) (File method) (Kymo method) (Slice method) __init__() (CalibrationResults method) (CalibrationSettings method) (CorrelatedStack method) (FdCurve method) (FdFit method) (FdRangeSelector method) (File method) (GaussianMixtureModel method) (Kymo method) (KymoLine method) (Model method) (PassiveCalibrationModel method) (PointScan method) (PowerSpectrum method) (Scan method) (Slice method)

A

add_data() (FdFit method) aic (FdFit attribute) (GaussianMixtureModel attribute)

aicc (FdFit attribute) append() (KymoLine method)

B

bic (FdFit attribute) (GaussianMixtureModel attribute)

bluelake_version (File attribute)

C

calculate_power_spectrum() (in module lumicks.pylake) calibration (Slice attribute) calibration_parameters() (PassiveCalibrationModel method) CalibrationResults (class in lumicks.pylake.force_calibration.power_spectrum_calibration) CalibrationSettings (class in lumicks.pylake)

center_point_um (Kymo attribute) (PointScan attribute) (Scan attribute) CorrelatedStack (class in lumicks.pylake.correlated_stack) cov (FdFit attribute)

D

d (FdCurve attribute) data (Slice attribute) derivative() (Model method) description (File attribute) dirty (FdFit attribute)

distance_offset() (in module lumicks.pylake) downsampled_by() (PowerSpectrum method) (Slice method) downsampled_like() (Slice method) downsampled_over() (Slice method) downsampled_to() (Slice method)

E

exit_flag (GaussianMixtureModel attribute) experiment (File attribute) export_tiff() (CorrelatedStack method) export_time (File attribute)

export_video_blue() (Scan method) export_video_green() (Scan method) export_video_red() (Scan method) export_video_rgb() (Scan method) extrapolate() (KymoLine method)

F

f (FdCurve attribute) FdCurve (class in lumicks.pylake.fdcurve) fdcurves (FdRangeSelector attribute) FdFit (class in lumicks.pylake) FdRangeSelector (class in lumicks.pylake) File (class in lumicks.pylake) filter_lines() (in module lumicks.pylake) fit() (FdFit method) fit_power_spectrum() (in module lumicks.pylake)

force_offset() (in module lumicks.pylake) format_version (File attribute) freely_jointed_chain() (in module lumicks.pylake) from_channel() (lumicks.pylake.GaussianMixtureModel class method) from_data() (lumicks.pylake.correlated_stack.CorrelatedStack class method) from_dataset() (lumicks.pylake.kymo.Kymo class method) (lumicks.pylake.point_scan.PointScan class method) (lumicks.pylake.scan.Scan class method) from_h5py() (lumicks.pylake.File class method)

G

GaussianMixtureModel (class in lumicks.pylake)

guid (File attribute)

H

has_derivative (Model attribute) has_fluorescence (Kymo attribute) (PointScan attribute) (Scan attribute) has_force (Kymo attribute) (PointScan attribute) (Scan attribute)

has_jacobian (FdFit attribute) (Model attribute) hist() (GaussianMixtureModel method)

I

in_range() (PowerSpectrum method) in_rect() (KymoLine method) interpolate() (KymoLine method) invert() (Model method)

inverted_freely_jointed_chain() (in module lumicks.pylake) inverted_marko_siggia_simplified() (in module lumicks.pylake) inverted_odijk() (in module lumicks.pylake) inverted_twistable_wlc() (in module lumicks.pylake)

J

jacobian() (Model method) json (Kymo attribute) (PointScan attribute) (Scan attribute)

K

Kymo (class in lumicks.pylake.kymo)

KymoLine (class in lumicks.pylake.kymotracker.kymoline)

L

label() (GaussianMixtureModel method)

line_time_seconds (Kymo attribute) log_likelihood() (FdFit method)

M

marko_siggia_ewlc_distance() (in module lumicks.pylake) marko_siggia_ewlc_force() (in module lumicks.pylake)

marko_siggia_simplified() (in module lumicks.pylake) means (GaussianMixtureModel attribute) Model (class in lumicks.pylake.fitting.model)

N

n_params (FdFit attribute)

n_residuals (FdFit attribute) num_frames (CorrelatedStack attribute)

O

odijk() (in module lumicks.pylake)

P

parameter_trace() (in module lumicks.pylake) params (FdFit attribute) PassiveCalibrationModel (class in lumicks.pylake) pdf() (GaussianMixtureModel method) pixelsize_um (Kymo attribute) (Scan attribute) plot() (CalibrationResults method) (CorrelatedStack method) (FdFit method) (GaussianMixtureModel method) (Model method) (PowerSpectrum method) (Slice method) plot_blue() (Kymo method) (PointScan method) (Scan method)

plot_correlated() (CorrelatedStack method) plot_green() (Kymo method) (PointScan method) (Scan method) plot_red() (Kymo method) (PointScan method) (Scan method) plot_rgb() (Kymo method) (PointScan method) (Scan method) plot_scatter() (FdCurve method) plot_with_force() (Kymo method) plot_with_position_histogram() (Kymo method) plot_with_time_histogram() (Kymo method) PointScan (class in lumicks.pylake.point_scan) PowerSpectrum (class in lumicks.pylake.force_calibration.power_spectrum) profile_likelihood() (FdFit method)

R

ranges (FdRangeSelector attribute)

raw (CorrelatedStack attribute) refine_lines_centroid() (in module lumicks.pylake)

S

sample_from_image() (KymoLine method) sample_rate (Slice attribute) save_as() (File method) save_tiff() (Kymo method) (Scan method) Scan (class in lumicks.pylake.scan) scan_width_um (Kymo attribute) (Scan attribute) seconds (Slice attribute)

sigma (FdFit attribute) size_um (Kymo attribute) (Scan attribute) Slice (class in lumicks.pylake.channel) start (CorrelatedStack attribute) (Slice attribute) std (GaussianMixtureModel attribute) stop (CorrelatedStack attribute) (Slice attribute) subtract_independent_offset() (Model method)

T

timestamps (CorrelatedStack attribute) (Kymo attribute) (Scan attribute) (Slice attribute)

track_greedy() (in module lumicks.pylake) track_lines() (in module lumicks.pylake) twistable_wlc() (in module lumicks.pylake)

U

update_params() (FdFit method)

V

variances (GaussianMixtureModel attribute)

verify_derivative() (Model method) verify_jacobian() (Model method)

W

weights (GaussianMixtureModel attribute) with_channels() (FdCurve method)

with_offset() (FdCurve method) (KymoLine method) with_spectrum() (PowerSpectrum method)