v0.13.0
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Force Calibration
F,d Fitting
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Diffusion constant estimation
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lumicks.pylake
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Index
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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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K
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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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__call__() (ActiveCalibrationModel method)
(DistanceCalibration method)
(Model method)
(PassiveCalibrationModel method)
__getitem__() (CorrelatedStack method)
(File method)
(Kymo method)
(Scan method)
(Slice method)
_samples (DwelltimeBootstrap attribute)
A
ActiveCalibrationModel (class in lumicks.pylake)
add_data() (FdFit method)
aic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
aicc (FdFit property)
amplitude_distributions (DwelltimeBootstrap property)
amplitudes (DwelltimeModel property)
axial (PassiveCalibrationModel attribute)
B
bead_diameter (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
bic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
blue_image (Kymo property)
(Scan property)
bluelake_version (File property)
C
calculate_power_spectrum() (in module lumicks.pylake)
calculate_stats() (DwelltimeBootstrap method)
calibrate_force() (in module lumicks.pylake)
calibrate_to_kbp() (Kymo method)
calibration (Slice property)
calibration_results() (ActiveCalibrationModel method)
(PassiveCalibrationModel method)
CalibrationResults() (in module lumicks.pylake.force_calibration.power_spectrum_calibration)
center_point_um (Kymo property)
(PointScan property)
(Scan property)
ColorAdjustment (class in lumicks.pylake)
coordinate_idx (KymoTrack property)
correct_data() (ForceBaseLine method)
CorrelatedStack (class in lumicks.pylake.correlated_stack)
cov (FdFit property)
crop_and_calibrate() (Kymo method)
crop_and_rotate() (CorrelatedStack method)
crop_by_distance() (Kymo method)
crop_by_pixels() (CorrelatedStack method)
(Scan method)
D
d (FdCurve property)
data (Slice property)
define_tether() (CorrelatedStack method)
derivative() (Model method)
description (File property)
dirty (FdFit property)
distance_offset() (in module lumicks.pylake)
distance_to_surface (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
DistanceCalibration (class in lumicks.pylake)
downsampled_by() (Kymo method)
(Slice method)
downsampled_like() (Slice method)
downsampled_over() (Slice method)
downsampled_to() (Slice method)
driving_amplitude (ActiveCalibrationModel attribute)
driving_frequency (ActiveCalibrationModel attribute)
DwelltimeBootstrap (class in lumicks.pylake.population.dwelltime)
DwelltimeModel (class in lumicks.pylake)
E
estimate_diffusion() (KymoTrack method)
estimate_diffusion_ols() (KymoTrack method)
exit_flag (GaussianMixtureModel property)
experiment (File property)
export_tiff() (CorrelatedStack method)
(Kymo method)
(Scan method)
export_time (File property)
export_video() (CorrelatedStack method)
(Scan method)
export_video_blue() (Scan method)
export_video_green() (Scan method)
export_video_red() (Scan method)
export_video_rgb() (Scan method)
extrapolate() (KymoTrack method)
F
f (FdCurve property)
fast_sensor (PassiveCalibrationModel attribute)
FdCurve (class in lumicks.pylake.fdcurve)
fdcurves (FdDistanceRangeSelector property)
(FdRangeSelector property)
FdDistanceRangeSelector (class in lumicks.pylake)
FdFit (class in lumicks.pylake)
FdRangeSelector (class in lumicks.pylake)
File (class in lumicks.pylake)
file (FdCurve attribute)
filter_tracks() (in module lumicks.pylake)
fit() (FdFit method)
fit_power_spectrum() (in module lumicks.pylake)
force_distance() (PiezoForceDistance method)
force_offset() (in module lumicks.pylake)
ForceBaseLine (class in lumicks.pylake)
format_version (File property)
frame_timestamp_ranges() (CorrelatedStack method)
(Scan method)
freely_jointed_chain() (in module lumicks.pylake)
frequency (in module lumicks.pylake.force_calibration.power_spectrum)
from_channel() (GaussianMixtureModel class method)
from_data() (CorrelatedStack class method)
from_dataset() (CorrelatedStack class method)
(Kymo class method)
(PointScan class method)
(Scan class method)
from_file() (DistanceCalibration class method)
from_h5py() (File class method)
G
GaussianMixtureModel (class in lumicks.pylake)
get_image() (CorrelatedStack method)
(Kymo method)
(Scan method)
green_image (Kymo property)
(Scan property)
guid (File property)
H
has_derivative (Model property)
has_jacobian (FdFit property)
(Model property)
hist() (DwelltimeModel method)
(GaussianMixtureModel method)
hydrodynamically_correct (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
I
in_rect() (KymoTrack method)
interpolate() (KymoTrack 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)
K
Kymo (class in lumicks.pylake.kymo)
KymoTrack (class in lumicks.pylake.kymotracker.kymotrack)
L
label() (GaussianMixtureModel method)
lifetime_distributions (DwelltimeBootstrap property)
lifetimes (DwelltimeModel property)
line_time_seconds (Kymo property)
line_timestamp_ranges() (Kymo method)
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 property)
Model (class in lumicks.pylake.fitting.model)
model (in module lumicks.pylake.force_calibration.power_spectrum_calibration)
msd() (KymoTrack method)
N
n_components (DwelltimeBootstrap property)
n_params (FdFit property)
n_residuals (FdFit property)
n_samples (DwelltimeBootstrap property)
name (FdCurve attribute)
num_frames (CorrelatedStack property)
num_windows (ActiveCalibrationModel attribute)
O
odijk() (in module lumicks.pylake)
P
parameter_trace() (in module lumicks.pylake)
params (FdFit property)
(in module lumicks.pylake.force_calibration.power_spectrum_calibration)
PassiveCalibrationModel (class in lumicks.pylake)
pdf() (DwelltimeModel method)
(GaussianMixtureModel method)
piezo_track() (PiezoTrackingCalibration method)
PiezoForceDistance (class in lumicks.pylake)
PiezoTrackingCalibration (class in lumicks.pylake)
pixel_time_seconds (Kymo property)
(PointScan property)
(Scan property)
pixelsize (Kymo property)
pixelsize_um (Kymo property)
(Scan property)
plot() (CorrelatedStack method)
(DistanceCalibration method)
(DwelltimeBootstrap method)
(DwelltimeModel method)
(FdFit method)
(ForceBaseLine method)
(GaussianMixtureModel method)
(Kymo method)
(Model method)
(PointScan method)
(Scan method)
(Slice method)
plot_blue() (Kymo method)
(PointScan method)
(Scan method)
plot_correlated() (CorrelatedStack method)
(Scan method)
plot_green() (Kymo method)
(PointScan method)
(Scan method)
plot_msd() (KymoTrack method)
plot_red() (Kymo method)
(PointScan method)
(Scan method)
plot_residual() (DistanceCalibration method)
(ForceBaseLine method)
plot_rgb() (Kymo method)
(PointScan method)
(Scan method)
plot_scatter() (FdCurve method)
plot_tether() (CorrelatedStack 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)
polynomial_baseline() (ForceBaseLine class method)
power (in module lumicks.pylake.force_calibration.power_spectrum)
PowerSpectrum() (in module lumicks.pylake.force_calibration.power_spectrum)
profile_likelihood() (FdFit method)
ps_data (in module lumicks.pylake.force_calibration.power_spectrum_calibration)
ps_model (in module lumicks.pylake.force_calibration.power_spectrum_calibration)
R
ranges (FdDistanceRangeSelector property)
(FdRangeSelector property)
raw (CorrelatedStack property)
red_image (Kymo property)
(Scan property)
refine_tracks_centroid() (in module lumicks.pylake)
refine_tracks_gaussian() (in module lumicks.pylake)
results (in module lumicks.pylake.force_calibration.power_spectrum_calibration)
rgb_image (Kymo property)
(Scan property)
rho_bead (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
rho_sample (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
S
sample_from_image() (KymoTrack method)
sample_rate (ActiveCalibrationModel attribute)
(in module lumicks.pylake.force_calibration.power_spectrum)
(Slice property)
save_as() (File method)
save_tiff() (Kymo method)
(Scan method)
Scan (class in lumicks.pylake.scan)
seconds (Slice property)
shape (Kymo property)
(Scan property)
sigma (FdFit property)
size_um (Kymo property)
(Scan property)
Slice (class in lumicks.pylake.channel)
start (CorrelatedStack property)
(Slice property)
std (GaussianMixtureModel property)
stop (CorrelatedStack property)
(Slice property)
subtract_independent_offset() (Model method)
T
temperature (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
timestamps (CorrelatedStack property)
(Kymo property)
(Scan property)
(Slice property)
total_duration (in module lumicks.pylake.force_calibration.power_spectrum)
track_greedy() (in module lumicks.pylake)
track_lines() (in module lumicks.pylake)
twistable_wlc() (in module lumicks.pylake)
U
update_params() (FdFit method)
V
valid_range() (ForceBaseLine method)
(PiezoForceDistance method)
variances (GaussianMixtureModel property)
verify_derivative() (Model method)
verify_jacobian() (Model method)
viscosity (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
viscosity_of_water() (in module lumicks.pylake)
W
weights (GaussianMixtureModel property)
with_baseline_corrected_x() (FdCurve method)
with_channels() (FdCurve method)
with_offset() (FdCurve method)
(KymoTrack method)
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