v0.13.2
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Literature
Force Calibration
F,d Fitting
Kymotracker
Diffusion constant estimation
References
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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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 (class in lumicks.pylake.force_calibration.power_spectrum_calibration)
center_point_um (Kymo property)
(PointScan property)
(Scan property)
ColorAdjustment (class in lumicks.pylake)
contiguous (Kymo property)
coordinate_idx (KymoTrack property)
correct_data() (ForceBaseLine method)
CorrelatedStack (class in lumicks.pylake.correlated_stack)
counts (EnsembleMSD attribute)
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)
(PowerSpectrum method)
(Slice method)
downsampled_like() (Slice method)
downsampled_over() (Slice method)
downsampled_to() (Slice method)
driving_amplitude (ActiveCalibrationModel attribute)
driving_frequency (ActiveCalibrationModel attribute)
duration (Kymo property)
DwelltimeBootstrap (class in lumicks.pylake.population.dwelltime)
DwelltimeModel (class in lumicks.pylake)
E
effective_sample_size (EnsembleMSD attribute)
efjc_distance() (in module lumicks.pylake)
efjc_force() (in module lumicks.pylake)
ensemble_msd() (KymoTrackGroup method)
EnsembleMSD (class in lumicks.pylake.kymotracker.detail.msd_estimation)
estimate_diffusion() (KymoTrack method)
(KymoTrackGroup method)
estimate_diffusion_ols() (KymoTrack method)
ewlc_marko_siggia_distance() (in module lumicks.pylake)
ewlc_marko_siggia_force() (in module lumicks.pylake)
ewlc_odijk_distance() (in module lumicks.pylake)
ewlc_odijk_force() (in module lumicks.pylake)
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_axis (Kymo property)
(Scan property)
fast_sensor (PassiveCalibrationModel attribute)
FdCurve (class in lumicks.pylake.fdcurve)
fdcurves (FdDistanceRangeSelector property)
(FdRangeSelector property)
(File 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_binding_times() (KymoTrackGroup method)
fit_power_spectrum() (in module lumicks.pylake)
flip() (Kymo method)
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)
frequency (PowerSpectrum attribute)
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_range() (PowerSpectrum method)
in_rect() (KymoTrack method)
interpolate() (KymoTrack method)
invert() (Model method)
J
jacobian() (Model method)
K
Kymo (class in lumicks.pylake.kymo)
kymos (File property)
KymoTrack (class in lumicks.pylake.kymotracker.kymotrack)
KymoTrackGroup (class in lumicks.pylake.kymotracker.kymotrack)
L
label() (GaussianMixtureModel method)
lags (EnsembleMSD attribute)
lifetime_distributions (DwelltimeBootstrap property)
lifetimes (DwelltimeModel property)
line_time_seconds (Kymo property)
line_timestamp_ranges() (Kymo method)
lines_per_frame (Scan property)
log_likelihood() (FdFit method)
M
markers (File property)
means (GaussianMixtureModel property)
model (CalibrationResults attribute)
Model (class in lumicks.pylake.fitting.model)
msd (EnsembleMSD attribute)
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)
(Scan property)
num_windows (ActiveCalibrationModel attribute)
P
parameter_trace() (in module lumicks.pylake)
params (CalibrationResults attribute)
(FdFit property)
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)
pixels_per_line (Kymo property)
(Scan property)
pixelsize (Kymo property)
pixelsize_um (Kymo property)
(Scan property)
plot() (CalibrationResults method)
(CorrelatedStack method)
(DistanceCalibration method)
(DwelltimeBootstrap method)
(DwelltimeModel method)
(FdFit method)
(ForceBaseLine method)
(GaussianMixtureModel method)
(Kymo method)
(Model method)
(PointScan method)
(PowerSpectrum method)
(Scan method)
(Slice method)
plot_binding_histogram() (KymoTrackGroup 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_spectrum_residual() (CalibrationResults method)
plot_tether() (CorrelatedStack method)
plot_with_force() (Kymo method)
plot_with_position_histogram() (Kymo method)
plot_with_time_histogram() (Kymo method)
point_scans (File property)
PointScan (class in lumicks.pylake.point_scan)
polynomial_baseline() (ForceBaseLine class method)
power (PowerSpectrum attribute)
PowerSpectrum (class in lumicks.pylake.force_calibration.power_spectrum)
profile_likelihood() (FdFit method)
ps_data (CalibrationResults attribute)
ps_model (CalibrationResults attribute)
R
ranges (FdDistanceRangeSelector property)
(FdRangeSelector property)
rate_constants (DwelltimeModel property)
raw (CorrelatedStack property)
red_image (Kymo property)
(Scan property)
refine_tracks_centroid() (in module lumicks.pylake)
refine_tracks_gaussian() (in module lumicks.pylake)
remove_lines_in_rect() (KymoTrackGroup method)
remove_tracks_in_rect() (KymoTrackGroup method)
results (CalibrationResults attribute)
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)
(PowerSpectrum attribute)
(Slice property)
save() (KymoTrackGroup method)
save_as() (File method)
save_tiff() (Kymo method)
(Scan method)
Scan (class in lumicks.pylake.scan)
scans (File property)
seconds (Slice property)
sem (EnsembleMSD attribute)
shape (Kymo property)
(Scan property)
sigma (FdFit property)
size_um (Kymo property)
(Scan property)
Slice (class in lumicks.pylake.channel)
src (CorrelatedStack property)
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 (PowerSpectrum attribute)
track_greedy() (in module lumicks.pylake)
track_lines() (in module lumicks.pylake)
twlc_distance() (in module lumicks.pylake)
twlc_force() (in module lumicks.pylake)
U
unit (EnsembleMSD attribute)
update_params() (FdFit method)
V
valid_range() (ForceBaseLine method)
(PiezoForceDistance method)
variance (EnsembleMSD attribute)
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)
with_spectrum() (PowerSpectrum method)
wlc_marko_siggia_distance() (in module lumicks.pylake)
wlc_marko_siggia_force() (in module lumicks.pylake)
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v: v0.13.2
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