1.7
Changelog
What’s new
Installation
User guide
Tutorial
Examples
API Reference
Fundamentals
Diffusion
Force Calibration
Literature
Force Calibration
F,d Fitting
Kymotracker
Diffusion constant estimation
References
lumicks.pylake
Index
Index
_
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A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
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O
|
P
|
R
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S
|
T
|
U
|
V
|
W
|
Y
_
__call__() (ActiveCalibrationModel method)
(CalibrationResults method)
(DiodeCalibrationModel method)
(DistanceCalibration method)
(Model method)
(PassiveCalibrationModel method)
__getitem__() (File method)
(ImageStack method)
(Kymo method)
(PointScan method)
(Scan method)
(Slice method)
A
active_calibration (CalibrationResults property)
(ForceCalibrationItem property)
ActiveCalibrationModel (class in lumicks.pylake)
add_data() (FdFit method)
aic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
aicc (FdFit property)
align_linear() (FdEnsemble method)
amplitude_distributions (DwelltimeBootstrap attribute)
amplitudes (DwelltimeModel property)
applied_at (CalibrationResults property)
(ForceCalibrationItem property)
B
backing (CalibrationResults property)
(ForceCalibrationItem property)
bead_diameter (CalibrationResults property)
(ForceCalibrationItem property)
bic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
blue (in module lumicks.pylake)
blue_power (Kymo property)
(PointScan property)
(Scan property)
bluelake_version (File property)
bootstrap (DwelltimeModel property)
C
calculate_bootstrap() (DwelltimeModel method)
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_params() (ForceCalibrationItem method)
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)
chi_squared_per_degree (CalibrationResults property)
(ForceCalibrationItem property)
ci() (Parameter method)
clear() (ForceCalibrationItem method)
close() (ImageStack method)
ColorAdjustment (class in lumicks.pylake)
colormaps (in module lumicks.pylake)
compress() (PowerSpectrum method)
connect_click_callback() (SliceRangeSelectorWidget method)
contiguous (Kymo property)
coordinate_idx (KymoTrack property)
corner_frequency (CalibrationResults property)
(ForceCalibrationItem property)
corner_frequency_std_err (CalibrationResults property)
(ForceCalibrationItem property)
correct_data() (ForceBaseLine method)
counts (EnsembleMSD attribute)
coupling_correction_2d() (in module lumicks.pylake)
cov (FdFit property)
crop_and_calibrate() (Kymo method)
crop_and_rotate() (ImageStack method)
crop_beads() (Kymo method)
crop_by_distance() (Kymo method)
crop_by_pixels() (ImageStack method)
(Scan method)
cyan (in module lumicks.pylake)
D
d (FdCurve property)
data (Slice property)
defaults (Model property)
define_tether() (ImageStack method)
density_of_water() (in module lumicks.pylake)
derivative() (Model method)
description (File property)
diffusion_constant (CalibrationResults property)
(ForceCalibrationItem property)
diffusion_constant_volts (CalibrationResults property)
(ForceCalibrationItem property)
diffusion_volts_std_err (CalibrationResults property)
(ForceCalibrationItem property)
DiffusionEstimate (class in lumicks.pylake.kymotracker.detail.msd_estimation)
diode_calibration (ForceCalibrationItem property)
diode_frequency (CalibrationResults property)
(ForceCalibrationItem property)
diode_frequency_std_err (CalibrationResults property)
(ForceCalibrationItem property)
diode_relaxation_factor (CalibrationResults property)
(ForceCalibrationItem property)
diode_relaxation_factor_std_err (CalibrationResults property)
(ForceCalibrationItem property)
DiodeCalibrationModel (class in lumicks.pylake.force_calibration.calibration_models)
dirty (FdFit property)
disconnect_click_callback() (SliceRangeSelectorWidget method)
displacement_sensitivity (CalibrationResults property)
(ForceCalibrationItem property)
displacement_sensitivity_std_err (CalibrationResults property)
(ForceCalibrationItem property)
distance_offset() (in module lumicks.pylake)
distance_range_selector() (FdCurve method)
distance_to_surface (CalibrationResults property)
(ForceCalibrationItem property)
DistanceCalibration (class in lumicks.pylake)
download_from_doi() (in module lumicks.pylake)
downsampled_by() (Kymo method)
(PowerSpectrum method)
(Slice method)
downsampled_like() (Slice method)
downsampled_over() (Slice method)
downsampled_to() (Slice method)
driving (ForceCalibrationItem property)
driving_amplitude (ActiveCalibrationModel attribute)
(CalibrationResults property)
(ForceCalibrationItem property)
driving_frequency (ActiveCalibrationModel attribute)
(CalibrationResults property)
(ForceCalibrationItem property)
driving_frequency_guess (CalibrationResults property)
(ForceCalibrationItem property)
driving_power (CalibrationResults property)
(ForceCalibrationItem property)
driving_sample_rate (CalibrationResults property)
(ForceCalibrationItem property)
dsdna_ewlc_odijk_distance() (in module lumicks.pylake)
duration (Kymo property)
(KymoTrack property)
DwelltimeBootstrap (class in lumicks.pylake.population.dwelltime)
DwelltimeModel (class in lumicks.pylake)
DwelltimeProfiles (class in lumicks.pylake.population.dwelltime)
E
effective_sample_size (EnsembleMSD attribute)
efjc_distance() (in module lumicks.pylake)
efjc_force() (in module lumicks.pylake)
emission_path() (GaussianMixtureModel method)
(HiddenMarkovModel method)
ensemble_diffusion() (KymoTrackGroup method)
ensemble_msd() (KymoTrackGroup method)
EnsembleMSD (class in lumicks.pylake.kymotracker.detail.msd_estimation)
err_amplitudes (DwelltimeModel property)
err_lifetimes (DwelltimeModel property)
estimate_bead_edges() (Kymo method)
estimate_diffusion() (KymoTrack method)
(KymoTrackGroup 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)
excluded_ranges (CalibrationResults property)
(ForceCalibrationItem property)
exit_flag (GaussianMixtureModel property)
experiment (File property)
export_tiff() (ImageStack method)
(Kymo method)
(Scan method)
export_time (File property)
export_video() (ImageStack method)
(Scan method)
extend() (DwelltimeBootstrap method)
(KymoTrackGroup method)
extract_dwell_times() (GaussianMixtureModel method)
(HiddenMarkovModel method)
extrapolate() (KymoTrack method)
F
f (FdCurve property)
fast_axis (Kymo property)
(Scan property)
fast_sensor (CalibrationResults property)
(ForceCalibrationItem property)
fd_curves (FdEnsemble attribute)
fd_curves_processed (FdEnsemble attribute)
FdCurve (class in lumicks.pylake.fdcurve)
fdcurves (FdDistanceRangeSelector property)
(FdRangeSelector property)
(File property)
FdDistanceRangeSelector (class in lumicks.pylake)
FdEnsemble (class in lumicks.pylake.fdensemble)
FdFit (class in lumicks.pylake)
FdRangeSelector (class in lumicks.pylake)
File (class in lumicks.pylake)
file (FdCurve attribute)
filter() (KymoTrackGroup method)
filter_tracks() (in module lumicks.pylake)
fit() (FdFit method)
fit_binding_times() (KymoTrackGroup method)
fit_info (GaussianMixtureModel property)
(HiddenMarkovModel property)
fit_power_spectrum() (in module lumicks.pylake)
fit_range (CalibrationResults property)
(ForceCalibrationItem property)
fitted_diode (CalibrationResults property)
(ForceCalibrationItem property)
fitted_params (CalibrationResults attribute)
fixed (Parameter attribute)
flip() (Kymo method)
force_distance() (PiezoForceDistance method)
force_offset() (in module lumicks.pylake)
force_sensitivity (CalibrationResults property)
(ForceCalibrationItem property)
ForceBaseLine (class in lumicks.pylake)
ForceCalibrationItem (class in lumicks.pylake.calibration)
format_version (File property)
frame_timestamp_ranges() (ImageStack method)
(Scan method)
frequency (PowerSpectrum attribute)
frequency_bin_width (PowerSpectrum property)
from_channel() (GaussianMixtureModel class method)
from_data() (PowerSpectrum static method)
from_dataset() (ImageStack class method)
(Kymo class method)
(PointScan class method)
(Scan class method)
from_file() (DistanceCalibration class method)
from_h5py() (File class method)
from_wavelength() (in module lumicks.pylake)
G
GaussianMixtureModel (class in lumicks.pylake)
get() (ForceCalibrationItem method)
get_image() (ImageStack method)
(Kymo method)
(Scan method)
get_interval() (DwelltimeBootstrap method)
(DwelltimeProfiles method)
green (in module lumicks.pylake)
green_power (Kymo property)
(PointScan property)
(Scan property)
guid (File property)
H
has_data (CalibrationResults property)
(ForceCalibrationItem property)
has_derivative (Model property)
has_jacobian (FdFit property)
(Model property)
HiddenMarkovModel (class in lumicks.pylake)
highlight_time_range() (Slice method)
hist() (DwelltimeBootstrap method)
(DwelltimeModel method)
(GaussianMixtureModel method)
(HiddenMarkovModel method)
hydrodynamically_correct (CalibrationResults property)
(ForceCalibrationItem property)
I
identify_peaks() (PowerSpectrum method)
image (ImageEditorWidget property)
ImageEditorWidget (class in lumicks.pylake.nb_widgets.image_editing)
ImageStack (class in lumicks.pylake)
in_range() (PowerSpectrum method)
in_rect() (KymoTrack method)
initial_state_probability (HiddenMarkovModel property)
interpolate() (KymoTrack method)
invert() (Model method)
items() (ForceCalibrationItem method)
J
jacobian() (Model method)
K
keys() (ForceCalibrationItem method)
Kymo (class in lumicks.pylake.kymo)
kymos (File property)
KymoTrack (class in lumicks.pylake.kymotracker.kymotrack)
KymoTrackGroup (class in lumicks.pylake.kymotracker.kymotrack)
KymoWidgetGreedy (class in lumicks.pylake)
L
label() (GaussianMixtureModel method)
lags (EnsembleMSD attribute)
lifetime_distributions (DwelltimeBootstrap attribute)
lifetimes (DwelltimeModel property)
line_time_seconds (Kymo property)
line_timestamp_ranges() (Kymo method)
lines_per_frame (Scan property)
load_tracks() (in module lumicks.pylake)
(KymoWidgetGreedy method)
local_drag_coefficient (CalibrationResults property)
(ForceCalibrationItem property)
localization_variance (DiffusionEstimate attribute)
log_likelihood() (FdFit method)
lower_bound (Parameter attribute)
M
magenta (in module lumicks.pylake)
markers (File property)
means (GaussianMixtureModel property)
(HiddenMarkovModel property)
measured_drag_coefficient (CalibrationResults property)
(ForceCalibrationItem property)
method (DiffusionEstimate attribute)
model (CalibrationResults attribute)
Model (class in lumicks.pylake.fitting.model)
model (DwelltimeBootstrap attribute)
(DwelltimeProfiles attribute)
motion_blur_constant (Kymo property)
msd (EnsembleMSD attribute)
msd() (KymoTrack method)
N
n_components (DwelltimeBootstrap property)
(DwelltimeProfiles property)
n_params (FdFit property)
n_residuals (FdFit property)
n_samples (DwelltimeBootstrap property)
name (FdCurve attribute)
notes (File property)
num_frames (ImageStack property)
(Scan property)
num_lags (DiffusionEstimate attribute)
num_points (DiffusionEstimate attribute)
num_points_per_block (ForceCalibrationItem property)
number_of_samples (CalibrationResults property)
(ForceCalibrationItem property)
O
offset (CalibrationResults property)
(ForceCalibrationItem property)
P
Parameter (class in lumicks.pylake.fitting.parameters)
parameter_trace() (in module lumicks.pylake)
params (CalibrationResults attribute)
Params (class in lumicks.pylake.fitting.parameters)
params (FdFit property)
PassiveCalibrationModel (class in lumicks.pylake)
pdf() (DwelltimeModel method)
(GaussianMixtureModel method)
photon_counts (KymoTrack property)
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 (ImageStack property)
(Kymo property)
(Scan property)
plot() (CalibrationResults method)
(DistanceCalibration method)
(DwelltimeBootstrap method)
(DwelltimeModel method)
(DwelltimeProfiles method)
(EnsembleMSD method)
(FdFit method)
(ForceBaseLine method)
(GaussianMixtureModel method)
(HiddenMarkovModel method)
(ImageStack method)
(Kymo method)
(KymoTrack method)
(KymoTrackGroup method)
(Model method)
(PointScan method)
(PowerSpectrum method)
(Scan method)
(Slice method)
plot_binding_histogram() (KymoTrackGroup method)
plot_correlated() (ImageStack method)
(Scan method)
plot_fit() (KymoTrack method)
(KymoTrackGroup method)
plot_msd() (KymoTrack method)
plot_path() (GaussianMixtureModel method)
(HiddenMarkovModel method)
plot_residual() (DistanceCalibration method)
(ForceBaseLine method)
plot_scatter() (FdCurve method)
plot_spectrum_residual() (CalibrationResults method)
(ForceCalibrationItem method)
plot_tether() (ImageStack method)
plot_with_channels() (Kymo 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)
pop() (ForceCalibrationItem method)
popitem() (ForceCalibrationItem method)
PopulationFitInfo (class in lumicks.pylake.population.detail.fit_info)
position (KymoTrack property)
power (PowerSpectrum attribute)
power_spectrum_params() (ForceCalibrationItem method)
PowerSpectrum (class in lumicks.pylake.force_calibration.power_spectrum)
profile (Parameter attribute)
profile_likelihood() (DwelltimeModel method)
(FdFit method)
profiles (DwelltimeProfiles attribute)
ps_data (CalibrationResults attribute)
ps_model (CalibrationResults attribute)
R
range_selector() (FdCurve method)
(Slice method)
ranges (FdDistanceRangeSelector property)
(FdRangeSelector property)
(SliceRangeSelectorWidget property)
rate_constants (DwelltimeModel property)
recalibrate_force() (Slice method)
recalibrate_with() (ForceCalibrationItem method)
red (in module lumicks.pylake)
red_power (Kymo property)
(PointScan property)
(Scan property)
refine_tracks_centroid() (in module lumicks.pylake)
refine_tracks_gaussian() (in module lumicks.pylake)
remove() (KymoTrackGroup method)
remove_tracks_in_rect() (KymoTrackGroup method)
results (CalibrationResults attribute)
rho_bead (CalibrationResults property)
(ForceCalibrationItem property)
rho_sample (CalibrationResults property)
(ForceCalibrationItem property)
S
sample_from_channel() (KymoTrack method)
sample_from_image() (KymoTrack method)
sample_rate (CalibrationResults property)
(ForceCalibrationItem property)
(PowerSpectrum attribute)
(Slice property)
save() (KymoTrackGroup method)
save_as() (File method)
save_tracks() (KymoWidgetGreedy method)
ScaleBar (class in lumicks.pylake)
Scan (class in lumicks.pylake.scan)
scans (File property)
seconds (KymoTrack property)
(Slice property)
sem (EnsembleMSD attribute)
setdefault() (ForceCalibrationItem method)
shape (Kymo property)
(Scan property)
shared (Parameter attribute)
sigma (FdFit property)
simulate_diffusive_tracks() (in module lumicks.pylake.simulation)
size_um (ImageStack property)
(Kymo property)
(Scan property)
Slice (class in lumicks.pylake.channel)
SliceRangeSelectorWidget (class in lumicks.pylake.nb_widgets.range_selector)
slices (SliceRangeSelectorWidget property)
ssdna_efjc_distance() (in module lumicks.pylake)
start (CalibrationResults property)
(ForceCalibrationItem property)
(ImageStack property)
(Slice property)
state_path() (GaussianMixtureModel method)
(HiddenMarkovModel method)
std (GaussianMixtureModel property)
(HiddenMarkovModel property)
std_err (DiffusionEstimate attribute)
stderr (Parameter attribute)
sted_power (Kymo property)
(PointScan property)
(Scan property)
stiffness (CalibrationResults property)
(ForceCalibrationItem property)
stiffness_std_err (CalibrationResults property)
(ForceCalibrationItem property)
stop (CalibrationResults property)
(ForceCalibrationItem property)
(ImageStack property)
(Slice property)
subtract_independent_offset() (Model method)
sum_voltage (ForceCalibrationItem property)
T
temperature (CalibrationResults property)
(ForceCalibrationItem property)
theoretical_bulk_drag (CalibrationResults property)
(ForceCalibrationItem property)
time_idx (KymoTrack property)
timestamps (Kymo property)
(Scan property)
(Slice property)
to_kymo() (ImageStack method)
total_duration (PowerSpectrum attribute)
track_greedy() (in module lumicks.pylake)
track_lines() (in module lumicks.pylake)
tracks (KymoWidgetGreedy property)
transferred_lateral_drag_coefficient (CalibrationResults property)
(ForceCalibrationItem property)
transition_matrix (HiddenMarkovModel property)
trap_power (ForceCalibrationItem property)
twlc_distance() (in module lumicks.pylake)
twlc_force() (in module lumicks.pylake)
U
unfiltered_frequency (PowerSpectrum property)
unfiltered_power (PowerSpectrum property)
unit (DiffusionEstimate attribute)
(EnsembleMSD attribute)
(Parameter attribute)
update() (ForceCalibrationItem method)
update_params() (FdFit method)
(Params method)
upper_bound (Parameter attribute)
V
valid_range() (ForceBaseLine method)
(PiezoForceDistance method)
value (DiffusionEstimate attribute)
(Parameter attribute)
values() (ForceCalibrationItem method)
variance (EnsembleMSD attribute)
variance_of_localization_variance (DiffusionEstimate attribute)
variances (GaussianMixtureModel property)
(HiddenMarkovModel property)
verify_derivative() (Model method)
verify_jacobian() (Model method)
viscosity (ActiveCalibrationModel attribute)
(CalibrationResults property)
(ForceCalibrationItem property)
viscosity_of_water() (in module lumicks.pylake)
voltage (ForceCalibrationItem property)
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)
Y
yellow (in module lumicks.pylake)