v0.13.3
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Force Calibration
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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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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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Y
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__call__() (ActiveCalibrationModel method)
(DistanceCalibration method)
(Model method)
(PassiveCalibrationModel method)
__getitem__() (File method)
(ImageStack method)
(Kymo method)
(Scan method)
(Slice method)
A
ActiveCalibrationModel (class in lumicks.pylake)
add_data() (FdFit method)
aic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
aicc (FdFit property)
amplitude_distributions (DwelltimeBootstrap attribute)
amplitudes (DwelltimeModel property)
axial (PassiveCalibrationModel attribute)
B
bead_diameter (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
bic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
blue (in module lumicks.pylake)
blue_image (Kymo 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_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)
colormaps (in module lumicks.pylake)
contiguous (Kymo property)
coordinate_idx (KymoTrack property)
correct_data() (ForceBaseLine method)
counts (EnsembleMSD attribute)
cov (FdFit property)
crop_and_calibrate() (Kymo method)
crop_and_rotate() (ImageStack 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)
define_tether() (ImageStack method)
derivative() (Model method)
description (File property)
DiffusionEstimate (class in lumicks.pylake.kymotracker.detail.msd_estimation)
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_diffusion() (KymoTrackGroup method)
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() (ImageStack method)
(Kymo method)
(Scan method)
export_time (File property)
export_video() (ImageStack method)
(Scan method)
export_video_blue() (Scan method)
export_video_green() (Scan method)
export_video_red() (Scan method)
export_video_rgb() (Scan method)
extend() (DwelltimeBootstrap method)
extract_dwell_times() (GaussianMixtureModel 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() (ImageStack method)
(Scan method)
frequency (PowerSpectrum attribute)
from_channel() (GaussianMixtureModel class method)
from_data() (ImageStack class 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)
G
GaussianMixtureModel (class in lumicks.pylake)
get_image() (ImageStack method)
(Kymo method)
(Scan method)
get_interval() (DwelltimeBootstrap method)
green (in module lumicks.pylake)
green_image (Kymo property)
(Scan property)
guid (File property)
H
has_derivative (Model property)
has_jacobian (FdFit property)
(Model property)
hist() (DwelltimeBootstrap method)
(DwelltimeModel method)
(GaussianMixtureModel method)
hydrodynamically_correct (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
I
ImageStack (class in lumicks.pylake)
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 attribute)
lifetimes (DwelltimeModel property)
line_time_seconds (Kymo property)
line_timestamp_ranges() (Kymo method)
lines_per_frame (Scan property)
localization_variance (DiffusionEstimate attribute)
log_likelihood() (FdFit method)
M
magenta (in module lumicks.pylake)
markers (File property)
means (GaussianMixtureModel property)
method (DiffusionEstimate attribute)
model (CalibrationResults attribute)
Model (class in lumicks.pylake.fitting.model)
model (DwelltimeBootstrap attribute)
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 (ImageStack property)
(Scan property)
num_lags (DiffusionEstimate attribute)
num_points (DiffusionEstimate attribute)
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)
(DistanceCalibration method)
(DwelltimeBootstrap method)
(DwelltimeModel method)
(EnsembleMSD method)
(FdFit method)
(ForceBaseLine method)
(GaussianMixtureModel 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_blue() (Kymo method)
(PointScan method)
(Scan method)
plot_correlated() (ImageStack 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() (ImageStack 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)
position (KymoTrack property)
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 (ImageStack property)
red (in module lumicks.pylake)
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 (KymoTrack property)
(Slice property)
sem (EnsembleMSD attribute)
shape (Kymo property)
(Scan property)
sigma (FdFit property)
simulate_diffusive_tracks() (in module lumicks.pylake.simulation)
size_um (Kymo property)
(Scan property)
Slice (class in lumicks.pylake.channel)
src (ImageStack property)
start (ImageStack property)
(Slice property)
std (GaussianMixtureModel property)
std_err (DiffusionEstimate attribute)
stop (ImageStack property)
(Slice property)
subtract_independent_offset() (Model method)
T
temperature (ActiveCalibrationModel attribute)
(PassiveCalibrationModel attribute)
timestamps (ImageStack 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 (DiffusionEstimate attribute)
(EnsembleMSD attribute)
update_params() (FdFit method)
V
valid_range() (ForceBaseLine method)
(PiezoForceDistance method)
value (DiffusionEstimate attribute)
variance (EnsembleMSD attribute)
variance_of_localization_variance (DiffusionEstimate 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)
Y
yellow (in module lumicks.pylake)
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