stable
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
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
P
|
R
|
S
|
T
|
U
|
V
|
W
|
Y
_
__call__() (ActiveCalibrationModel method)
(DistanceCalibration method)
(Model method)
(PassiveCalibrationModel method)
__getitem__() (File method)
(ImageStack method)
(Kymo method)
(PointScan 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)
align_linear() (FdEnsemble method)
amplitude_distributions (DwelltimeBootstrap attribute)
amplitudes (DwelltimeModel property)
B
bic (DwelltimeModel property)
(FdFit property)
(GaussianMixtureModel property)
blue (in module lumicks.pylake)
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)
close() (ImageStack method)
ColorAdjustment (class in lumicks.pylake)
colormaps (in module lumicks.pylake)
connect_click_callback() (SliceRangeSelectorWidget method)
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_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)
define_tether() (ImageStack method)
density_of_water() (in module lumicks.pylake)
derivative() (Model method)
description (File property)
DiffusionEstimate (class in lumicks.pylake.kymotracker.detail.msd_estimation)
dirty (FdFit property)
disconnect_click_callback() (SliceRangeSelectorWidget method)
distance_offset() (in module lumicks.pylake)
distance_range_selector() (FdCurve method)
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_amplitude (ActiveCalibrationModel attribute)
driving_frequency (ActiveCalibrationModel attribute)
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)
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)
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)
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)
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)
frequency_bin_width (PowerSpectrum property)
from_channel() (GaussianMixtureModel 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)
from_wavelength() (in module lumicks.pylake)
G
GaussianMixtureModel (class in lumicks.pylake)
get_image() (ImageStack method)
(Kymo method)
(Scan method)
get_interval() (DwelltimeBootstrap method)
(DwelltimeProfiles method)
green (in module lumicks.pylake)
guid (File property)
H
has_derivative (Model property)
has_jacobian (FdFit property)
(Model property)
HiddenMarkovModel (class in lumicks.pylake)
hist() (DwelltimeBootstrap method)
(DwelltimeModel method)
(GaussianMixtureModel method)
(HiddenMarkovModel method)
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)
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)
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)
localization_variance (DiffusionEstimate attribute)
log_likelihood() (FdFit method)
M
magenta (in module lumicks.pylake)
markers (File property)
means (GaussianMixtureModel property)
(HiddenMarkovModel 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)
P
parameter_trace() (in module lumicks.pylake)
params (CalibrationResults attribute)
(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)
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)
PopulationFitInfo (class in lumicks.pylake.population.detail.fit_info)
position (KymoTrack property)
power (PowerSpectrum attribute)
PowerSpectrum (class in lumicks.pylake.force_calibration.power_spectrum)
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)
red (in module lumicks.pylake)
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)
S
sample_from_image() (KymoTrack method)
sample_rate (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)
shape (Kymo property)
(Scan property)
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 (ImageStack property)
(Slice property)
state_path() (GaussianMixtureModel method)
(HiddenMarkovModel method)
std (GaussianMixtureModel property)
(HiddenMarkovModel property)
std_err (DiffusionEstimate attribute)
stop (ImageStack property)
(Slice property)
subtract_independent_offset() (Model method)
T
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)
transition_matrix (HiddenMarkovModel property)
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)
(HiddenMarkovModel property)
verify_derivative() (Model method)
verify_jacobian() (Model method)
viscosity (ActiveCalibrationModel 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)
Read the Docs
v: stable
Versions
latest
stable
3.10
v1.4.0
v1.3.1
v1.3.0
v1.2.1
v1.2.0
v1.1.1
v1.1.0
v1.0.0
v0.13.3
v0.13.2
v0.13.1
v0.13.0
v0.12.1
v0.12.0
v0.11.1
v0.11.0
v0.10.1
v0.10.0
v0.9.0
v0.8.2
wavelength_cmap
tiffclose
testdoc
swap
scalebar
salty_branch
robert-robust-fitting-example
release_v1_4_0
prettier_docs
prep_1.3.0
pin_jupyter_client
piezo_docs
option_2
no_track_uuids
nbwidgets_docs
minor_fixups
kymotracking_docs_fixup
jupyter_issue
installation_warning
installation_faq_condassl
hidden_markov
global_analysis
fun_with_css
fodocs
fixup_gmm_api
fixup_force_calib_docs
fit_what_you_need
find_beads
filter_by_length
dwelltime_theory
docstring_oops
docs_reorg
docs_diffusion_intro
discrete_pdf
coupling
count_dem_photons
correlated_movie
bugfix_gaussian
bring_on_the_pattern_matching
binding_kinetics_intro
better_dta
assert_other
assert_kymo
assert_fdfit
all_the_plot_docs
add-zenodo-link
add_logic_example
Downloads
On Read the Docs
Project Home
Builds