api.rst

API Reference

This detailed reference lists all the classes and functions contained in the package. If you are just looking to get started, read the :doc:`/tutorial/index` first.

.. currentmodule:: lumicks.pylake

.. autosummary::
    :toctree: _api

    File
    channel.Slice
    fdcurve.FdCurve
    kymo.Kymo
    scan.Scan
    point_scan.PointScan
    correlated_stack.CorrelatedStack
    ColorAdjustment

Force calibration

.. autosummary::
    :toctree: _api

    calibrate_force
    calculate_power_spectrum
    fit_power_spectrum
    PassiveCalibrationModel
    ActiveCalibrationModel
    force_calibration.power_spectrum.PowerSpectrum
    force_calibration.power_spectrum_calibration.CalibrationResults
    viscosity_of_water

FD Fitting

.. autosummary::
    :toctree: _api

    fitting.model.Model
    FdFit
    parameter_trace

Available models

.. autosummary::
    :toctree: _api

    force_offset
    distance_offset
    marko_siggia_ewlc_force
    marko_siggia_ewlc_distance
    marko_siggia_simplified
    inverted_marko_siggia_simplified
    odijk
    inverted_odijk
    freely_jointed_chain
    inverted_freely_jointed_chain
    twistable_wlc
    inverted_twistable_wlc

Kymotracking

.. autosummary::
    :toctree: _api

    kymotracker.kymoline.KymoLine
    kymotracker.kymoline.KymoLine.estimate_diffusion
    track_greedy
    track_lines
    filter_lines
    refine_lines_centroid
    refine_lines_gaussian

Notebook widgets

.. autosummary::
    :toctree: _api

    FdRangeSelector
    FdDistanceRangeSelector

Population Dynamics

.. autosummary::
    :toctree: _api

    GaussianMixtureModel
    DwelltimeModel
    population.dwelltime.DwelltimeBootstrap