calibrate_force

lumicks.pylake.calibrate_force

calibrate_force(force_voltage_data, bead_diameter, temperature, *, sample_rate, viscosity=None, active_calibration=False, driving_data=array([], dtype=float64), driving_frequency_guess=None, axial=False, hydrodynamically_correct=False, rho_sample=None, rho_bead=1060.0, distance_to_surface=None, fast_sensor=False, num_points_per_block=2000, fit_range=(100.0, 23000.0), excluded_ranges=[], fixed_diode=None, fixed_alpha=None, drag=None) → lumicks.pylake.force_calibration.power_spectrum_calibration.CalibrationResults

Determine force calibration factors.

The power spectrum calibration algorithm implemented here is based on 1 2 3 4 5 6.

References

1

Berg-Sørensen, K. & Flyvbjerg, H. Power spectrum analysis for optical tweezers. Rev. Sci. Instrum. 75, 594 (2004).

2

Tolić-Nørrelykke, I. M., Berg-Sørensen, K. & Flyvbjerg, H. MatLab program for precision calibration of optical tweezers. Comput. Phys. Commun. 159, 225–240 (2004).

3

Hansen, P. M., Tolic-Nørrelykke, I. M., Flyvbjerg, H. & Berg-Sørensen, K. tweezercalib 2.1: Faster version of MatLab package for precise calibration of optical tweezers. Comput. Phys. Commun. 175, 572–573 (2006).

4

Berg-Sørensen, K., Peterman, E. J. G., Weber, T., Schmidt, C. F. & Flyvbjerg, H. Power spectrum analysis for optical tweezers. II: Laser wavelength dependence of parasitic filtering, and how to achieve high bandwidth. Rev. Sci. Instrum. 77, 063106 (2006).

5

Tolić-Nørrelykke, S. F, and Flyvbjerg, H, “Power spectrum analysis with least-squares fitting: amplitude bias and its elimination, with application to optical tweezers and atomic force microscope cantilevers.” Review of Scientific Instruments 81.7 (2010)

6

Tolić-Nørrelykke S. F, Schäffer E, Howard J, Pavone F. S, Jülicher F and Flyvbjerg, H. Calibration of optical tweezers with positional detection in the back focal plane, Review of scientific instruments 77, 103101 (2006).

Parameters

  • force_voltage_data (array_like) – Uncalibrated force data in volts.

  • bead_diameter (float) – Bead diameter [um].

  • temperature (float) – Liquid temperature [Celsius].

  • sample_rate (float) – Sample rate at which the signals were acquired.

  • viscosity (float, optional) – Liquid viscosity [Pa*s]. When omitted, the temperature will be used to look up the viscosity of water at that particular temperature.

  • active_calibration (bool, optional) – Active calibration, when set to True, driving_data must also be provided.

  • driving_data (array_like, optional) – Array of driving data.

  • driving_frequency_guess (float, optional) – Guess of the driving frequency. Required for active calibration.

  • axial (bool, optional) – Is this an axial calibration? Only valid for a passive calibration.

  • hydrodynamically_correct (bool, optional) – Enable hydrodynamically correct model.

  • rho_sample (float, optional) – Density of the sample [kg/m**3]. Only used when using hydrodynamically correct model.

  • rho_bead (float, optional) – Density of the bead [kg/m**3]. Only used when using hydrodynamically correct model.

  • distance_to_surface (float, optional) – Distance from bead center to the surface [um] When specifying None, the model will use an approximation which is only suitable for measurements performed deep in bulk.

  • fast_sensor (bool, optional) – Fast sensor? Fast sensors do not have the diode effect included in the model.

  • fit_range (tuple of float, optional) – Tuple of two floats (f_min, f_max), indicating the frequency range to use for the full model fit. [Hz]

  • num_points_per_block (int, optional) – The spectrum is first block averaged by this number of points per block. Default: 2000.

  • excluded_ranges (list of tuple of float, optional) – List of ranges to exclude specified as a list of (frequency_min, frequency_max).

  • drag (float, optional) – Overrides the drag coefficient to this particular value.

  • fixed_diode (float, optional) – Fix diode frequency to a particular frequency.

  • fixed_alpha (float, optional) – Fix diode relaxation factor to particular value.