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 Tutorial first.
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A convenient HDF5 file wrapper for reading data exported from Bluelake |
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A lazily evaluated slice of a timeline/HDF5 channel |
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An FD curve exported from Bluelake |
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A Kymograph exported from Bluelake |
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A confocal scan exported from Bluelake |
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A confocal point scan exported from Bluelake |
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CorrelatedStack acquired with Bluelake. |
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Color adjustment for plotting |
Force calibration¶
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Determine force calibration factors. |
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Compute power spectrum and returns it as a |
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Power Spectrum Calibration |
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Model to fit data acquired during passive calibration. |
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Model to fit data acquired during active calibration. |
Power spectrum data for a time series. |
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Power spectrum calibration results. |
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Computes the viscosity of water in [Pa*s] at a particular temperature. |
FD Fitting¶
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Object which is used for fitting. |
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Invert a model with respect to one parameter. |
Available models
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Offset on the the model output. |
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Offset on the the model output. |
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Marko Siggia's Worm-like Chain model with force as dependent parameter. |
Marko Siggia's Worm-like Chain model with distance as dependent parameter. |
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Marko Siggia's Worm-like Chain model based on only entropic contributions (valid for F << 10 pN). |
Marko Siggia's Worm-like Chain model based on only entropic contributions (valid for F << 10 pN). |
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Odijk's Extensible Worm-Like Chain model with distance as dependent variable (useful for 10 pN < F < 30 pN). |
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Odijk's Extensible Worm-Like Chain model with force as dependent variable (useful for 10 pN < F < 30 pN). |
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Freely-Jointed Chain with distance as dependent parameter. |
Inverted Freely-Jointed Chain with force as dependent parameter. |
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Twistable Worm-like Chain model. |
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Twistable Worm-like Chain model. |
Kymotracking¶
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A line on a kymograph. |
Estimate diffusion constant |
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Track particles on an image using a greedy algorithm. |
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Track particles on an image using an algorithm that looks for line-like structures. |
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Remove lines below a specific minimum number of points from the list. |
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Refine the lines based on the brightness-weighted centroid. |
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Refine the lines by gaussian peak MLE. |
Notebook widgets¶
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Population Dynamics¶
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A wrapper around scikit-learn's GMM. |
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Exponential mixture model optimization for dwelltime analysis. |
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Bootstrap distributions for a dwelltime model. |