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.
|
A convenient HDF5 file wrapper for reading data exported from Bluelake |
|
A lazily evaluated slice of a timeline/HDF5 channel |
|
An FD curve exported from Bluelake |
|
A Kymograph exported from Bluelake |
|
A confocal scan exported from Bluelake |
|
A confocal point scan exported from Bluelake |
|
CorrelatedStack acquired with Bluelake. |
|
Utility class to adjust the min/max values of image colormaps. |
Force calibration¶
|
Model to fit data acquired during passive calibration. |
|
Model to fit data acquired during active calibration. |
|
Determine force calibration factors. |
|
Compute power spectrum and returns it as a |
|
Power Spectrum Calibration |
Power spectrum data for a time series. |
|
|
Power spectrum calibration results. |
|
Computes the viscosity of water in [Pa*s] at a particular temperature. |
FD Fitting¶
|
|
|
Object which is used for fitting. |
|
Invert a model with respect to one parameter. |
Available models
|
Offset on the the model output. |
|
Offset on the the model output. |
|
Marko Siggia's Worm-like Chain model with force as dependent parameter. |
Marko Siggia's Worm-like Chain model with distance as dependent parameter |
|
|
Marko Siggia's Worm-like Chain model. |
Marko Siggia's Worm-like Chain model. |
|
|
Odijk's Extensible Worm-Like Chain model with distance as dependent variable |
|
Odijk's Extensible Worm-Like Chain model with force as dependent variable |
|
Freely-Jointed Chain with distance as dependent parameter. |
Freely-Jointed Chain model with distance as the dependent parameter. |
|
|
Twistable Worm-like Chain model with distance as dependent variable. |
|
Twistable Worm-like Chain model with force as the dependent variable. |
Kymotracking¶
|
A tracked particle on a kymograph. |
|
Track particles on an image using a greedy algorithm. |
|
Track particles on an image using an algorithm that looks for line-like structures. |
|
Remove tracks shorter than a minimum number of time points from the list. |
|
Refine the tracks based on the brightness-weighted centroid. |
|
Refine the tracks by gaussian peak MLE. |
Notebook widgets¶
|
|
|
Population Dynamics¶
|
A wrapper around scikit-learn's GMM. |
|
Exponential mixture model optimization for dwelltime analysis. |
|
Bootstrap distributions for a dwelltime model. |
Piezo tracking¶
|
Class to calibrate trap position to camera distance |
|
A force baseline as a function of trap position |
|
Class to handle piezo tracking calibration |
|
Class to determine both piezo distance and baseline corrected force |