v0.13.3

New features

• Added KymoTrackGroup.ensemble_diffusion() for estimating an average diffusion constant for a collection of tracks.
• Added diffusion theory section which details methods used for quantifying diffusive motion. Note that this documentation can be downloaded and run inside a Jupyter notebook.
• Added KymoTrack.plot() and KymoTrackGroup.plot() methods to conveniently plot the coordinates of tracked lines. See the kymotracking documentation for more details.
• Added the lk.GaussianMixtureModel.extract_dwell_times() method to calculate dwell-times for all states from channel data.
• Added lk.colormaps with custom colormaps for plotting single-channel images. Note: this is a namedtuple so you can access the attributes using the dot notation (for example kymo.plot("blue", cmap=lk.colormaps.cyan)). The available attributes are red, green, blue, magenta, yellow, cyan.
• Added localization_variance to DiffusionEstimate. This quantity is useful for determining the diffusive SNR.
• Added variance_of_localization_variance to DiffusionEstimate when calculating an ensemble CVE. This provides an estimate of the variance of the averaged localization uncertainty.
• Added option to pass a localization variance and its uncertainty to KymoTrack.estimate_diffusion().
• Added option to calculate a diffusion estimate based on the ensemble MSDs using the Ordinary Least Squares (OLS) method.
• Added DwelltimeBootstrap.extend() to draw additional samples for the distribution.

Bug fixes

• Fixed a bug that resulted in an incorrect round-off of the window size to pixels when kymotracking. This bug resulted in using one more pixel on each side than intended for specific track_widths. Track width is selected by rounding to the next odd window size. Prior to this change, the number of points used would increase on even window sizes. As a result, requesting a track width of 2.5 pixels, would result in using a window of size 5. Currently, requested a track width of 3 pixels results in a window of size 3, while 3.1 rounds up to the next odd window size (5). This bug affected the kymo tracking widget (tracking, refinement and photon count sampling during saving), lk.track_greedy() and lk.refine_tracks_centroid().
• Updated default slider ranges for the Kymotracker widget to reflect minimum track width required for tracking.
• Fixed issue with model description not being available in Jupyter notebooks for some force-distance models.
• Show validity criterion for Marko Siggia WLC models in terms of model parameters. Prior to this change the limit was simply denoted as 10 pN where in reality it depends on the model parameters. The 10 pN was a reasonable value for most DNA constructs.
• Fixed bug which occurred when exporting images to TIFF files of a numerical type with insufficient range for the data with the flag clip=True. Prior to this change, values exceeding the range of the numerical type were not clearly defined. After this change values below and above the supported range are clipped to the lowest or highest value of the data type respectively.
• Fixed bug in DwelltimeBootstrap.hist() (previously named DwelltimeBootstrap.plot(), see below). Previously, only up to two components were plotted; now all components are plotted appropriately.
• DwelltimeBootstrap.hist() now displays the original parameter estimate rather than the mean of the bootstrap distribution; the bootstrap distribution is used solely to calculate the confidence intervals via DwelltimeBootstrap.get_interval().
• Fixed a bug where Scan.export_video() and ImageStack.export_video() would show elements from a previous plot.
• Fixed a bug that caused a misalignment of half a pixel between the kymograph and its position histogram when using Kymo.plot_with_position_histogram().

Deprecations

• Renamed CorrelatedStack to ImageStack.
• Deprecated the DwelltimeModel.bootstrap attribute; this attribute will be removed in a future release. Instead, DwelltimeModel.calculate_bootstrap() now returns a DwelltimeBootstrap instance directly. See the population dynamics documentation for more details.
• Deprecated DwelltimeBootstrap.plot() and renamed to DwelltimeBootstrap.hist() to more closely match the figure that is generated.
• Deprecated DwelltimeBootstrap.calculate_stats(). This method is replaced with DwelltimeBootstrap.get_interval() which returns the 100*(1-alpha) % confidence interval; unlike DwelltimeBootstrap.calculate_stats(), it does not return the mean.

Other changes

• DwelltimeBootstrap is now a frozen dataclass.
• Attempting to access DwelltimeModel.bootstrap before sampling now raises a RuntimeError; however, see the deprecation note above for proper API to access bootstrapping distributions.
• Suppress legend entry for outline when invoking KymoTrack.plot().
• Allow pickling force calibration results (CalibrationResults). Prior to this change two functions involved in calculating upper parameter bounds prevented this class from being pickled.