v0.12.1

New features

• Added Scan.pixel_time_seconds and Kymo.pixel_time_seconds to obtain the pixel dwell time. See Confocal images for more information.
• Allow cropping CorrelatedStack using multidimensional indexing, i.e. stack[start_frame : end_frame, start_row : end_row, start_column : end_column]. See Correlated stacks for more information.
• Added KymoLine.estimate_diffusion() which provides additional information regarding the diffusion constant estimation. This dataclass can be converted to floating point to get just the estimate, but also contains the number of points used to compute the estimate, and the number of lags used in the analysis. In addition to that, it provides a std_err field which reports the standard error for the estimate.
• Added generalized least squares method as method option for KymoLine.estimate_diffusion(). Please refer to the kymotracker documentation for more information.
• Added offline piezo tracking functionality (documentation pending).
• Added lk.benchmark() that can be used to estimate the performance of your computer with various pylake tasks.

Bug fixes

• Changed the internal calculation of the extent argument in Kymo.plot() such that the spatial limits are now defined at the center of the pixel (same functionality that is used for the temporal axis). Previously the limits were defined at the edge of the pixel resulting in a subtle misalignment between the coordinates of the tracked lines and the actual image.
• Fixed an issue where the pixel dwell time stored in TIFFs exported from Pylake could be incorrect. Prior to this fix, Pylake exported the value entered in the Bluelake UI as pixel dwell time. In reality, the true pixel dwell time is a multiple of the acquisition sample rate. After the fix, TIFF files correctly report the achieved pixel dwell time.
• Changed the internal calculation of the hydrodynamically correct force spectrum. Before this change, the computation of the power spectral density relied on the frequencies always being positive. While this change does not affect any results, it allows evaluating the power spectral density for negative frequencies.
• Fixed an issue where evaluating the hydrodynamically correct spectrum up to very high frequencies could lead to precision losses. These precision losses typically occur at frequencies upwards of 30 kHz and manifest themselves as visible discontinuities.
• Perform better input validation on the kymotracking functions track_greedy and track_lines. The line width and pixel threshold must be larger than zero. The diffusion parameter must be positive. Previously, failure to provide values respecting these limits would produce cryptic error messages.
• Perform better input validation on refine_lines_centroid. Line width must now be at least one pixel. Previously, negative values produced a cryptic error message, while a line width smaller than one pixel would silently result in no refinement taking place.
• Fixed bug in force calibration convenience function where setting fixed_alpha or fixed_diode to zero resulted in those parameters still being fitted. After this change, setting fixed_alpha to zero will result in the diode model having a fixed alpha of zero, whereas setting f_diode to zero raises an exception.
• Include one extra sample when requesting frame timestamp ranges from a scan (Scan.frame_timestamp_ranges(exclude=True)). Previously, when slicing using these timestamps, you would omit the last sample of the scan. Now this sample will be included.

Deprecations

• KymoLine.estimate_diffusion_ols() is now deprecated; use KymoLine.estimate_diffusion(method="ols") instead. This new method returns the same estimate of the diffusion coefficient as before but includes additional information about the fit.