lumicks/pylake: v0.11.1

New features Added support for Python 3.10. Added CorrelatedStack.define_tether() which can be used to define the endpoints of the tether between two beads and return image data rotated such that the tether is horizontal. Check out the documentation for more information. Added function to correlate Scan frames to channel data. See Confocal images. Added CorrelatedStack.crop_and_rotate() for interactive editing of the image stack. Actions include scrolling through image frames with the mouse wheel, and left-clicking to define the tether coordinates, and right-click/drag to define a cropping region. Check out the documentation for more information. Added KymoLineGroup.plot_binding_histogram() to plot histograms of binding events for tracked lines. See Kymotracking for more details. Allow fixing the photon background parameter in refine_lines_gaussian(). See kymotracking for more information. Added option to specify a custom label when plotting fit with FdFit.plot(). See the tutorial section on Fd Fitting for more information. Added functionality to slice Scan objects by frame indices. See Confocal images. Added convenience function which allows users to perform a force calibration procedure with a single function call calibrate_force(). See force calibration. Added Kymo.crop_and_calibrate() for interactive cropping of a kymograph. If the optional tether_length_kbp argument is supplied, the resulting kymograph will be automatically calibrated to this length. Check out the documentation for more information. Added fallback to the function Kymo.plot_with_force() when only low-frequency force data is available. Added option to undo/redo actions in the kymotracker widget. Added option to fit peaks simultaneously in refine_lines_gaussian() using the flag overlap_strategy="fit_multiple". See kymotracking for more information. Added ability to manually connect two lines from any points (not just the ends) in the kymotracker widget. Bug fixes Fixed issue which resulted in the offset parameter added by Model.subtract_independent_offset() not having a unit associated with it. Fixed bug which resulted in erroneous standard errors on parameter estimates computed from an FdFit with fixed parameters. For such a fitting problem, the covariance matrix was evaluated for the unconstrained problem (without the fixed parameter constraints). As a result, standard errors were always overestimated. Note that uncertainty estimation by profile likelihood was unaffected. Fixed issue which resulted in overly stringent positional tolerance when using the kymotracker widget. This tolerance has now been made proportional to the axis viewport. Removed axial parameter from lk.ActiveCalibrationModel() as we do not support active force calibration in the axial direction. Improved default scaling behaviour for CorrelatedStack.plot_correlated() and Scan.plot_correlated(). It now ensures the ratio between the image and temporal plot is according to the aspect ratio of the scan or stack. Slicing CorrelatedStack in reverse (i.e., stack[5:3]) or resulting in an empty stack (i.e., stack[5:5]) now throws an exception. Resolved DeprecationWarning for tifffile.imsave() and tifffile.TiffWriter.save() with tifffile >= 2020.9.30. Fixed a bug in refine_lines_gaussian() which incorrectly rounded the pixel position instead of flooring it. For pixels with a subpixel position larger than half the pixel, this resulted in shifting the window by one pixel in the positive direction. Typically, this would have little or no effect since the majority of the peak should still be covered. Deprecations Deprecated CorrelatedStack.timestamps and replaced with CorrelatedStack.frame_timestamp_ranges. The reason for this change is that per-pixel timestamps are not defined for camera based images; therefore, this previous use was not in line with the use of the timestamps property of confocal image classes. This change also brings consistency with Scan.frame_timestamp_ranges. Deprecated plot_red(), plot_green(), plot_blue(), and plot_rgb() methods for PointScan, Scan, and Kymo. These methods have been replaced with a single .plot(channel={color}) method