New features Added fitting mode "simultaneous" to lk.refine_tracks_gaussian() which enforces optimization bounds between the peak positions. This helps prevent lk.refine_tracks_gaussian() from reassigning points to the wrong track when a track momentarily disappears and overlap_strategy is set to "multiple" and refine_missing_frames is set to True. When fitting mode is set to "simultaneous", bounds ensure that the individual Gaussians cannot switch position. In addition, this mode uses a better initial guess for the peak amplitudes based on the maximum photon count observed in each range. Added the option to take into account discretization effects in DwelltimeModel by passing a discretization_timestep to the model when constructing it. Added the option to take into account discretization effects when performing dwell time analysis on a KymoTrackGroup. Simply pass discrete_model=True to KymoTrackGroup.fit_binding_times() to make use of this new functionality. Added the optional parameter loss_function to fit_power_spectrum(). Implemented loss functions are "gaussian" (default) and "lorentzian". The default corresponds to regular least-squares fitting, whereas "lorentzian" invokes a robust fitting method that is less susceptible to spurious peaks in the power spectrum which comes at the cost of a small bias in the estimates for a spectrum without noise peaks. Furthermore, no estimates of the errors in the fitted parameters are provided. This is beta functionality. While usable, this has not yet been tested in a large number of different scenarios. The API can still be subject to change without any prior deprecation notice! Added PowerSpectrum.identify_peaks() method to the PowerSpectrum class. This method uses probability to identify peaks in the spectrum that are not due to the movement of beads in an optical trap. This is beta functionality. While usable, this has not yet been tested in a large number of different scenarios. The API can still be subject to change without any prior deprecation notice! Added KymoTrack.plot_fit() and KymoTrackGroup.plot_fit() to show the fitted model obtained from gaussian refinement. Added the ability to specify a cropping region when exporting to an h5-file using file.save_as(filename, crop_time_range=(starting_timestamp, ending_timestamp)). Added method to create colormaps approximating a color from emission wavelength. See lk.colormaps.from_wavelength() for more information. Added support for accessing Kymo, Scan and PointScan by path (e.g. file["Kymograph"]["my_kymo"] or file["Kymograph/my_kymo"]). Added support for slicing PointScan. Bug fixes Fixed issue in dwell time analysis that could lead to biased estimates for kymographs with very few events. Before this fix KymoTrackGroup.fit_binding_times() relied on the assumption that the shortest observed track is actually the minimum observable dwell time. This assumption is valid for kymographs with many events; however, this becomes problematic when multiple kymographs with few events each are analyzed globally. In this case, binding times will be underestimated. With this fix, the minimum observable dwell time is calculated from the kymograph scan line time and the set minimum track length. The old (incorrect) behavior is maintained as default until the next major release (v2.0.0) to ensure backward compatibility. To enable the fixed behavior immediately (recommended), specify observed_minimum=False when calling KymoTrackGroup.fit_binding_times(). To maintain the old legacy behavior use observed_minimum=True. Note that CSVs exported from the kymotracking widget before v1.2.0 will contain insufficient metadata to make use of the improved analysis. To recover this metadata, use lk.filter_tracks() on the KymoTrackGroup with a specified min_length. This filters short events and stores the new minimum observable duration in the group. Other changes File.save_as() data now allows passing in a single string for the omit_data parameter. Gracefully handle empty Scan after slicing. Previously, a slice operation on a Scan that resulted in no frames remaining raised a NotImplementedError. Now it returns an EmptyScan. Improved performance of Scan.pixel_time_seconds, Kymo.pixel_time_seconds and Kymo.line_time_seconds. Dropped opencv dependency which was only used for calculating rotation matrices and performing the affine transformations required for image alignment. Pylake now uses scikit-image for this purpose. Marked functions that take file paths as arguments with the os.PathLike type hint to idicate that pathlib.Path and similar types are also accepted (not just str). Use Unicode characters for µ and ² when plotting rather than TeX strings. Deprecations Deprecated fitting mode "multiple" in lk.refine_tracks_gaussian() as it could lead to spurious track crossings. See the entry for the fitting mode "simultaneous" under New Features for more information.