Pylake 1.5.0

Pylake v1.5.0 has been released with new features and improvements to existing analyses. Here’s some of the highlights:

Plotting with channel data

Added Kymo.plot_with_channels() to plot kymograph data along with data from multiple channels.

A plot of a kymograph with force data and photon counts where we customized color, labels and down-sampling.

This function allows for fine grained plot customization. See correlated plotting for more information.

Improved customization of correlated plots

Added option to disable down-sampling channel data to frame rates when plotting or exporting correlated channel data with scans and images. This option is now available in the plotting methods ImageStack.plot_correlated(), Scan.plot_correlated() and video export methods ImageStack.export_video() and Scan.export_video().

A correlated movie of a multi-frame scan with a customized level of down-sampling.

Improved returned statistics force calibration

A bug in the calculation of the goodness of fit in force calibration routine was fixed. For more information on this quantity, please see the section on goodness of fit. Note that this bug did not affect force calibration results, only the value of this statistic. In addition, the force calibration routine now returns standard errors on the stiffness and displacement sensitivity in the table of fit results.

Updated dependencies

Starting from Pylake 1.5.0, we have updated some of our dependencies.

If you installed Pylake with jupyter notebook, you may have to update uses of %matplotlib notebook with %matplotlib widget in existing notebooks. See the FAQ for more information.

We also dropped support for Python 3.9 in favor of the newer 3.12.

Other changes

In addition, this release contains several other bug-fixes and improvements. For a full list of all the changes, please refer to the full changelog.

Happy Pylake-ing!