Pylake 1.7.0

Here is an overview of features that were released in Pylake v1.7.0.

Calculating effective on-rates from a kymograph

We’ve introduced a new example analysis workflow for calculating the effective on-rate, \(k'_{on}\) (the inverse of the time between binding events as shown in the figure below), for proteins binding to a target site. This workflow guides users through measuring the intervals between binding events of fluorescently labeled proteins on a kymograph, making it possible to determine effective on-rates and analyze binding dynamics. For more information, refer to the examples examples section.

../../_images/kon_whatsnew.png

Improved force calibration

Pylake v1.7.0 comes with several improvements to the force calibration workflow, making it easier to work with force calibration data. Force calibration items now have properties containing the raw calibration data voltage, driving and sum_voltage.

Note

The properties voltage, driving and sum_voltage are only available if the raw data was exported in Bluelake 2.7.0 or newer with this functionality enabled.

Previously, the voltage had to be computed manually to recalibrate the force. Now, recalibrating a force with a single calibration setting overridden becomes a simple three lines:

calibration = file.force1x.calibration[0]
recalibrated = calibration.recalibrate_with(hydrodynamically_correct=True)
recalibrated_force1x = file.force1x.recalibrate_force(recalibrated)

For more information, please refer to the updated tutorial.

Faster bootstraps

Calculating confidence intervals for dwelltime models using bootstrapping can be very time consuming, especially for large datasets. To speed up the process, we have added the option to calculate bootstraps in parallel. This can be done by setting the num_processes parameter in the calculate_bootstrap() method.

Bigger TIF files

Added the option to save TIFF files bigger than 4 GB with export_tiff().

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!