Pylake 1.1.0

Pylake v1.1.0 has been released, with new features and an important bugfix. Here’s some of the highlights.

Bugfix KymoTrackGroup.sample_from_image

Prior to version 1.1.0, the method sample_from_image() had a bug that assumed the origin of a pixel to be at the edge rather than the center of the pixel. Consequently, the sampled window would be off by one pixel half the time. For reasonably sized sampling windows (more than 4 pixels wide), the effect of this bug should be small. Note that the bug does not impact the position estimates.

Important

The old (incorrect) behavior is maintained until the next major release (2.0) to ensure backward compatibility and allow assessment of the impact of the bug. When using sample_from_image() or KymoWidgetGreedy(), it is recommended to include the argument correct_origin=True which results in using the correct origin.

Global analysis

Previously, downstream analyses from kymotracking were limited to tracks from a single kymograph. With global analysis, you can combine tracking results from multiple kymographs to get better statistics when estimating binding lifetimes or calculating diffusion constants. For more information on this feature, please refer to the relevant section of the kymotracking tutorial.

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Global analysis allows you to analyze multiple kymographs in a single analysis. This results in improved estimates of the biophysical parameters of your experiment.

Splitting tracks

You can now split tracks in the Kymotracker widget.

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Clicking with the right mouse button splits an existing line into two segments.

Profile likelihood for dwell time analysis

We added a second method for calculating uncertainty intervals for dwell time analysis. This method can be used to determine confidence intervals and assess whether a dwell time model has too many parameters (i.e., if a model with fewer components would be sufficient to fit the data).

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Profile likelihood curves for a dwell time model. The intersection points between the blue curve and the dashed lines indicate the 95% confidence interval for that particular parameter.

Other changes

As always, we implemented various other bug-fixes and improvements. For a full list of all the changes, please refer to the full changelog.

Happy Pylake-ing!