Palmari

Description¶

Palmari allows you to process your SPT recordings (PALM or other modalities, 2D) with an all-inclusive pipeline: spot detection, sub-pixel localization, tracking & more. Start quickly with default parameters or customize your pipeline, and run it on entire folder of microscope recordings.

Quickstart¶

On a single recording¶

To run Palmari on a single microscope recording, click on "Palmari > run Palmari on file..." You'll see a panel open on the right with a pre-loaded default analysis pipeline.

You can run steps of the pipeline one after the other and tweak the parameters so that they suit your experimental setup. Don't forget to set the pixel size and exposure. You can also add and remove processing steps by clicking on the "Edit pipeline" button.

When you're satisfied with te results, just click on "Save locs and tracks" to export localizations and trajectories in a CSV format.

On a series of files¶

Once you've set up your processing pipeline, you can save it under the form of a yaml file by clicking on "save pipeline". Then, to use it to process all your acquisitions within a same series of experimental recordings, click on "palmari > run Palmari on folder...", load the pipeline, select the folder where your files lie, and click process !

What to do next ? Try Tracktor¶

If you want to test the statistical significance of the difference between the sets of trajectories observed in one or the other experiment (or set of experiments), you may want to try Tracktor. It's an online platform developed at tout lab that allows to statistically compare sets of trajectories.

It notably

1. estimates the p-value of the following null hypothesis "Both these sets of trajectories were generated by the same stochastic process",
2. identifies trajectories that are more found in one set than in another,
3. provides nice visualizations of various standard metrics.

Documentation¶

Find more details on Palmari in the documentation.

Getting Help¶

Email Hippolyte Verdier : hverdier@pasteur.fr