Welcome to Palmari’s documentation!#

What’s included ?#

Palmari is a Python package providing tools to process movies of PALM experiments (photo-activated localization microscopy). It provides a customizable pipeline scheme with the following features :

  • Get your trajectories in a few clicks with built-in, ready-to-use processing steps : localizer, tracker, drift corrector, …

  • Napari widget to adjust a pipeline’s parameters : intuitively visualize the effect of one or the other parameter. Want to test your results’ robustness to different processing pipelines ? Palmari stores the localizations and trajectories output from each pipeline so that they can be easily compared afterwards.

  • Designed from the start to process series of PALM acquisitions using a same pipeline : don’t loose time writing scripts to go through all files in a folder. Palmari’s Experiment class allows you to keep track of your entire series of acquisition and stores your processing results.

  • Easily include your favorite processing steps in your Palmari pipeline, see here for more details. If it’s worth sharing, consider a merge request ! 🫵


Visualize processing steps and tweak their parameters with the Napari interface.#


This package is under development, if you wish to contribute, report a bug or suggest an addition, raise an issue or send an email to hverdier@pasteur.fr. Constibutions enriching the set of built-in image processing steps, among others, are very welcome !


pip install palmari