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
Experimentclass 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 !
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 email@example.com. Constibutions enriching the set of built-in image processing steps, among others, are very welcome !
pip install palmari
- TIF processing pipeline
- Data structure
- Napari plugin
- API index