Palmari

Palmari provides a plugin to analyze PALM movies, as well as microscope recordings of other SMLM-based SPT modalities. Set up your pipeline on one file, run it on a folder !

  • Hippolyte Verdier

Documentation Status Python Version tests napari hub License

A processing pipeline for PALM movies analysis (pre-processing, localization, drift correction, tracking).

Check out the documentation to get started.

napari_plugin


This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install palmari via pip:

pip install palmari

To install latest development version :

pip install git+https://github.com/hippover/palmari.git

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the CeCILL license.

Issues

If you encounter any problems, please file an issue along with a detailed description.

Version:

  • 0.3.0

Last updated:

  • 2023-05-01

First released:

  • 2022-05-06

License:

  • "CeCILL"...

Supported data:

  • Information not submitted

Plugin type:

Open extension:

Save extension:

Python versions supported:

Operating system:

  • Information not submitted

Requirements:

  • click
  • dask (>=2022.1.0)
  • dask-image (>=2021.12.0)
  • imageio-ffmpeg
  • magicgui (>=0.5.0)
  • matplotlib (>=3.5)
  • munkres
  • napari
  • napari-aicsimageio
  • numpy
  • pandas
  • pyyaml
  • qtpy
  • scikit-image (>=0.18.3)
  • scikit-learn
  • toml
  • tqdm
  • trackpy (>=0.5.0)
  • tox ; extra == 'testing'
  • PyQt5 ; extra == 'testing'
  • pytest ; extra == 'testing'
  • pytest-cov ; extra == 'testing'
  • pytest-qt ; extra == 'testing'
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