small-particle-detection 0.0.1a6

Small Particle Detection, a shapes library-based object detector.

SPADE: Small PArticle DEtection

An algorithm primarily design to detect objects whose sizes aren’t larger a few pixels (particles) on fluorescence microscopy images.

It is an simplified version of marked point process.

Requirements

SPADE has only been tested with Python 3.5 but should work with older versions. The only strict requirement is the package numpy. In order to use SPADE to its full extent, we recommend installing the scikit-image package and the full scipy ecosystem.

Usage

You can install the package using PIP. The main function, spade2d, is in the spade.detection_2d module. It takes an image, a shapes library and a threshold as input. See the examples in the example folder for more information.

Also provided is a command line interface, that can be used as following:

python -m spade.cli INPUT_IMAGE THRESHOLD -o /path/to/output_image.png

Launch this command with -h for more information on its usage.

Take a look at the files in the example folder to see how to use SPADE from within a python script.

Authors & Acknowledgments

SPADE was developed by Nicolas Cedilnik, Éric Debreuve and Xavier Descombes at the MORPHEME team.

If you use SPADE for your scientific work, please include this bibtex (or equivalent) entry:

@misc{cedilnik2016spade,
  title={SPADE: Small particle detection}
  author={Cedilnik, Nicolas and Debreuve, Éric and Descombes, Xavier}
  url={https://pypi.python.org/pypi/small-particle-detection}
  year={2016}
}

License

SPADE is released under the CeCILL-2.1 licence.